Starting phenix.real_space_refine
on Wed Sep 17 06:18:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvq_44941/09_2025/9bvq_44941.cif"
  }
  resolution = 3.3
  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=   0.019
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       2      5.49       5
     S      25      5.16       5
     C    3906      2.51       5
     N     977      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5977
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5490
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 35, 'TRANS': 629}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 293
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
          Chain breaks: 1
    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: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 110
          Unusual residues: {'6PL': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   6PL A 801 " occ=0.60
      ... (44 atoms not shown)
      pdb=" P   6PL A 801 " occ=0.60
    residue:
      pdb=" N   6PL A 802 " occ=0.60
      ... (48 atoms not shown)
      pdb=" P   6PL A 802 " occ=0.60
  Time building chain proxies: 1.58, per 1000 atoms: 0.26
  Number of scatterers: 5977
  At special positions: 0
  Unit cell: (86.7626, 85.8773, 108.896, 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       2     15.00
     O    1067      8.00
     N     977      7.00
     C    3906      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
      
  Atom "HETATM 5851  O5  NAG D   1 .*.     O  " rejected from bonding due to valence issues.
  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 803 " - " 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: 0.55
  Conformation dependent library (CDL) restraints added in 304.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      55.3% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 41 through 46
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 61 through 79
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   LYS A  91 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    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
      removed outlier: 3.747A  pdb=" N   ASP A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
      removed outlier: 3.777A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.209A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 174 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.509A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.776A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 244
      removed outlier: 3.863A  pdb=" N   LEU A 232 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   SER A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 234 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 4.024A  pdb=" N   LEU A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 294
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 308 through 311
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.823A  pdb=" N   LYS A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 319 " --> pdb=" O   TRP A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 377
      removed outlier: 3.539A  pdb=" N   ALA A 364 " --> pdb=" O   HIS A 360 " (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 384 through 388
      removed outlier: 3.700A  pdb=" N   TYR A 387 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.596A  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 511 through 523
      removed outlier: 4.111A  pdb=" N   LYS A 515 " --> pdb=" O   PRO A 511 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLN A 517 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 627
    Processing helix  chain 'A' and resid 638 through 644
    Processing helix  chain 'A' and resid 653 through 674
    Processing helix  chain 'A' and resid 676 through 709
      removed outlier: 3.598A  pdb=" N   ARG A 680 " --> pdb=" O   PRO A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 724
    Processing helix  chain 'P' and resid 33 through 38
      removed outlier: 3.725A  pdb=" N   GLN P  38 " --> pdb=" O   PRO P  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 3.661A  pdb=" N   GLN A 479 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   HIS A 410 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   HIS A 408 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TYR A 425 " --> pdb=" O   LEU P  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 534
      removed outlier: 6.573A  pdb=" N   CYS A 598 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.614A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    816 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: 0.77

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1008
        1.33 -     1.45: 1734
        1.45 -     1.57: 3357
        1.57 -     1.69: 4
        1.69 -     1.81: 42
  Bond restraints: 6145
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.77e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.41e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 6140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 8109
        1.21 -     2.42: 167
        2.42 -     3.63: 45
        3.63 -     4.84: 5
        4.84 -     6.04: 4
  Bond angle restraints: 8330
  Sorted by residual:
  angle pdb=" N   VAL P  30 "
        pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     112.96  110.14    2.82 1.00e+00 1.00e+00 7.97e+00
  angle pdb=" N   PRO P  34 "
        pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
      ideal   model   delta    sigma   weight residual
     110.70  113.08   -2.38 1.22e+00 6.72e-01 3.80e+00
  angle pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
        pdb=" N   PRO P  35 "
      ideal   model   delta    sigma   weight residual
     117.93  120.18   -2.25 1.20e+00 6.94e-01 3.51e+00
  angle pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
        pdb=" O   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     119.29  120.74   -1.45 8.40e-01 1.42e+00 2.99e+00
  angle pdb=" N   PHE A 268 "
        pdb=" CA  PHE A 268 "
        pdb=" C   PHE A 268 "
      ideal   model   delta    sigma   weight residual
     112.90  115.13   -2.23 1.31e+00 5.83e-01 2.89e+00
  ... (remaining 8325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.96: 3573
       24.96 -    49.92: 96
       49.92 -    74.88: 27
       74.88 -    99.85: 8
       99.85 -   124.81: 17
  Dihedral angle restraints: 3721
    sinusoidal: 1670
      harmonic: 2051
  Sorted by residual:
  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   61.85 -124.81     1      3.00e+01 1.11e-03 1.68e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C6  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -68.78 -120.06     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C4  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   55.88 -119.99     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 3718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.332: 898
       0.332 -    0.664: 2
       0.664 -    0.996: 3
       0.996 -    1.329: 0
       1.329 -    1.661: 2
  Chirality restraints: 905
  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   -1.02   -1.38 2.00e-02 2.50e+03 4.73e+03
  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   -1.48   -0.92 2.00e-02 2.50e+03 2.13e+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   -1.70   -0.70 2.00e-02 2.50e+03 1.21e+03
  ... (remaining 902 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 570 "    0.003 2.00e-02 2.50e+03   5.51e-02 3.79e+01
        pdb=" CG  ASN A 570 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 570 "   -0.050 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 570 "    0.094 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 550 "   -0.046 2.00e-02 2.50e+03   5.28e-02 3.49e+01
        pdb=" CG  ASN A 550 "    0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 550 "    0.015 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 550 "    0.080 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 459 "   -0.008 2.00e-02 2.50e+03   1.90e-02 4.51e+00
        pdb=" CG  ASN A 459 "    0.005 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 459 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 459 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG A 803 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 460
        2.74 -     3.28: 5532
        3.28 -     3.82: 9313
        3.82 -     4.36: 10638
        4.36 -     4.90: 19258
  Nonbonded interactions: 45201
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  60 "
            pdb=" OH  TYR A 200 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" NE2 HIS A 256 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OD2 ASP A 153 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" NH1 ARG A 704 "
            pdb=" OE2 GLU A 719 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OD1 ASP A 417 "
            pdb=" OG1 THR A 461 "
     model   vdw
     2.351 3.040
  ... (remaining 45196 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=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.020
  Find NCS groups from input model:        0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
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      :  0.004   0.200   6153  Z= 0.210
  Angle     :  1.392  55.479   8353  Z= 0.496
  Chirality :  0.096   1.661    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 15.642 124.808   2398
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  4.59 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  0.89 (0.33), residues: 692
  helix:  1.34 (0.28), residues: 348
  sheet:  1.62 (0.58), residues: 73
  loop : -0.65 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 406 
 TYR   0.010   0.001   TYR A 590 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.006   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6145)
  covalent geometry    : angle       0.47055 ( 8330)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.42604 (    2)
  hydrogen bonds       : bond        0.13855 (  286)
  hydrogen bonds       : angle       5.67442 (  816)
  link_BETA1-4         : bond        0.06797 (    3)
  link_BETA1-4         : angle      28.34613 (    9)
  link_NAG-ASN         : bond        0.11272 (    4)
  link_NAG-ASN         : angle      24.34865 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8528 (mt) cc_final: 0.8313 (mp)
REVERT: A  115 MET cc_start: 0.8407 (mmt) cc_final: 0.7898 (mmt)
REVERT: A  180 TRP cc_start: 0.7480 (t60) cc_final: 0.7112 (t-100)
REVERT: A  680 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.6993 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6959 (p90)
  outliers start: 10
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1282
  time to fit residues: 17.7125
Evaluate side-chains
  59 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
P  38 GLN
P  44 HIS
P  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.132532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.094858 restraints weight = 9330.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.71
r_work: 0.2987 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6153  Z= 0.146
  Angle     :  0.671  11.490   8353  Z= 0.297
  Chirality :  0.043   0.284    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 14.850  79.379   1011
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  7.12 %
    Favored  : 91.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.34), residues: 692
  helix:  1.80 (0.29), residues: 355
  sheet:  1.72 (0.58), residues: 73
  loop : -0.39 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 726 
 TYR   0.011   0.001   TYR A 285 
 PHE   0.008   0.001   PHE A 299 
 TRP   0.008   0.001   TRP A 315 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6145)
  covalent geometry    : angle       0.62292 ( 8330)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.23164 (    2)
  hydrogen bonds       : bond        0.04375 (  286)
  hydrogen bonds       : angle       4.21165 (  816)
  link_BETA1-4         : bond        0.00829 (    3)
  link_BETA1-4         : angle       2.10108 (    9)
  link_NAG-ASN         : bond        0.00885 (    4)
  link_NAG-ASN         : angle       6.35904 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8499 (t0) cc_final: 0.8264 (t0)
REVERT: A  180 TRP cc_start: 0.7840 (t60) cc_final: 0.7276 (t-100)
REVERT: A  663 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8483 (tp-100)
REVERT: A  680 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.6832 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6709 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 63
  average time/residue: 0.1211
  time to fit residues: 9.5014
Evaluate side-chains
  57 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0070
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0070
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7418

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.130685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.093210 restraints weight = 9219.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.71
r_work: 0.2959 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6153  Z= 0.137
  Angle     :  0.585   7.578   8353  Z= 0.269
  Chirality :  0.042   0.295    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 12.565  76.158   1011
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  7.59 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  1.69 (0.34), residues: 692
  helix:  2.04 (0.29), residues: 355
  sheet:  1.78 (0.59), residues: 73
  loop : -0.34 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 671 
 TYR   0.015   0.001   TYR A 285 
 PHE   0.008   0.001   PHE A 684 
 TRP   0.008   0.001   TRP A 198 
 HIS   0.007   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6145)
  covalent geometry    : angle       0.55599 ( 8330)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.15686 (    2)
  hydrogen bonds       : bond        0.04171 (  286)
  hydrogen bonds       : angle       3.95871 (  816)
  link_BETA1-4         : bond        0.00580 (    3)
  link_BETA1-4         : angle       1.89286 (    9)
  link_NAG-ASN         : bond        0.00500 (    4)
  link_NAG-ASN         : angle       4.56239 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8523 (t0) cc_final: 0.8308 (t0)
REVERT: A  180 TRP cc_start: 0.7828 (t60) cc_final: 0.7202 (t-100)
REVERT: A  183 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8222 (m-30)
REVERT: A  417 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7919 (t0)
REVERT: A  619 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8625 (tm-30)
REVERT: A  663 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: A  680 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.6871 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6710 (p90)
  outliers start: 10
  outliers final: 1
  residues processed: 64
  average time/residue: 0.1066
  time to fit residues: 8.8078
Evaluate side-chains
  57 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  417 ASP
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.6260

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.130164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.092979 restraints weight = 9341.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.72
r_work: 0.2952 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6153  Z= 0.124
  Angle     :  0.584  10.595   8353  Z= 0.264
  Chirality :  0.042   0.294    905
  Planarity :  0.004   0.051   1034
  Dihedral  : 11.224  66.086   1011
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.75 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.34), residues: 692
  helix:  2.18 (0.29), residues: 355
  sheet:  1.79 (0.58), residues: 73
  loop : -0.29 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 671 
 TYR   0.016   0.001   TYR A 285 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.009   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6145)
  covalent geometry    : angle       0.55860 ( 8330)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.12856 (    2)
  hydrogen bonds       : bond        0.03920 (  286)
  hydrogen bonds       : angle       3.83585 (  816)
  link_BETA1-4         : bond        0.00446 (    3)
  link_BETA1-4         : angle       1.70293 (    9)
  link_NAG-ASN         : bond        0.00526 (    4)
  link_NAG-ASN         : angle       4.35275 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.9066 (tppt) cc_final: 0.8816 (tppt)
REVERT: A  153 ASP cc_start: 0.8524 (t0) cc_final: 0.8300 (t0)
REVERT: A  183 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (m-30)
REVERT: A  619 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8496 (tm-30)
REVERT: A  663 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8510 (tp-100)
REVERT: A  680 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.6865 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6644 (p90)
  outliers start: 7
  outliers final: 2
  residues processed: 65
  average time/residue: 0.1082
  time to fit residues: 9.0508
Evaluate side-chains
  59 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.124369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.086306 restraints weight = 9492.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.85
r_work: 0.2857 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6153  Z= 0.137
  Angle     :  0.588  10.047   8353  Z= 0.266
  Chirality :  0.042   0.295    905
  Planarity :  0.004   0.051   1034
  Dihedral  : 11.477  89.145   1011
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.07 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.03 (0.34), residues: 692
  helix:  2.40 (0.29), residues: 348
  sheet:  1.75 (0.58), residues: 73
  loop : -0.16 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 683 
 TYR   0.013   0.001   TYR A 285 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.009   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6145)
  covalent geometry    : angle       0.55242 ( 8330)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.13775 (    2)
  hydrogen bonds       : bond        0.03962 (  286)
  hydrogen bonds       : angle       3.79727 (  816)
  link_BETA1-4         : bond        0.00301 (    3)
  link_BETA1-4         : angle       1.60852 (    9)
  link_NAG-ASN         : bond        0.01034 (    4)
  link_NAG-ASN         : angle       5.22015 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8533 (t0) cc_final: 0.8321 (t0)
REVERT: A  183 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8398 (m-30)
REVERT: A  417 ASP cc_start: 0.8273 (t0) cc_final: 0.7885 (t0)
REVERT: A  619 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8484 (tm-30)
REVERT: A  663 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8504 (tp-100)
REVERT: A  671 ARG cc_start: 0.9433 (tmm-80) cc_final: 0.8992 (ttp80)
REVERT: A  680 ARG cc_start: 0.7742 (mtp-110) cc_final: 0.6871 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6594 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 63
  average time/residue: 0.0981
  time to fit residues: 8.0422
Evaluate side-chains
  61 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0050
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.124293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.086182 restraints weight = 9371.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.84
r_work: 0.2856 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6153  Z= 0.127
  Angle     :  0.556  10.276   8353  Z= 0.254
  Chirality :  0.040   0.189    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.920  97.504   1011
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.02 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.09 (0.34), residues: 692
  helix:  2.46 (0.29), residues: 348
  sheet:  1.94 (0.59), residues: 71
  loop : -0.20 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.010   0.001   TYR A 285 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.009   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6145)
  covalent geometry    : angle       0.52905 ( 8330)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.12056 (    2)
  hydrogen bonds       : bond        0.03891 (  286)
  hydrogen bonds       : angle       3.76353 (  816)
  link_BETA1-4         : bond        0.00346 (    3)
  link_BETA1-4         : angle       1.49485 (    9)
  link_NAG-ASN         : bond        0.00451 (    4)
  link_NAG-ASN         : angle       4.34141 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8519 (t0) cc_final: 0.8300 (t0)
REVERT: A  183 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8391 (m-30)
REVERT: A  236 TRP cc_start: 0.8677 (p-90) cc_final: 0.8475 (p-90)
REVERT: A  285 TYR cc_start: 0.8323 (t80) cc_final: 0.7867 (t80)
REVERT: A  417 ASP cc_start: 0.8288 (t0) cc_final: 0.7882 (t0)
REVERT: A  520 LYS cc_start: 0.8532 (tppp) cc_final: 0.8322 (tttm)
REVERT: A  619 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8488 (tm-30)
REVERT: A  663 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8498 (tp-100)
REVERT: A  680 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.6895 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6630 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 63
  average time/residue: 0.0914
  time to fit residues: 7.4721
Evaluate side-chains
  62 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0770
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.124948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.086834 restraints weight = 9332.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.85
r_work: 0.2871 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6153  Z= 0.115
  Angle     :  0.552   9.802   8353  Z= 0.254
  Chirality :  0.040   0.202    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.873 107.189   1011
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  9.34 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.23 (0.34), residues: 692
  helix:  2.55 (0.29), residues: 348
  sheet:  1.97 (0.59), residues: 70
  loop : -0.06 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.024   0.001   TYR A 285 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6145)
  covalent geometry    : angle       0.51940 ( 8330)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.06726 (    2)
  hydrogen bonds       : bond        0.03751 (  286)
  hydrogen bonds       : angle       3.69755 (  816)
  link_BETA1-4         : bond        0.00374 (    3)
  link_BETA1-4         : angle       1.42660 (    9)
  link_NAG-ASN         : bond        0.00845 (    4)
  link_NAG-ASN         : angle       4.82388 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8520 (t0) cc_final: 0.8300 (t70)
REVERT: A  183 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8404 (m-30)
REVERT: A  619 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8488 (tm-30)
REVERT: A  663 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8519 (tp-100)
REVERT: A  680 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.6908 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8207 (tp40) cc_final: 0.8003 (tp40)
REVERT: P   94 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6642 (p90)
  outliers start: 5
  outliers final: 3
  residues processed: 62
  average time/residue: 0.1029
  time to fit residues: 8.2946
Evaluate side-chains
  63 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0050
   chunk 41 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.8396

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.123618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.085388 restraints weight = 9411.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.86
r_work: 0.2846 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6153  Z= 0.141
  Angle     :  0.548   7.994   8353  Z= 0.256
  Chirality :  0.040   0.213    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.440 105.614   1011
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.65 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.19 (0.34), residues: 692
  helix:  2.53 (0.29), residues: 348
  sheet:  1.94 (0.59), residues: 71
  loop : -0.12 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.016   0.001   TYR A 285 
 PHE   0.008   0.001   PHE A 286 
 TRP   0.008   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6145)
  covalent geometry    : angle       0.52841 ( 8330)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.09351 (    2)
  hydrogen bonds       : bond        0.03982 (  286)
  hydrogen bonds       : angle       3.72902 (  816)
  link_BETA1-4         : bond        0.00362 (    3)
  link_BETA1-4         : angle       1.39191 (    9)
  link_NAG-ASN         : bond        0.00298 (    4)
  link_NAG-ASN         : angle       3.66543 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8537 (t0) cc_final: 0.8323 (t70)
REVERT: A  183 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8364 (m-30)
REVERT: A  285 TYR cc_start: 0.8169 (t80) cc_final: 0.7733 (t80)
REVERT: A  417 ASP cc_start: 0.8368 (t0) cc_final: 0.7924 (t0)
REVERT: A  619 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8491 (tm-30)
REVERT: A  663 GLN cc_start: 0.8891 (tp-100) cc_final: 0.7739 (tp-100)
REVERT: A  667 GLN cc_start: 0.9575 (mt0) cc_final: 0.9123 (mt0)
REVERT: A  680 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.6938 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8211 (tp40) cc_final: 0.8007 (tp40)
REVERT: P   94 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6641 (p90)
  outliers start: 7
  outliers final: 3
  residues processed: 67
  average time/residue: 0.1067
  time to fit residues: 9.1120
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0980
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.124648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.086424 restraints weight = 9452.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.84
r_work: 0.2860 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6153  Z= 0.112
  Angle     :  0.544   9.860   8353  Z= 0.254
  Chirality :  0.039   0.150    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.339 106.230   1011
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.44 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.25 (0.34), residues: 692
  helix:  2.58 (0.29), residues: 349
  sheet:  1.96 (0.59), residues: 70
  loop : -0.07 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.017   0.001   TYR A 285 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.010   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6145)
  covalent geometry    : angle       0.51447 ( 8330)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.05267 (    2)
  hydrogen bonds       : bond        0.03781 (  286)
  hydrogen bonds       : angle       3.68084 (  816)
  link_BETA1-4         : bond        0.00391 (    3)
  link_BETA1-4         : angle       1.36692 (    9)
  link_NAG-ASN         : bond        0.00950 (    4)
  link_NAG-ASN         : angle       4.60743 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8507 (t0) cc_final: 0.8279 (t70)
REVERT: A  183 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8359 (m-30)
REVERT: A  285 TYR cc_start: 0.8110 (t80) cc_final: 0.7782 (t80)
REVERT: A  619 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8504 (tm-30)
REVERT: A  663 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8402 (tp-100)
REVERT: A  680 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.6914 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8195 (tp40) cc_final: 0.7981 (tp40)
REVERT: P   94 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6593 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0967
  time to fit residues: 8.0820
Evaluate side-chains
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.123394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.085059 restraints weight = 9524.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 2.88
r_work: 0.2838 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6153  Z= 0.146
  Angle     :  0.554   8.433   8353  Z= 0.262
  Chirality :  0.040   0.169    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.341 109.162   1011
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.28 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.25 (0.34), residues: 692
  helix:  2.53 (0.29), residues: 349
  sheet:  1.87 (0.58), residues: 75
  loop : -0.02 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 683 
 TYR   0.011   0.001   TYR A 285 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.008   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6145)
  covalent geometry    : angle       0.53394 ( 8330)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.10273 (    2)
  hydrogen bonds       : bond        0.04059 (  286)
  hydrogen bonds       : angle       3.71828 (  816)
  link_BETA1-4         : bond        0.00339 (    3)
  link_BETA1-4         : angle       1.40934 (    9)
  link_NAG-ASN         : bond        0.00379 (    4)
  link_NAG-ASN         : angle       3.79800 (   12)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8533 (t0) cc_final: 0.8326 (t70)
REVERT: A  183 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8372 (m-30)
REVERT: A  619 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: A  663 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8446 (tp-100)
REVERT: A  680 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.6946 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8218 (tp40) cc_final: 0.8006 (tp40)
REVERT: P   94 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6629 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 64
  average time/residue: 0.0960
  time to fit residues: 7.8480
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.123281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.085369 restraints weight = 9467.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.82
r_work: 0.2842 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6153  Z= 0.142
  Angle     :  0.561  11.075   8353  Z= 0.265
  Chirality :  0.040   0.163    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.347 107.312   1011
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.28 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 aren not related in a simple way.
  whole:  2.23 (0.34), residues: 692
  helix:  2.52 (0.29), residues: 349
  sheet:  1.87 (0.58), residues: 75
  loop : -0.03 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.013   0.001   TYR A 458 
 PHE   0.007   0.001   PHE A 684 
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6145)
  covalent geometry    : angle       0.53146 ( 8330)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.09385 (    2)
  hydrogen bonds       : bond        0.04040 (  286)
  hydrogen bonds       : angle       3.72537 (  816)
  link_BETA1-4         : bond        0.00348 (    3)
  link_BETA1-4         : angle       1.39767 (    9)
  link_NAG-ASN         : bond        0.00270 (    4)
  link_NAG-ASN         : angle       4.61745 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1510.08 seconds
wall clock time: 26 minutes 34.68 seconds (1594.68 seconds total)