Starting phenix.real_space_refine
on Tue Feb 11 14:34:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvq_44941/02_2025/9bvq_44941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvq_44941/02_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_44941/02_2025/9bvq_44941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvq_44941/02_2025/9bvq_44941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvq_44941/02_2025/9bvq_44941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvq_44941/02_2025/9bvq_44941.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.38, per 1000 atoms: 0.73
  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: 1.71
  Conformation dependent library (CDL) restraints added in 819.6 milliseconds
  

  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: 0.82
  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: 1.61

  Time building geometry restraints manager: 1.74 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:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.940
-------------------------------------------------------------------------------
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      :  0.003   0.027   6145  Z= 0.179
  Angle     :  0.471   6.045   8330  Z= 0.235
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (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
 TRP   0.006   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 406 

*********************** 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  : 0.604 
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: 0.2899
  time to fit residues: 40.2047
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  : 0.661 
-------------------------------------------------------------------------------
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 58 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0010
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5706

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.129645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.091720 restraints weight = 9155.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.77
r_work: 0.2931 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    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 = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6145  Z= 0.186
  Angle     :  0.618  11.523   8330  Z= 0.282
  Chirality :  0.043   0.292    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 14.530  77.767   1011
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 2.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.34), residues: 692
  helix:  1.80 (0.29), residues: 355
  sheet:  1.73 (0.58), residues: 73
  loop : -0.37 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 315 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.011   0.001   TYR A 285 
 ARG   0.006   0.001   ARG A 671 

*********************** 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
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8499 (t0) cc_final: 0.8285 (t0)
REVERT: A  180 TRP cc_start: 0.7858 (t60) cc_final: 0.7216 (t-100)
REVERT: A  663 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8537 (tp-100)
REVERT: A  680 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.6835 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6584 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 65
  average time/residue: 0.2521
  time to fit residues: 20.6966
Evaluate side-chains
  56 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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 6 optimal weight:    0.0270
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.1444

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.128811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.090728 restraints weight = 9406.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.73
r_work: 0.2920 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6145  Z= 0.286
  Angle     :  0.588   7.553   8330  Z= 0.280
  Chirality :  0.044   0.318    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 12.457  75.473   1011
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.34), residues: 692
  helix:  1.95 (0.29), residues: 355
  sheet:  1.74 (0.58), residues: 73
  loop : -0.37 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 315 
 HIS   0.007   0.001   HIS P  44 
 PHE   0.010   0.001   PHE A 299 
 TYR   0.012   0.001   TYR A 285 
 ARG   0.006   0.000   ARG A 671 

*********************** 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
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8532 (t0) cc_final: 0.8317 (t0)
REVERT: A  183 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (m-30)
REVERT: A  619 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8609 (tm-30)
REVERT: A  663 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8548 (tp-100)
REVERT: A  680 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.6878 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6696 (p90)
  outliers start: 10
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2381
  time to fit residues: 20.0368
Evaluate side-chains
  60 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0870
   chunk 1 optimal weight:    0.2980
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0770
   overall best weight:    0.4316

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.125632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.087563 restraints weight = 9340.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.85
r_work: 0.2877 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6145  Z= 0.153
  Angle     :  0.543  10.176   8330  Z= 0.251
  Chirality :  0.040   0.235    905
  Planarity :  0.004   0.049   1034
  Dihedral  : 10.842  62.968   1011
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.39 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.34), residues: 692
  helix:  2.19 (0.29), residues: 355
  sheet:  1.75 (0.58), residues: 73
  loop : -0.31 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 
 PHE   0.007   0.001   PHE P  90 
 TYR   0.009   0.001   TYR A 285 
 ARG   0.006   0.000   ARG A 671 

*********************** 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: 6
    poor density    : 60
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8516 (t0) cc_final: 0.8278 (t0)
REVERT: A  183 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (m-30)
REVERT: A  229 MET cc_start: 0.8839 (mtt) cc_final: 0.8424 (mtt)
REVERT: A  520 LYS cc_start: 0.8535 (tppp) cc_final: 0.8189 (mmmt)
REVERT: A  619 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8489 (tm-30)
REVERT: A  663 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: A  680 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.6870 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6565 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 65
  average time/residue: 0.2254
  time to fit residues: 18.7994
Evaluate side-chains
  59 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0980
   chunk 68 optimal weight:    3.9990
   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 = 0.3571 r_free = 0.3571 target = 0.124269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.086061 restraints weight = 9395.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.85
r_work: 0.2856 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6145  Z= 0.210
  Angle     :  0.559   8.046   8330  Z= 0.259
  Chirality :  0.042   0.247    905
  Planarity :  0.004   0.050   1034
  Dihedral  : 10.288  59.239   1011
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.34), residues: 692
  helix:  2.25 (0.29), residues: 355
  sheet:  1.90 (0.59), residues: 71
  loop : -0.29 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.005   0.001   HIS P  44 
 PHE   0.008   0.001   PHE A 684 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

*********************** 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
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8505 (t0) cc_final: 0.8305 (t0)
REVERT: A  183 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8394 (m-30)
REVERT: A  236 TRP cc_start: 0.8675 (p-90) cc_final: 0.8467 (p-90)
REVERT: A  285 TYR cc_start: 0.8320 (t80) cc_final: 0.7985 (t80)
REVERT: A  619 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8494 (tm-30)
REVERT: A  663 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8518 (tp-100)
REVERT: A  671 ARG cc_start: 0.9423 (tmm-80) cc_final: 0.8975 (ttp80)
REVERT: A  680 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.6766 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6602 (p90)
  outliers start: 7
  outliers final: 2
  residues processed: 65
  average time/residue: 0.2067
  time to fit residues: 17.4807
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  : 0.629 
-------------------------------------------------------------------------------
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 66 optimal weight:    0.0770
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0980
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.125125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.087134 restraints weight = 9242.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.83
r_work: 0.2874 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6145  Z= 0.161
  Angle     :  0.528   7.735   8330  Z= 0.248
  Chirality :  0.040   0.248    905
  Planarity :  0.004   0.051   1034
  Dihedral  : 11.103 105.541   1011
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.86 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.34), residues: 692
  helix:  2.35 (0.29), residues: 355
  sheet:  1.92 (0.59), residues: 71
  loop : -0.24 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.007   0.001   PHE P  90 
 TYR   0.011   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 683 

*********************** 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  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8511 (t0) cc_final: 0.8289 (t0)
REVERT: A  183 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8390 (m-30)
REVERT: A  285 TYR cc_start: 0.8311 (t80) cc_final: 0.7841 (t80)
REVERT: A  417 ASP cc_start: 0.8258 (t0) cc_final: 0.7870 (t0)
REVERT: A  520 LYS cc_start: 0.8525 (tppp) cc_final: 0.8317 (tttm)
REVERT: A  619 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: A  663 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8549 (tp-100)
REVERT: A  671 ARG cc_start: 0.9442 (tmm-80) cc_final: 0.8973 (ttp80)
REVERT: A  680 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.6772 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6598 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 64
  average time/residue: 0.2508
  time to fit residues: 21.5320
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  : 0.779 
-------------------------------------------------------------------------------
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  228 SER
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 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.1980
   chunk 44 optimal weight:    0.0870
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.125452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.087351 restraints weight = 9402.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.86
r_work: 0.2873 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6145  Z= 0.157
  Angle     :  0.507   8.002   8330  Z= 0.241
  Chirality :  0.039   0.172    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.519 106.009   1011
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.34 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.34), residues: 692
  helix:  2.40 (0.29), residues: 355
  sheet:  1.75 (0.58), residues: 73
  loop : -0.20 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.017   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 683 

*********************** 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: 7
    poor density    : 57
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8511 (t0) cc_final: 0.8291 (t70)
REVERT: A  183 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8394 (m-30)
REVERT: A  619 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: A  663 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8553 (tp-100)
REVERT: A  680 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.6797 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8175 (tp40) cc_final: 0.7960 (tp40)
REVERT: P   94 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6651 (p90)
  outliers start: 7
  outliers final: 3
  residues processed: 62
  average time/residue: 0.2191
  time to fit residues: 18.0306
Evaluate side-chains
  60 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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 A residue  713 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 41 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.123882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.086032 restraints weight = 9265.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.83
r_work: 0.2871 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6145  Z= 0.172
  Angle     :  0.510   7.302   8330  Z= 0.243
  Chirality :  0.039   0.166    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.273 109.243   1011
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  9.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.34), residues: 692
  helix:  2.40 (0.29), residues: 356
  sheet:  1.97 (0.58), residues: 71
  loop : -0.20 (0.42), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.023   0.001   TYR A 285 
 ARG   0.006   0.000   ARG A 683 

*********************** 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
  63 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8515 (t0) cc_final: 0.8299 (t70)
REVERT: A  183 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8379 (m-30)
REVERT: A  619 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8517 (tm-30)
REVERT: A  663 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8540 (tp-100)
REVERT: A  680 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.6807 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8205 (tp40) cc_final: 0.7995 (tp40)
REVERT: P   94 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6649 (p90)
  outliers start: 5
  outliers final: 2
  residues processed: 61
  average time/residue: 0.2272
  time to fit residues: 18.0361
Evaluate side-chains
  60 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 6 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   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 = 0.3587 r_free = 0.3587 target = 0.124188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.086296 restraints weight = 9356.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.85
r_work: 0.2911 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6145  Z= 0.164
  Angle     :  0.512   7.229   8330  Z= 0.245
  Chirality :  0.039   0.148    905
  Planarity :  0.004   0.046   1034
  Dihedral  : 10.320 110.821   1011
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.34), residues: 692
  helix:  2.43 (0.29), residues: 356
  sheet:  2.03 (0.59), residues: 70
  loop : -0.13 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.006   0.001   PHE A 286 
 TYR   0.029   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 683 

*********************** 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
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8396 (m-30)
REVERT: A  619 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8526 (tm-30)
REVERT: A  663 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8019 (tp-100)
REVERT: A  667 GLN cc_start: 0.9581 (mt0) cc_final: 0.9139 (mt0)
REVERT: A  680 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.6814 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8197 (tp40) cc_final: 0.7987 (tp40)
REVERT: P   94 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6657 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 63
  average time/residue: 0.2061
  time to fit residues: 17.0931
Evaluate side-chains
  62 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
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 38 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 57 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 44 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.125507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.087216 restraints weight = 9382.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.89
r_work: 0.2875 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6145  Z= 0.156
  Angle     :  0.509   7.084   8330  Z= 0.244
  Chirality :  0.039   0.147    905
  Planarity :  0.004   0.044   1034
  Dihedral  : 10.311 113.521   1011
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.34), residues: 692
  helix:  2.44 (0.29), residues: 356
  sheet:  2.01 (0.58), residues: 71
  loop : -0.15 (0.42), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.033   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 683 

********************** 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
  64 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8375 (m-30)
REVERT: A  459 ASN cc_start: 0.7562 (t0) cc_final: 0.7328 (t0)
REVERT: A  619 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8515 (tm-30)
REVERT: A  663 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8385 (tp-100)
REVERT: A  667 GLN cc_start: 0.9582 (mt0) cc_final: 0.9370 (mt0)
REVERT: A  680 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.6805 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8175 (tp40) cc_final: 0.7963 (tp40)
REVERT: P   94 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6649 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 63
  average time/residue: 0.2082
  time to fit residues: 17.4582
Evaluate side-chains
  63 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.123911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.085547 restraints weight = 9497.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.89
r_work: 0.2848 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    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 = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6145  Z= 0.214
  Angle     :  0.544   9.673   8330  Z= 0.259
  Chirality :  0.040   0.156    905
  Planarity :  0.004   0.044   1034
  Dihedral  : 10.285 112.376   1011
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.44 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.35), residues: 692
  helix:  2.36 (0.29), residues: 356
  sheet:  1.77 (0.57), residues: 78
  loop : -0.13 (0.43), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.009   0.001   PHE A 286 
 TYR   0.029   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 683 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2884.55 seconds
wall clock time: 52 minutes 4.82 seconds (3124.82 seconds total)