Starting phenix.real_space_refine
on Tue Feb 11 07:05:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xps_38560/02_2025/8xps_38560.cif"
  }
  resolution = 3.22
  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=  -0.024 sd=   0.413
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: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    2874      2.51       5
     N     727      2.21       5
     O     942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4568
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 898
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
    Chain: "A"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3376
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 402}
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.35, per 1000 atoms: 0.73
  Number of scatterers: 4568
  At special positions: 0
  Unit cell: (84.812, 84.812, 110.908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O     942      8.00
     N     727      7.00
     C    2874      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 216 " - pdb=" SG  CYS A 240 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 499 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 493 " - pdb=" SG  CYS A 503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 565 " - pdb=" SG  CYS A 574 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA D   3 " - " MAN D   6 "
      " BMA G   3 " - " MAN G   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   4 "
      " MAN C   4 " - " MAN C   5 "
      " BMA D   3 " - " MAN D   4 "
      " MAN D   4 " - " MAN D   5 "
      " BMA E   3 " - " MAN E   4 "
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 417 "
      " NAG D   1 " - " ASN A 306 "
      " NAG E   1 " - " ASN A 195 "
      " NAG F   1 " - " ASN A 529 "
      " NAG G   1 " - " ASN A 378 "
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 496.0 milliseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 13 sheets defined
      3.1% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.517A  pdb=" N   THR B  91 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
    Processing helix  chain 'A' and resid 393 through 399
      removed outlier: 3.590A  pdb=" N   MET A 399 " --> pdb=" O   CYS A 395 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.627A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.572A  pdb=" N   SER B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 225
      removed outlier: 5.994A  pdb=" N   SER A 232 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 222 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA A 230 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 224 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLN A 247 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 225
      removed outlier: 5.994A  pdb=" N   SER A 232 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 222 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA A 230 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 224 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU A 254 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   MET A 267 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 279 through 284
      removed outlier: 5.324A  pdb=" N   HIS A 281 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA A 296 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LEU A 314 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 350
      removed outlier: 3.836A  pdb=" N   MET A 349 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A 363 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE A 356 " --> pdb=" O   TYR A 363 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 350
      removed outlier: 3.836A  pdb=" N   MET A 349 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 442 through 447
    Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 471
      removed outlier: 3.667A  pdb=" N   GLN A 470 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL A 476 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 512 through 515
      removed outlier: 6.465A  pdb=" N   ILE A 520 " --> pdb=" O   ILE A 514 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 540 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   TYR A 547 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 561 through 567
      removed outlier: 3.532A  pdb=" N   SER A 576 " --> pdb=" O   PHE A 593 " (cutoff:3.500A)

    101 hydrogen bonds defined for protein.
    264 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: 1.25

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 956
        1.33 -     1.45: 1143
        1.45 -     1.57: 2531
        1.57 -     1.69: 3
        1.69 -     1.81: 34
  Bond restraints: 4667
  Sorted by residual:
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.587 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" N   LEU A 475 "
       pdb=" CA  LEU A 475 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.038 1.30e-02 5.92e+03 8.68e+00
  bond pdb=" N   ASN A 473 "
       pdb=" CA  ASN A 473 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.026 9.50e-03 1.11e+04 7.35e+00
  bond pdb=" C4  BMA F   3 "
       pdb=" C5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.582 -0.054 2.00e-02 2.50e+03 7.24e+00
  bond pdb=" N   VAL A 477 "
       pdb=" CA  VAL A 477 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.20e-02 6.94e+03 6.28e+00
  ... (remaining 4662 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 6169
        2.28 -     4.56: 134
        4.56 -     6.84: 37
        6.84 -     9.12: 3
        9.12 -    11.41: 2
  Bond angle restraints: 6345
  Sorted by residual:
  angle pdb=" N   GLN A 470 "
        pdb=" CA  GLN A 470 "
        pdb=" C   GLN A 470 "
      ideal   model   delta    sigma   weight residual
     113.88  105.95    7.93 1.23e+00 6.61e-01 4.16e+01
  angle pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
        pdb=" C   PRO A 474 "
      ideal   model   delta    sigma   weight residual
     112.47  101.06   11.41 2.06e+00 2.36e-01 3.07e+01
  angle pdb=" CA  ASN A 478 "
        pdb=" C   ASN A 478 "
        pdb=" O   ASN A 478 "
      ideal   model   delta    sigma   weight residual
     120.98  116.51    4.47 1.08e+00 8.57e-01 1.72e+01
  angle pdb=" CA  LEU A 475 "
        pdb=" C   LEU A 475 "
        pdb=" O   LEU A 475 "
      ideal   model   delta    sigma   weight residual
     121.02  116.56    4.46 1.15e+00 7.56e-01 1.50e+01
  angle pdb=" N   PRO A 474 "
        pdb=" CD  PRO A 474 "
        pdb=" CG  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     103.20   98.30    4.90 1.50e+00 4.44e-01 1.07e+01
  ... (remaining 6340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.21: 2918
       24.21 -    48.41: 88
       48.41 -    72.62: 20
       72.62 -    96.83: 47
       96.83 -   121.03: 25
  Dihedral angle restraints: 3098
    sinusoidal: 1516
      harmonic: 1582
  Sorted by residual:
  dihedral pdb=" C   ASN A 473 "
           pdb=" N   ASN A 473 "
           pdb=" CA  ASN A 473 "
           pdb=" CB  ASN A 473 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.34   11.74     0      2.50e+00 1.60e-01 2.21e+01
  dihedral pdb=" N   ASN A 473 "
           pdb=" C   ASN A 473 "
           pdb=" CA  ASN A 473 "
           pdb=" CB  ASN A 473 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.58  -10.78     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" C2  MAN D   4 "
           pdb=" C1  MAN D   4 "
           pdb=" O5  MAN D   4 "
           pdb=" C5  MAN D   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   63.41 -121.03     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 3095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 684
       0.087 -    0.174: 81
       0.174 -    0.260: 7
       0.260 -    0.347: 2
       0.347 -    0.434: 1
  Chirality restraints: 775
  Sorted by residual:
  chirality pdb=" CA  ASN A 473 "
            pdb=" N   ASN A 473 "
            pdb=" C   ASN A 473 "
            pdb=" CB  ASN A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.71e+00
  chirality pdb=" CA  VAL A 477 "
            pdb=" N   VAL A 477 "
            pdb=" C   VAL A 477 "
            pdb=" CB  VAL A 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 772 not shown)

  Planarity restraints: 783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 473 "    0.014 2.00e-02 2.50e+03   2.71e-02 7.37e+00
        pdb=" C   ASN A 473 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASN A 473 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A 474 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 467 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.21e+00
        pdb=" C   GLY A 467 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A 467 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 468 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 473 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 474 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 474 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 474 "    0.022 5.00e-02 4.00e+02
  ... (remaining 780 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 418
        2.75 -     3.28: 4268
        3.28 -     3.82: 7226
        3.82 -     4.36: 8373
        4.36 -     4.90: 14560
  Nonbonded interactions: 34845
  Sorted by model distance:
  nonbonded pdb=" O3  NAG G   2 "
            pdb=" O2  BMA G   3 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR B  32 "
            pdb=" O   ASP A 257 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR A 454 "
            pdb=" O   ASN A 509 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O3  NAG F   2 "
            pdb=" O2  BMA F   3 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O3  NAG D   2 "
            pdb=" O2  BMA D   3 "
     model   vdw
     2.348 3.040
  ... (remaining 34840 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 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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=1.00 max=1.00 mean=1.00
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:             0.890
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.020
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
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      :  0.005   0.068   4667  Z= 0.278
  Angle     :  0.852  11.406   6345  Z= 0.429
  Chirality :  0.057   0.434    775
  Planarity :  0.003   0.039    778
  Dihedral  : 20.478 121.032   2064
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.04 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  :  5.62 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.20 %
  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: -4.49 (0.29), residues: 542
  helix: -1.38 (2.33), residues: 6
  sheet: -2.13 (0.35), residues: 173
  loop : -3.70 (0.25), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 310 
 HIS   0.001   0.000   HIS A 233 
 PHE   0.005   0.001   PHE A 537 
 TYR   0.004   0.001   TYR A 454 
 ARG   0.001   0.000   ARG B  98 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8858 (mt) cc_final: 0.8345 (mt)
REVERT: A  197 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8311 (tp)
REVERT: A  360 ASP cc_start: 0.7905 (t0) cc_final: 0.7643 (t0)
  outliers start: 22
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2206
  time to fit residues: 38.8083
Evaluate side-chains
  103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  472 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
A 326 ASN
A 334 GLN
A 358 GLN
A 394 ASN
A 478 ASN
A 534 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.062041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.055022 restraints weight = 15409.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.95
r_work: 0.2935 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4667  Z= 0.267
  Angle     :  0.818  10.844   6345  Z= 0.381
  Chirality :  0.050   0.214    775
  Planarity :  0.005   0.043    778
  Dihedral  : 21.072 108.381   1084
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 12.71 %
    Favored  : 81.88 %
  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: -3.80 (0.31), residues: 542
  helix: -3.32 (0.78), residues: 6
  sheet: -1.55 (0.36), residues: 183
  loop : -3.27 (0.27), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 573 
 HIS   0.001   0.000   HIS A 406 
 PHE   0.017   0.002   PHE A 364 
 TYR   0.016   0.002   TYR B  50 
 ARG   0.005   0.001   ARG A 372 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.7935 (t0) cc_final: 0.7651 (t0)
REVERT: B   76 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8105 (mmtt)
REVERT: B  103 VAL cc_start: 0.8064 (m) cc_final: 0.7692 (m)
REVERT: A  291 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8319 (t80)
REVERT: A  360 ASP cc_start: 0.8515 (t0) cc_final: 0.8158 (t0)
REVERT: A  394 ASN cc_start: 0.8702 (m110) cc_final: 0.8490 (m-40)
REVERT: A  470 GLN cc_start: 0.8399 (pt0) cc_final: 0.8194 (pt0)
  outliers start: 26
  outliers final: 12
  residues processed: 123
  average time/residue: 0.1978
  time to fit residues: 30.1770
Evaluate side-chains
  105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.054905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.047920 restraints weight = 15708.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.93
r_work: 0.2736 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   4667  Z= 0.433
  Angle     :  0.903   9.462   6345  Z= 0.432
  Chirality :  0.052   0.262    775
  Planarity :  0.006   0.039    778
  Dihedral  : 19.487 107.540   1074
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 14.79 %
    Favored  : 80.62 %
  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: -3.11 (0.33), residues: 542
  helix:  0.08 (2.06), residues: 7
  sheet: -0.78 (0.38), residues: 175
  loop : -3.00 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 104 
 HIS   0.007   0.002   HIS A 233 
 PHE   0.024   0.003   PHE A 537 
 TYR   0.023   0.002   TYR A 351 
 ARG   0.009   0.001   ARG A 242 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8105 (t0) cc_final: 0.7708 (t0)
REVERT: B   76 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8083 (mmtt)
REVERT: A  261 GLU cc_start: 0.8608 (tp30) cc_final: 0.8271 (tp30)
REVERT: A  291 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8352 (t80)
REVERT: A  326 ASN cc_start: 0.8577 (p0) cc_final: 0.7990 (p0)
REVERT: A  360 ASP cc_start: 0.8619 (t0) cc_final: 0.8217 (t0)
REVERT: A  450 GLN cc_start: 0.8210 (tt0) cc_final: 0.7912 (tt0)
REVERT: A  466 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8130 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1696
  time to fit residues: 22.8732
Evaluate side-chains
  96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  518 ASN
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.056761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.049632 restraints weight = 15681.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 2.93
r_work: 0.2791 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4667  Z= 0.216
  Angle     :  0.800  12.762   6345  Z= 0.369
  Chirality :  0.049   0.285    775
  Planarity :  0.004   0.034    778
  Dihedral  : 17.781 110.152   1072
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 16.67 %
    Favored  : 78.75 %
  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: -2.77 (0.33), residues: 542
  helix:  1.41 (2.17), residues: 6
  sheet: -0.41 (0.39), residues: 175
  loop : -2.86 (0.28), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.015   0.002   PHE B  68 
 TYR   0.016   0.002   TYR A 351 
 ARG   0.009   0.001   ARG B  19 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8032 (t0) cc_final: 0.7681 (t0)
REVERT: B   76 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8204 (mmtt)
REVERT: B   85 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.7475 (p)
REVERT: A  235 GLU cc_start: 0.8186 (mp0) cc_final: 0.7722 (mp0)
REVERT: A  261 GLU cc_start: 0.8491 (tp30) cc_final: 0.8124 (tp30)
REVERT: A  291 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8238 (t80)
REVERT: A  360 ASP cc_start: 0.8514 (t0) cc_final: 0.8159 (t0)
REVERT: A  450 GLN cc_start: 0.8113 (tt0) cc_final: 0.7866 (tt0)
REVERT: A  466 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7900 (m-10)
  outliers start: 22
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1801
  time to fit residues: 23.4674
Evaluate side-chains
  97 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 HIS
A 332 GLN
A 394 ASN
A 600 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.056100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.049033 restraints weight = 15738.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 2.93
r_work: 0.2772 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4667  Z= 0.254
  Angle     :  0.820  12.510   6345  Z= 0.379
  Chirality :  0.050   0.280    775
  Planarity :  0.004   0.035    778
  Dihedral  : 16.993 110.347   1072
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.08 %
    Favored  : 78.75 %
  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: -2.54 (0.33), residues: 542
  helix:  1.72 (2.29), residues: 6
  sheet: -0.18 (0.39), residues: 175
  loop : -2.74 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.018   0.002   PHE B  68 
 TYR   0.014   0.002   TYR B  80 
 ARG   0.007   0.001   ARG B  67 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.490 
Fit side-chains
REVERT: B   73 ASP cc_start: 0.8010 (t0) cc_final: 0.7650 (t0)
REVERT: B   76 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8234 (mmtt)
REVERT: A  235 GLU cc_start: 0.8132 (mp0) cc_final: 0.7702 (mp0)
REVERT: A  291 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.8250 (t80)
REVERT: A  360 ASP cc_start: 0.8502 (t0) cc_final: 0.8110 (t0)
REVERT: A  394 ASN cc_start: 0.8750 (m110) cc_final: 0.8501 (m-40)
REVERT: A  450 GLN cc_start: 0.8169 (tt0) cc_final: 0.7925 (tt0)
REVERT: A  466 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (m-10)
  outliers start: 20
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1873
  time to fit residues: 22.9959
Evaluate side-chains
  98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  600 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0370
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 600 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.057105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.049786 restraints weight = 15367.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.98
r_work: 0.2791 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4667  Z= 0.245
  Angle     :  0.848  12.632   6345  Z= 0.394
  Chirality :  0.051   0.280    775
  Planarity :  0.004   0.045    778
  Dihedral  : 16.348 110.966   1072
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.67 %
    Favored  : 80.00 %
  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: -2.39 (0.34), residues: 542
  helix:  2.06 (2.37), residues: 6
  sheet: -0.10 (0.39), residues: 178
  loop : -2.65 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.016   0.002   PHE B  68 
 TYR   0.013   0.001   TYR A 351 
 ARG   0.006   0.000   ARG A 242 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.536 
Fit side-chains
REVERT: B   67 ARG cc_start: 0.7786 (mmt-90) cc_final: 0.7274 (mmt-90)
REVERT: B   73 ASP cc_start: 0.8062 (t0) cc_final: 0.7724 (t0)
REVERT: B   76 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8273 (mmtt)
REVERT: B  113 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8410 (p)
REVERT: A  235 GLU cc_start: 0.8174 (mp0) cc_final: 0.7706 (mp0)
REVERT: A  291 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8188 (t80)
REVERT: A  360 ASP cc_start: 0.8480 (t0) cc_final: 0.8110 (t0)
REVERT: A  394 ASN cc_start: 0.8730 (m110) cc_final: 0.8518 (m-40)
REVERT: A  466 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7834 (m-10)
  outliers start: 16
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1818
  time to fit residues: 21.7800
Evaluate side-chains
  97 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 24 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.048034 restraints weight = 15534.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.94
r_work: 0.2742 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4667  Z= 0.306
  Angle     :  0.863  12.214   6345  Z= 0.407
  Chirality :  0.050   0.279    775
  Planarity :  0.005   0.040    778
  Dihedral  : 15.385 111.010   1072
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.12 %
    Favored  : 78.33 %
  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: -2.30 (0.34), residues: 542
  helix:  1.15 (2.43), residues: 7
  sheet: -0.09 (0.39), residues: 184
  loop : -2.58 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 104 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.023   0.002   PHE B  68 
 TYR   0.020   0.002   TYR B  80 
 ARG   0.006   0.001   ARG A 242 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.502 
Fit side-chains
REVERT: B   73 ASP cc_start: 0.8121 (t0) cc_final: 0.7689 (t0)
REVERT: B   76 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8307 (mmtt)
REVERT: B   78 THR cc_start: 0.9112 (p) cc_final: 0.8887 (p)
REVERT: A  235 GLU cc_start: 0.8208 (mp0) cc_final: 0.7673 (mp0)
REVERT: A  291 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.8196 (t80)
REVERT: A  360 ASP cc_start: 0.8563 (t0) cc_final: 0.8154 (t0)
REVERT: A  466 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7994 (m-10)
REVERT: A  585 ASP cc_start: 0.8513 (m-30) cc_final: 0.7445 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1808
  time to fit residues: 20.9277
Evaluate side-chains
  93 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.056714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.049263 restraints weight = 15378.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 3.09
r_work: 0.2773 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.5317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4667  Z= 0.228
  Angle     :  0.809  12.830   6345  Z= 0.381
  Chirality :  0.048   0.275    775
  Planarity :  0.004   0.045    778
  Dihedral  : 14.648 112.302   1072
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.96 %
    Favored  : 77.50 %
  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: -2.18 (0.35), residues: 542
  helix:  1.04 (2.33), residues: 7
  sheet:  0.07 (0.39), residues: 184
  loop : -2.54 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.021   0.002   PHE B  68 
 TYR   0.013   0.001   TYR A 351 
 ARG   0.009   0.001   ARG A 242 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8110 (t0) cc_final: 0.7635 (t0)
REVERT: B   76 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8333 (mmtt)
REVERT: B   78 THR cc_start: 0.9054 (p) cc_final: 0.8763 (p)
REVERT: A  235 GLU cc_start: 0.8233 (mp0) cc_final: 0.7672 (mp0)
REVERT: A  291 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8105 (t80)
REVERT: A  360 ASP cc_start: 0.8555 (t0) cc_final: 0.8040 (t0)
REVERT: A  394 ASN cc_start: 0.8798 (m110) cc_final: 0.8570 (m-40)
REVERT: A  466 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7876 (m-10)
REVERT: A  569 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8427 (ptmm)
  outliers start: 17
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1861
  time to fit residues: 22.8015
Evaluate side-chains
  101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.056452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.049342 restraints weight = 15516.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 2.93
r_work: 0.2785 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.5372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4667  Z= 0.235
  Angle     :  0.815  12.746   6345  Z= 0.385
  Chirality :  0.048   0.270    775
  Planarity :  0.006   0.084    778
  Dihedral  : 14.307 111.946   1072
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.12 %
    Favored  : 78.75 %
  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: -2.07 (0.35), residues: 542
  helix:  1.03 (2.32), residues: 7
  sheet:  0.19 (0.39), residues: 183
  loop : -2.49 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 479 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.029   0.002   PHE B  68 
 TYR   0.025   0.001   TYR B  80 
 ARG   0.012   0.001   ARG B  67 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.652 
Fit side-chains
REVERT: B    3 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8057 (mm110)
REVERT: B   73 ASP cc_start: 0.8100 (t0) cc_final: 0.7644 (t0)
REVERT: B   76 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8342 (mmtt)
REVERT: B   78 THR cc_start: 0.9031 (p) cc_final: 0.8755 (p)
REVERT: A  235 GLU cc_start: 0.8187 (mp0) cc_final: 0.7639 (mp0)
REVERT: A  291 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8103 (t80)
REVERT: A  360 ASP cc_start: 0.8471 (t0) cc_final: 0.8029 (t0)
REVERT: A  394 ASN cc_start: 0.8794 (m110) cc_final: 0.8583 (m-40)
REVERT: A  450 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7913 (tt0)
REVERT: A  466 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7850 (m-10)
REVERT: A  569 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8373 (ptmm)
  outliers start: 15
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1857
  time to fit residues: 21.5018
Evaluate side-chains
  95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  450 GLN
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.055969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.048707 restraints weight = 15537.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.95
r_work: 0.2765 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.5449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4667  Z= 0.266
  Angle     :  0.837  12.822   6345  Z= 0.400
  Chirality :  0.049   0.267    775
  Planarity :  0.006   0.118    778
  Dihedral  : 14.027 111.693   1072
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.71 %
    Favored  : 78.96 %
  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: -2.01 (0.36), residues: 542
  helix:  1.07 (2.33), residues: 7
  sheet:  0.22 (0.40), residues: 184
  loop : -2.45 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 504 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.026   0.002   PHE B  68 
 TYR   0.012   0.001   TYR A 351 
 ARG   0.013   0.001   ARG A 242 

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.541 
Fit side-chains
REVERT: B    3 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8052 (mm110)
REVERT: B   73 ASP cc_start: 0.8116 (t0) cc_final: 0.7660 (t0)
REVERT: B   76 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8372 (mmtt)
REVERT: B   78 THR cc_start: 0.9090 (p) cc_final: 0.8842 (p)
REVERT: A  291 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: A  360 ASP cc_start: 0.8497 (t0) cc_final: 0.7957 (t0)
REVERT: A  394 ASN cc_start: 0.8795 (m110) cc_final: 0.8593 (m-40)
REVERT: A  466 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7903 (m-10)
REVERT: A  585 ASP cc_start: 0.8430 (m-30) cc_final: 0.8173 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1813
  time to fit residues: 20.3667
Evaluate side-chains
  94 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  329 SER
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.2980
   chunk 5 optimal weight:    0.1980
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.057014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.049523 restraints weight = 15109.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.06
r_work: 0.2784 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4667  Z= 0.233
  Angle     :  0.834  12.854   6345  Z= 0.397
  Chirality :  0.048   0.262    775
  Planarity :  0.006   0.096    778
  Dihedral  : 13.633 111.895   1072
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.96 %
    Favored  : 77.92 %
  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: -1.95 (0.36), residues: 542
  helix:  1.00 (2.30), residues: 7
  sheet:  0.25 (0.40), residues: 184
  loop : -2.39 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.027   0.002   PHE B  68 
 TYR   0.011   0.001   TYR A 351 
 ARG   0.012   0.001   ARG A 242 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2215.65 seconds
wall clock time: 40 minutes 11.11 seconds (2411.11 seconds total)