Starting phenix.real_space_refine
on Tue Feb  3 17:12:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvo_44939/02_2026/9bvo_44939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvo_44939/02_2026/9bvo_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_44939/02_2026/9bvo_44939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvo_44939/02_2026/9bvo_44939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvo_44939/02_2026/9bvo_44939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvo_44939/02_2026/9bvo_44939.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.25
  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: 0.43
  Conformation dependent library (CDL) restraints added in 319.6 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: 0.18
  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: 0.80

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 975
        1.33 -     1.45: 1556
        1.45 -     1.57: 3049
        1.57 -     1.69: 2
        1.69 -     1.81: 42
  Bond restraints: 5624
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.01e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.22e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.14e+00
  bond pdb=" C   ASN A 427 "
       pdb=" N   PRO A 428 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.021 1.30e-02 5.92e+03 2.71e+00
  ... (remaining 5619 not shown)

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1704
        2.84 -     3.35: 4499
        3.35 -     3.87: 8505
        3.87 -     4.38: 8958
        4.38 -     4.90: 15784
  Nonbonded interactions: 39450
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 236 "
            pdb=" OG  SER A 239 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   ARG A 671 "
            pdb=" OG1 THR A 675 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   ASP A 524 "
            pdb=" OG1 THR A 527 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   PRO A 654 "
            pdb=" OG1 THR A 658 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" ND2 ASN A 389 "
            pdb=" O   GLY A 393 "
     model   vdw
     2.386 3.120
  ... (remaining 39445 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.60 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.830
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6820
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG A 276 
 TYR   0.014   0.001   TYR A 590 
 PHE   0.011   0.001   PHE A 299 
 TRP   0.011   0.001   TRP A 501 
 HIS   0.007   0.001   HIS A 160 

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

*********************** 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  : 0.208 
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: 0.8383 (Cg_exo) cc_final: 0.8084 (Cg_endo)
REVERT: A  101 PHE cc_start: 0.8476 (m-80) cc_final: 0.8235 (m-10)
REVERT: A  143 LEU cc_start: 0.7702 (tp) cc_final: 0.7151 (tt)
REVERT: A  146 TYR cc_start: 0.7638 (t80) cc_final: 0.6455 (t80)
REVERT: A  147 TRP cc_start: 0.5010 (OUTLIER) cc_final: 0.4353 (m100)
REVERT: A  152 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7505 (tt)
REVERT: A  153 ASP cc_start: 0.7934 (t70) cc_final: 0.7546 (t0)
REVERT: A  235 HIS cc_start: 0.8889 (t-90) cc_final: 0.8146 (t-90)
REVERT: A  296 ILE cc_start: 0.9137 (pt) cc_final: 0.8883 (tp)
REVERT: A  376 PHE cc_start: 0.7563 (t80) cc_final: 0.7276 (t80)
REVERT: A  379 TYR cc_start: 0.8767 (m-80) cc_final: 0.8558 (m-80)
REVERT: A  401 MET cc_start: 0.2997 (ptt) cc_final: 0.1943 (ptt)
REVERT: A  402 MET cc_start: 0.7866 (mmt) cc_final: 0.7267 (mtm)
REVERT: A  405 SER cc_start: 0.8905 (m) cc_final: 0.8682 (t)
REVERT: A  416 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7502 (ttp-110)
REVERT: A  427 ASN cc_start: 0.8230 (t0) cc_final: 0.8030 (t0)
REVERT: A  436 ARG cc_start: 0.7501 (tpt170) cc_final: 0.5750 (ttm170)
REVERT: A  443 MET cc_start: 0.8924 (mtp) cc_final: 0.8721 (mtp)
REVERT: A  455 LEU cc_start: 0.7764 (mt) cc_final: 0.7538 (tp)
REVERT: A  468 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8122 (m-30)
REVERT: A  474 ASN cc_start: 0.8012 (m-40) cc_final: 0.7798 (p0)
REVERT: A  477 PHE cc_start: 0.8274 (m-80) cc_final: 0.7969 (m-10)
REVERT: A  503 GLN cc_start: 0.8850 (mm110) cc_final: 0.8483 (mm-40)
REVERT: A  505 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.7882 (tt)
REVERT: A  541 GLU cc_start: 0.7698 (tt0) cc_final: 0.7322 (pp20)
REVERT: A  555 LEU cc_start: 0.8266 (tp) cc_final: 0.7486 (tt)
REVERT: A  559 GLU cc_start: 0.6582 (tt0) cc_final: 0.6002 (tp30)
REVERT: A  563 GLU cc_start: 0.7687 (tt0) cc_final: 0.7455 (tt0)
REVERT: A  574 ARG cc_start: 0.6764 (mpt-90) cc_final: 0.6332 (mmm160)
REVERT: A  575 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7712 (tm-30)
REVERT: A  607 THR cc_start: 0.7965 (m) cc_final: 0.7604 (p)
REVERT: A  609 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.2113 (tp)
REVERT: A  681 PHE cc_start: 0.8501 (t80) cc_final: 0.8189 (t80)
REVERT: A  689 LEU cc_start: 0.8335 (tp) cc_final: 0.7997 (mt)
REVERT: A  705 ASN cc_start: 0.8624 (m-40) cc_final: 0.8280 (t0)
  outliers start: 33
  outliers final: 5
  residues processed: 238
  average time/residue: 0.0878
  time to fit residues: 25.8918
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  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0770
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.162732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.122442 restraints weight = 9150.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.124145 restraints weight = 6783.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.125841 restraints weight = 4824.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.126693 restraints weight = 4116.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.126706 restraints weight = 3650.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3623

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= 0.149
  Angle     :  0.738  16.150   7652  Z= 0.344
  Chirality :  0.047   0.344    838
  Planarity :  0.005   0.051    944
  Dihedral  : 13.717  91.265    903
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.09 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.27 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.33), residues: 636
  helix:  1.09 (0.28), residues: 319
  sheet:  1.39 (0.63), residues: 70
  loop : -0.72 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 476 
 TYR   0.020   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 535 
 TRP   0.026   0.002   TRP A 493 
 HIS   0.008   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5624)
  covalent geometry    : angle       0.67619 ( 7629)
  SS BOND              : bond        0.02646 (    1)
  SS BOND              : angle       6.00320 (    2)
  hydrogen bonds       : bond        0.04207 (  267)
  hydrogen bonds       : angle       4.30630 (  768)
  link_BETA1-4         : bond        0.00556 (    3)
  link_BETA1-4         : angle       1.33652 (    9)
  link_NAG-ASN         : bond        0.01489 (    4)
  link_NAG-ASN         : angle       7.03584 (   12)

*********************** 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
  159 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8584 (mmm) cc_final: 0.8321 (mmm)
REVERT: A  198 TRP cc_start: 0.8804 (p-90) cc_final: 0.8233 (p-90)
REVERT: A  235 HIS cc_start: 0.9218 (t-90) cc_final: 0.8372 (t-90)
REVERT: A  293 LEU cc_start: 0.9575 (tp) cc_final: 0.9301 (tp)
REVERT: A  376 PHE cc_start: 0.8217 (t80) cc_final: 0.7915 (t80)
REVERT: A  401 MET cc_start: 0.3541 (ptt) cc_final: 0.2574 (ptt)
REVERT: A  416 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7473 (ttp-110)
REVERT: A  436 ARG cc_start: 0.7575 (tpt170) cc_final: 0.5947 (ttm170)
REVERT: A  505 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7691 (tt)
REVERT: A  507 MET cc_start: 0.6996 (tmm) cc_final: 0.5692 (ttt)
REVERT: A  554 GLN cc_start: 0.6334 (tm-30) cc_final: 0.6082 (tm-30)
REVERT: A  559 GLU cc_start: 0.6650 (tt0) cc_final: 0.6210 (tp30)
REVERT: A  575 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7771 (tm-30)
REVERT: A  600 MET cc_start: 0.7540 (ptm) cc_final: 0.6968 (ptm)
REVERT: A  680 ARG cc_start: 0.8619 (ptp-110) cc_final: 0.7610 (ptt180)
REVERT: A  698 MET cc_start: 0.7885 (mmm) cc_final: 0.7527 (tpp)
REVERT: A  705 ASN cc_start: 0.8534 (m-40) cc_final: 0.8258 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0808
  time to fit residues: 16.3998
Evaluate side-chains
  111 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8184

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.162434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.126440 restraints weight = 8740.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.126802 restraints weight = 7425.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.128364 restraints weight = 6825.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.129140 restraints weight = 5080.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.129744 restraints weight = 4947.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5632  Z= 0.162
  Angle     :  0.745  12.733   7652  Z= 0.349
  Chirality :  0.048   0.319    838
  Planarity :  0.005   0.046    944
  Dihedral  : 12.090  88.868    903
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.71
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.34), residues: 636
  helix:  1.49 (0.30), residues: 324
  sheet:  1.22 (0.62), residues: 70
  loop : -0.77 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 190 
 TYR   0.022   0.002   TYR A 397 
 PHE   0.017   0.001   PHE A 535 
 TRP   0.022   0.002   TRP A 390 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 5624)
  covalent geometry    : angle       0.68344 ( 7629)
  SS BOND              : bond        0.01222 (    1)
  SS BOND              : angle       3.40254 (    2)
  hydrogen bonds       : bond        0.04192 (  267)
  hydrogen bonds       : angle       4.19116 (  768)
  link_BETA1-4         : bond        0.00789 (    3)
  link_BETA1-4         : angle       1.72387 (    9)
  link_NAG-ASN         : bond        0.00636 (    4)
  link_NAG-ASN         : angle       7.26383 (   12)

*********************** 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
  139 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.7730 (m-30) cc_final: 0.7045 (p0)
REVERT: A  131 LEU cc_start: 0.8742 (mt) cc_final: 0.8498 (mt)
REVERT: A  235 HIS cc_start: 0.9126 (t-90) cc_final: 0.8346 (t-90)
REVERT: A  293 LEU cc_start: 0.9531 (tp) cc_final: 0.9296 (tp)
REVERT: A  376 PHE cc_start: 0.8255 (t80) cc_final: 0.7945 (t80)
REVERT: A  397 TYR cc_start: 0.8916 (p90) cc_final: 0.8714 (p90)
REVERT: A  401 MET cc_start: 0.4149 (ptt) cc_final: 0.3630 (ptt)
REVERT: A  416 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7470 (ttp-110)
REVERT: A  436 ARG cc_start: 0.7509 (tpt170) cc_final: 0.5824 (ttm110)
REVERT: A  505 LEU cc_start: 0.8223 (tt) cc_final: 0.7642 (tt)
REVERT: A  507 MET cc_start: 0.7049 (tmm) cc_final: 0.5745 (ttt)
REVERT: A  559 GLU cc_start: 0.6677 (tt0) cc_final: 0.6367 (tp30)
REVERT: A  575 GLU cc_start: 0.8692 (mt-10) cc_final: 0.7863 (tm-30)
REVERT: A  615 LEU cc_start: 0.9004 (tt) cc_final: 0.8793 (tt)
REVERT: A  680 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.7371 (ptt180)
REVERT: A  698 MET cc_start: 0.8269 (mmm) cc_final: 0.7975 (mmm)
REVERT: A  705 ASN cc_start: 0.8700 (m-40) cc_final: 0.8171 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0729
  time to fit residues: 13.3553
Evaluate side-chains
  104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0170
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.8222

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.160673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125307 restraints weight = 8571.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124945 restraints weight = 6966.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.126714 restraints weight = 7138.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.127005 restraints weight = 5102.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.127523 restraints weight = 4686.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3433
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5632  Z= 0.163
  Angle     :  0.675   8.406   7652  Z= 0.328
  Chirality :  0.046   0.262    838
  Planarity :  0.005   0.061    944
  Dihedral  : 10.581  73.508    903
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.35), residues: 636
  helix:  1.77 (0.30), residues: 325
  sheet:  0.91 (0.57), residues: 75
  loop : -0.63 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 476 
 TYR   0.022   0.002   TYR A 397 
 PHE   0.025   0.002   PHE A 682 
 TRP   0.026   0.002   TRP A 390 
 HIS   0.004   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5624)
  covalent geometry    : angle       0.64451 ( 7629)
  SS BOND              : bond        0.00744 (    1)
  SS BOND              : angle       2.90464 (    2)
  hydrogen bonds       : bond        0.04116 (  267)
  hydrogen bonds       : angle       4.15811 (  768)
  link_BETA1-4         : bond        0.00455 (    3)
  link_BETA1-4         : angle       1.62118 (    9)
  link_NAG-ASN         : bond        0.00889 (    4)
  link_NAG-ASN         : angle       4.76004 (   12)

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

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.213 
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: 0.7755 (m-30) cc_final: 0.7041 (p0)
REVERT: A  153 ASP cc_start: 0.8477 (t70) cc_final: 0.8275 (t0)
REVERT: A  235 HIS cc_start: 0.8910 (t-90) cc_final: 0.8018 (t-90)
REVERT: A  237 LEU cc_start: 0.9250 (mt) cc_final: 0.8401 (mt)
REVERT: A  292 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8411 (mm-40)
REVERT: A  293 LEU cc_start: 0.9532 (tp) cc_final: 0.9226 (tp)
REVERT: A  376 PHE cc_start: 0.8289 (t80) cc_final: 0.7968 (t80)
REVERT: A  397 TYR cc_start: 0.8933 (p90) cc_final: 0.8658 (p90)
REVERT: A  401 MET cc_start: 0.4274 (ptt) cc_final: 0.3721 (ptt)
REVERT: A  416 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7511 (ttp-110)
REVERT: A  493 TRP cc_start: 0.7884 (t60) cc_final: 0.7530 (t60)
REVERT: A  507 MET cc_start: 0.6983 (tmm) cc_final: 0.5812 (ttt)
REVERT: A  559 GLU cc_start: 0.6832 (tt0) cc_final: 0.6405 (tp30)
REVERT: A  615 LEU cc_start: 0.9015 (tt) cc_final: 0.8792 (tt)
REVERT: A  680 ARG cc_start: 0.8093 (ptp-110) cc_final: 0.7392 (ptt180)
REVERT: A  705 ASN cc_start: 0.8857 (m-40) cc_final: 0.8260 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0687
  time to fit residues: 12.3404
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  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.159946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125249 restraints weight = 8670.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.124975 restraints weight = 7595.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.126754 restraints weight = 7679.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.127379 restraints weight = 5350.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127794 restraints weight = 5042.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    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 = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5632  Z= 0.139
  Angle     :  0.622   7.662   7652  Z= 0.307
  Chirality :  0.044   0.253    838
  Planarity :  0.004   0.040    944
  Dihedral  :  9.867  66.921    903
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.33
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.36), residues: 636
  helix:  1.81 (0.31), residues: 320
  sheet:  0.97 (0.55), residues: 78
  loop : -0.40 (0.45), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 476 
 TYR   0.022   0.001   TYR A 397 
 PHE   0.012   0.001   PHE A 535 
 TRP   0.017   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5624)
  covalent geometry    : angle       0.60403 ( 7629)
  SS BOND              : bond        0.00766 (    1)
  SS BOND              : angle       2.40546 (    2)
  hydrogen bonds       : bond        0.03952 (  267)
  hydrogen bonds       : angle       4.08949 (  768)
  link_BETA1-4         : bond        0.00539 (    3)
  link_BETA1-4         : angle       1.39809 (    9)
  link_NAG-ASN         : bond        0.00770 (    4)
  link_NAG-ASN         : angle       3.47153 (   12)

*********************** 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
  127 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.190 
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: 0.7127 (mmt180) cc_final: 0.6224 (mmm160)
REVERT: A  113 ASP cc_start: 0.7696 (m-30) cc_final: 0.7034 (p0)
REVERT: A  153 ASP cc_start: 0.8542 (t70) cc_final: 0.8330 (t0)
REVERT: A  235 HIS cc_start: 0.8973 (t-90) cc_final: 0.8030 (t-90)
REVERT: A  237 LEU cc_start: 0.9220 (mt) cc_final: 0.8376 (mt)
REVERT: A  293 LEU cc_start: 0.9529 (tp) cc_final: 0.9226 (tp)
REVERT: A  376 PHE cc_start: 0.8326 (t80) cc_final: 0.8018 (t80)
REVERT: A  397 TYR cc_start: 0.8929 (p90) cc_final: 0.8574 (p90)
REVERT: A  401 MET cc_start: 0.4093 (ptt) cc_final: 0.3563 (ptt)
REVERT: A  416 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7625 (ttp-110)
REVERT: A  443 MET cc_start: 0.8842 (ptp) cc_final: 0.8548 (ptp)
REVERT: A  559 GLU cc_start: 0.6731 (tt0) cc_final: 0.6326 (tp30)
REVERT: A  615 LEU cc_start: 0.9020 (tt) cc_final: 0.8806 (tt)
REVERT: A  705 ASN cc_start: 0.8898 (m-40) cc_final: 0.8339 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0626
  time to fit residues: 10.7487
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.157484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121651 restraints weight = 8973.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119833 restraints weight = 8201.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.121808 restraints weight = 7047.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.122299 restraints weight = 5658.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.122646 restraints weight = 4831.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5632  Z= 0.181
  Angle     :  0.696  11.155   7652  Z= 0.337
  Chirality :  0.046   0.233    838
  Planarity :  0.004   0.037    944
  Dihedral  :  9.577  59.639    903
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.35), residues: 636
  helix:  1.70 (0.30), residues: 327
  sheet:  0.85 (0.55), residues: 78
  loop : -0.38 (0.46), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 476 
 TYR   0.021   0.002   TYR A 397 
 PHE   0.015   0.001   PHE A 535 
 TRP   0.018   0.002   TRP A 390 
 HIS   0.004   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 5624)
  covalent geometry    : angle       0.65730 ( 7629)
  SS BOND              : bond        0.01346 (    1)
  SS BOND              : angle       3.07100 (    2)
  hydrogen bonds       : bond        0.04370 (  267)
  hydrogen bonds       : angle       4.19014 (  768)
  link_BETA1-4         : bond        0.00477 (    3)
  link_BETA1-4         : angle       1.57073 (    9)
  link_NAG-ASN         : bond        0.01208 (    4)
  link_NAG-ASN         : angle       5.58834 (   12)

*********************** 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
  123 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.218 
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: 0.7133 (mmt180) cc_final: 0.6798 (mmm160)
REVERT: A  113 ASP cc_start: 0.7661 (m-30) cc_final: 0.7084 (p0)
REVERT: A  235 HIS cc_start: 0.9102 (t-90) cc_final: 0.8393 (t-90)
REVERT: A  237 LEU cc_start: 0.9245 (mt) cc_final: 0.8724 (mt)
REVERT: A  293 LEU cc_start: 0.9534 (tp) cc_final: 0.9297 (tp)
REVERT: A  376 PHE cc_start: 0.8401 (t80) cc_final: 0.8119 (t80)
REVERT: A  391 THR cc_start: 0.7917 (p) cc_final: 0.7652 (p)
REVERT: A  401 MET cc_start: 0.4156 (ptt) cc_final: 0.3572 (ptt)
REVERT: A  507 MET cc_start: 0.7246 (tmm) cc_final: 0.6188 (ttt)
REVERT: A  559 GLU cc_start: 0.6851 (tt0) cc_final: 0.6370 (tp30)
REVERT: A  599 TYR cc_start: 0.8533 (p90) cc_final: 0.8053 (p90)
REVERT: A  615 LEU cc_start: 0.9111 (tt) cc_final: 0.8909 (tt)
REVERT: A  681 PHE cc_start: 0.8575 (t80) cc_final: 0.8191 (t80)
REVERT: A  705 ASN cc_start: 0.8954 (m-40) cc_final: 0.8398 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0706
  time to fit residues: 11.6623
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  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 49 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0470
   chunk 47 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.159806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.124092 restraints weight = 8885.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121650 restraints weight = 8571.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123394 restraints weight = 8551.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.124966 restraints weight = 5821.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.124923 restraints weight = 5037.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5632  Z= 0.134
  Angle     :  0.645  11.431   7652  Z= 0.314
  Chirality :  0.044   0.247    838
  Planarity :  0.004   0.038    944
  Dihedral  :  9.032  59.431    903
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.35), residues: 636
  helix:  1.83 (0.30), residues: 324
  sheet:  0.82 (0.56), residues: 78
  loop : -0.39 (0.45), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 416 
 TYR   0.032   0.001   TYR A 397 
 PHE   0.029   0.001   PHE A 682 
 TRP   0.018   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5624)
  covalent geometry    : angle       0.61226 ( 7629)
  SS BOND              : bond        0.01195 (    1)
  SS BOND              : angle       2.10772 (    2)
  hydrogen bonds       : bond        0.04029 (  267)
  hydrogen bonds       : angle       4.12752 (  768)
  link_BETA1-4         : bond        0.00576 (    3)
  link_BETA1-4         : angle       1.32849 (    9)
  link_NAG-ASN         : bond        0.00819 (    4)
  link_NAG-ASN         : angle       4.95599 (   12)

*********************** 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
  124 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7188 (mmt180) cc_final: 0.6842 (mmm160)
REVERT: A  113 ASP cc_start: 0.7654 (m-30) cc_final: 0.7040 (p0)
REVERT: A  153 ASP cc_start: 0.8490 (t70) cc_final: 0.8274 (t0)
REVERT: A  235 HIS cc_start: 0.9078 (t-90) cc_final: 0.8340 (t-90)
REVERT: A  237 LEU cc_start: 0.9204 (mt) cc_final: 0.8682 (mt)
REVERT: A  272 PHE cc_start: 0.7229 (m-80) cc_final: 0.7014 (m-80)
REVERT: A  292 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8514 (mm-40)
REVERT: A  293 LEU cc_start: 0.9529 (tp) cc_final: 0.9279 (tp)
REVERT: A  376 PHE cc_start: 0.8365 (t80) cc_final: 0.8117 (t80)
REVERT: A  391 THR cc_start: 0.7957 (p) cc_final: 0.7687 (p)
REVERT: A  397 TYR cc_start: 0.8977 (p90) cc_final: 0.8518 (p90)
REVERT: A  401 MET cc_start: 0.4112 (ptt) cc_final: 0.3486 (ptt)
REVERT: A  559 GLU cc_start: 0.6800 (tt0) cc_final: 0.6336 (tp30)
REVERT: A  599 TYR cc_start: 0.8532 (p90) cc_final: 0.8113 (p90)
REVERT: A  615 LEU cc_start: 0.9082 (tt) cc_final: 0.8805 (tt)
REVERT: A  681 PHE cc_start: 0.8358 (t80) cc_final: 0.8022 (t80)
REVERT: A  705 ASN cc_start: 0.8912 (m-40) cc_final: 0.8423 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0686
  time to fit residues: 11.4582
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.0010
   chunk 38 optimal weight:    0.5980
   chunk 39 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.4786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.159675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124461 restraints weight = 8738.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122913 restraints weight = 7435.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.124546 restraints weight = 7586.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125324 restraints weight = 5249.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.125738 restraints weight = 4626.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3403
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.5430

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= 0.121
  Angle     :  0.625  10.455   7652  Z= 0.305
  Chirality :  0.043   0.245    838
  Planarity :  0.004   0.041    944
  Dihedral  :  8.467  58.252    903
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.35), residues: 636
  helix:  1.83 (0.30), residues: 325
  sheet:  0.90 (0.56), residues: 77
  loop : -0.37 (0.45), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  68 
 TYR   0.030   0.001   TYR A 397 
 PHE   0.020   0.001   PHE A 682 
 TRP   0.015   0.001   TRP A 390 
 HIS   0.003   0.001   HIS A 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5624)
  covalent geometry    : angle       0.59695 ( 7629)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       1.75296 (    2)
  hydrogen bonds       : bond        0.03814 (  267)
  hydrogen bonds       : angle       4.05518 (  768)
  link_BETA1-4         : bond        0.00495 (    3)
  link_BETA1-4         : angle       1.29867 (    9)
  link_NAG-ASN         : bond        0.00837 (    4)
  link_NAG-ASN         : angle       4.56136 (   12)

*********************** 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
  124 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.209 
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: 0.7338 (mmt180) cc_final: 0.6816 (mmm160)
REVERT: A  113 ASP cc_start: 0.7636 (m-30) cc_final: 0.7048 (p0)
REVERT: A  153 ASP cc_start: 0.8568 (t70) cc_final: 0.8362 (t0)
REVERT: A  235 HIS cc_start: 0.9070 (t-90) cc_final: 0.8279 (t-90)
REVERT: A  237 LEU cc_start: 0.9184 (mt) cc_final: 0.8639 (mt)
REVERT: A  292 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8497 (mm-40)
REVERT: A  293 LEU cc_start: 0.9474 (tp) cc_final: 0.9223 (tp)
REVERT: A  391 THR cc_start: 0.7873 (p) cc_final: 0.7643 (p)
REVERT: A  397 TYR cc_start: 0.8986 (p90) cc_final: 0.8589 (p90)
REVERT: A  401 MET cc_start: 0.4062 (ptt) cc_final: 0.3459 (ptt)
REVERT: A  507 MET cc_start: 0.7180 (tmm) cc_final: 0.6186 (ttt)
REVERT: A  559 GLU cc_start: 0.6697 (tt0) cc_final: 0.6184 (tp30)
REVERT: A  599 TYR cc_start: 0.8491 (p90) cc_final: 0.8153 (p90)
REVERT: A  615 LEU cc_start: 0.9068 (tt) cc_final: 0.8796 (tt)
REVERT: A  681 PHE cc_start: 0.8371 (t80) cc_final: 0.8021 (t80)
REVERT: A  705 ASN cc_start: 0.8898 (m-40) cc_final: 0.8422 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0624
  time to fit residues: 10.6392
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  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0870
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0070
   chunk 61 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
A 479 GLN
** 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 = 0.3871 r_free = 0.3871 target = 0.158693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124180 restraints weight = 8771.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.121933 restraints weight = 9507.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123413 restraints weight = 7594.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.124390 restraints weight = 6503.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125706 restraints weight = 5859.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.5526

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= 0.120
  Angle     :  0.646  11.127   7652  Z= 0.309
  Chirality :  0.043   0.250    838
  Planarity :  0.004   0.040    944
  Dihedral  :  8.149  57.650    903
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.35), residues: 636
  helix:  1.79 (0.30), residues: 322
  sheet:  0.96 (0.56), residues: 77
  loop : -0.36 (0.44), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  68 
 TYR   0.029   0.001   TYR A 397 
 PHE   0.021   0.001   PHE A 682 
 TRP   0.014   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 5624)
  covalent geometry    : angle       0.62059 ( 7629)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       1.44616 (    2)
  hydrogen bonds       : bond        0.03790 (  267)
  hydrogen bonds       : angle       4.10638 (  768)
  link_BETA1-4         : bond        0.00555 (    3)
  link_BETA1-4         : angle       1.34383 (    9)
  link_NAG-ASN         : bond        0.00853 (    4)
  link_NAG-ASN         : angle       4.39272 (   12)

*********************** 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
  121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.126 
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: 0.7379 (mmt180) cc_final: 0.6814 (mmm160)
REVERT: A  113 ASP cc_start: 0.7714 (m-30) cc_final: 0.7144 (p0)
REVERT: A  153 ASP cc_start: 0.8628 (t70) cc_final: 0.8339 (t0)
REVERT: A  235 HIS cc_start: 0.9048 (t-90) cc_final: 0.8256 (t-90)
REVERT: A  237 LEU cc_start: 0.9166 (mt) cc_final: 0.8610 (mt)
REVERT: A  292 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8457 (mm-40)
REVERT: A  293 LEU cc_start: 0.9480 (tp) cc_final: 0.9219 (tp)
REVERT: A  319 LEU cc_start: 0.8322 (mp) cc_final: 0.7965 (mt)
REVERT: A  391 THR cc_start: 0.7846 (p) cc_final: 0.7641 (p)
REVERT: A  397 TYR cc_start: 0.8968 (p90) cc_final: 0.8555 (p90)
REVERT: A  401 MET cc_start: 0.4160 (ptt) cc_final: 0.3544 (ptt)
REVERT: A  507 MET cc_start: 0.7098 (tmm) cc_final: 0.6296 (ttt)
REVERT: A  559 GLU cc_start: 0.6600 (tt0) cc_final: 0.6071 (tp30)
REVERT: A  599 TYR cc_start: 0.8430 (p90) cc_final: 0.8202 (p90)
REVERT: A  698 MET cc_start: 0.8081 (mmt) cc_final: 0.7644 (mmt)
REVERT: A  705 ASN cc_start: 0.8883 (m-40) cc_final: 0.8389 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0663
  time to fit residues: 10.7589
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.150086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115414 restraints weight = 8856.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117891 restraints weight = 10609.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119373 restraints weight = 7903.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.119743 restraints weight = 5450.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120045 restraints weight = 5692.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5632  Z= 0.155
  Angle     :  0.680   9.304   7652  Z= 0.332
  Chirality :  0.045   0.257    838
  Planarity :  0.005   0.065    944
  Dihedral  :  8.045  58.312    903
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.35), residues: 636
  helix:  1.74 (0.30), residues: 324
  sheet:  0.45 (0.55), residues: 84
  loop : -0.34 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 476 
 TYR   0.030   0.001   TYR A 397 
 PHE   0.020   0.002   PHE A 682 
 TRP   0.017   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5624)
  covalent geometry    : angle       0.65774 ( 7629)
  SS BOND              : bond        0.00534 (    1)
  SS BOND              : angle       2.06506 (    2)
  hydrogen bonds       : bond        0.04274 (  267)
  hydrogen bonds       : angle       4.20690 (  768)
  link_BETA1-4         : bond        0.00422 (    3)
  link_BETA1-4         : angle       1.36413 (    9)
  link_NAG-ASN         : bond        0.00822 (    4)
  link_NAG-ASN         : angle       4.19913 (   12)

********************** 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
  120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.154 
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: 0.7192 (mmt180) cc_final: 0.6767 (mmm160)
REVERT: A  113 ASP cc_start: 0.7610 (m-30) cc_final: 0.7163 (p0)
REVERT: A  130 MET cc_start: 0.8170 (tmm) cc_final: 0.7623 (ttt)
REVERT: A  131 LEU cc_start: 0.8747 (mt) cc_final: 0.8314 (mt)
REVERT: A  153 ASP cc_start: 0.8640 (t70) cc_final: 0.8341 (t70)
REVERT: A  235 HIS cc_start: 0.8937 (t-90) cc_final: 0.8244 (t-90)
REVERT: A  237 LEU cc_start: 0.9164 (mt) cc_final: 0.8664 (mt)
REVERT: A  292 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8323 (mm-40)
REVERT: A  293 LEU cc_start: 0.9510 (tp) cc_final: 0.9276 (tp)
REVERT: A  319 LEU cc_start: 0.8323 (mp) cc_final: 0.8001 (mt)
REVERT: A  397 TYR cc_start: 0.8992 (p90) cc_final: 0.8624 (p90)
REVERT: A  401 MET cc_start: 0.4243 (ptt) cc_final: 0.3537 (ptt)
REVERT: A  507 MET cc_start: 0.7024 (tmm) cc_final: 0.6160 (ttt)
REVERT: A  559 GLU cc_start: 0.6790 (tt0) cc_final: 0.6270 (tp30)
REVERT: A  705 ASN cc_start: 0.8843 (m-40) cc_final: 0.8350 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0662
  time to fit residues: 10.7456
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  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 63 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0770
   chunk 62 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.4940

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.160124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124608 restraints weight = 8776.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123736 restraints weight = 7177.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.125487 restraints weight = 7701.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.126183 restraints weight = 4944.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.126241 restraints weight = 4638.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5796

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= 0.122
  Angle     :  0.636   9.107   7652  Z= 0.309
  Chirality :  0.043   0.261    838
  Planarity :  0.005   0.052    944
  Dihedral  :  7.652  55.254    903
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.35), residues: 636
  helix:  1.79 (0.30), residues: 323
  sheet:  0.52 (0.56), residues: 84
  loop : -0.29 (0.46), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 476 
 TYR   0.028   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 682 
 TRP   0.012   0.001   TRP A 390 
 HIS   0.004   0.001   HIS A 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5624)
  covalent geometry    : angle       0.61420 ( 7629)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       1.45558 (    2)
  hydrogen bonds       : bond        0.03861 (  267)
  hydrogen bonds       : angle       4.09330 (  768)
  link_BETA1-4         : bond        0.00536 (    3)
  link_BETA1-4         : angle       1.23270 (    9)
  link_NAG-ASN         : bond        0.00785 (    4)
  link_NAG-ASN         : angle       4.09018 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1051.87 seconds
wall clock time: 18 minutes 49.65 seconds (1129.65 seconds total)