Starting phenix.real_space_refine
on Fri Jul 25 05:17:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2025/9izp_61038.cif"
  }
  resolution = 2.89
  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
-------------------------------------------------------------------------------
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=   0.014 sd=   0.231
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: 6
    Type Number    sf(0)   Gaussians
     P      92      5.49       5
     Mg      3      5.21       5
     S      25      5.16       5
     C    4263      2.51       5
     N    1199      2.21       5
     O    1604      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-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7186
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 5246
          Classifications: {'peptide': 628}
          Link IDs: {'PTRANS': 8, 'TRANS': 619}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1127
          Classifications: {'RNA': 53}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 9, 'rna3p': 43}
    Chain: "C"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 265
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 545
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.76, per 1000 atoms: 0.66
  Number of scatterers: 7186
  At special positions: 0
  Unit cell: (89.64, 94.62, 110.805, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P      92     15.00
     Mg      3     11.99
     O    1604      8.00
     N    1199      7.00
     C    4263      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 2.05
  Conformation dependent library (CDL) restraints added in 620.0 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      57.0% alpha, 10.0% beta
      37 base pairs and 61 stacking pairs defined.
    Time for finding SS restraints: 2.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 37
      removed outlier: 3.591A  pdb=" N   ILE A  20 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 55
    Processing helix  chain 'A' and resid 58 through 63
    Processing helix  chain 'A' and resid 73 through 79
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 119 through 134
      removed outlier: 3.762A  pdb=" N   THR A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 165
      removed outlier: 3.577A  pdb=" N   GLN A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 181
      removed outlier: 3.807A  pdb=" N   TRP A 172 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASP A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 203
      removed outlier: 3.691A  pdb=" N   TYR A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS A 201 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN A 203 " --> pdb=" O   CYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 218
    Processing helix  chain 'A' and resid 277 through 287
      removed outlier: 3.520A  pdb=" N   TYR A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 353
    Processing helix  chain 'A' and resid 355 through 360
    Processing helix  chain 'A' and resid 363 through 375
      removed outlier: 3.556A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 397 through 418
    Processing helix  chain 'A' and resid 420 through 459
      removed outlier: 3.733A  pdb=" N   GLY A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 472
      removed outlier: 6.686A  pdb=" N   ASP A 472 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 483 through 517
      removed outlier: 3.645A  pdb=" N   ASN A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A 488 " --> pdb=" O   PRO A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 548
    Processing helix  chain 'A' and resid 562 through 571
    Processing helix  chain 'A' and resid 590 through 610
      removed outlier: 3.795A  pdb=" N   MET A 606 " --> pdb=" O   PHE A 602 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   MET A 607 " --> pdb=" O   PHE A 603 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS A 608 " --> pdb=" O   ASN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 4.370A  pdb=" N   SER A 305 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ASN A 290 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245
    Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 379
      removed outlier: 4.942A  pdb=" N   VAL A 377 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE A 332 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 335 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLY A 322 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 10.210A  pdb=" N   LYS A 337 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 13.177A  pdb=" N   THR A 320 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LYS A 319 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   ALA A 524 " --> pdb=" O   LYS A 319 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL A 321 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   GLU A 526 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU A 323 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 577
      removed outlier: 3.792A  pdb=" N   ASP A 586 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)

    268 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      89 hydrogen bonds
      174 hydrogen bond angles
      0 basepair planarities
      37 basepair parallelities
      61 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 2.37 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: 1212
        1.33 -     1.45: 2355
        1.45 -     1.57: 3722
        1.57 -     1.69: 182
        1.69 -     1.81: 39
  Bond restraints: 7510
  Sorted by residual:
  bond pdb=" CG1 ILE A   5 "
       pdb=" CD1 ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.23e+00
  bond pdb=" CG1 ILE A 514 "
       pdb=" CD1 ILE A 514 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.01e+00
  bond pdb=" CB  VAL A 273 "
       pdb=" CG1 VAL A 273 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" CB  LYS A 246 "
       pdb=" CG  LYS A 246 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" CG1 ILE A 238 "
       pdb=" CD1 ILE A 238 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.07e+00
  ... (remaining 7505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 9992
        1.14 -     2.29: 458
        2.29 -     3.43: 72
        3.43 -     4.57: 6
        4.57 -     5.71: 2
  Bond angle restraints: 10530
  Sorted by residual:
  angle pdb=" N   GLN A 272 "
        pdb=" CA  GLN A 272 "
        pdb=" C   GLN A 272 "
      ideal   model   delta    sigma   weight residual
     113.12  110.00    3.12 1.25e+00 6.40e-01 6.25e+00
  angle pdb=" C2'   G B   1 "
        pdb=" C1'   G B   1 "
        pdb=" N9    G B   1 "
      ideal   model   delta    sigma   weight residual
     112.00  115.73   -3.73 1.50e+00 4.44e-01 6.17e+00
  angle pdb=" CA  TYR A  60 "
        pdb=" CB  TYR A  60 "
        pdb=" CG  TYR A  60 "
      ideal   model   delta    sigma   weight residual
     113.90  118.07   -4.17 1.80e+00 3.09e-01 5.37e+00
  angle pdb=" CG1 VAL A 273 "
        pdb=" CB  VAL A 273 "
        pdb=" CG2 VAL A 273 "
      ideal   model   delta    sigma   weight residual
     110.80  106.13    4.67 2.20e+00 2.07e-01 4.51e+00
  angle pdb=" C2'   G B -33 "
        pdb=" C1'   G B -33 "
        pdb=" N9    G B -33 "
      ideal   model   delta    sigma   weight residual
     112.00  115.15   -3.15 1.50e+00 4.44e-01 4.41e+00
  ... (remaining 10525 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.07: 3810
       18.07 -    36.13: 432
       36.13 -    54.20: 171
       54.20 -    72.26: 95
       72.26 -    90.33: 7
  Dihedral angle restraints: 4515
    sinusoidal: 2636
      harmonic: 1879
  Sorted by residual:
  dihedral pdb=" CA  GLN A 272 "
           pdb=" C   GLN A 272 "
           pdb=" N   VAL A 273 "
           pdb=" CA  VAL A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  GLU A  68 "
           pdb=" C   GLU A  68 "
           pdb=" N   TRP A  69 "
           pdb=" CA  TRP A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.33  -16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ASN A 270 "
           pdb=" C   ASN A 270 "
           pdb=" N   ARG A 271 "
           pdb=" CA  ARG A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.42   16.58     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 743
       0.033 -    0.065: 315
       0.065 -    0.098: 97
       0.098 -    0.131: 40
       0.131 -    0.163: 3
  Chirality restraints: 1198
  Sorted by residual:
  chirality pdb=" C1'   G B   1 "
            pdb=" O4'   G B   1 "
            pdb=" C2'   G B   1 "
            pdb=" N9    G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" C1'   G B -33 "
            pdb=" O4'   G B -33 "
            pdb=" C2'   G B -33 "
            pdb=" N9    G B -33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" C1'   A B -24 "
            pdb=" O4'   A B -24 "
            pdb=" C2'   A B -24 "
            pdb=" N9    A B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1195 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   1 "   -0.031 2.00e-02 2.50e+03   1.32e-02 5.25e+00
        pdb=" N9    G B   1 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    G B   1 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B   1 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G B   1 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   1 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G B   1 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B   1 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B -33 "   -0.025 2.00e-02 2.50e+03   1.10e-02 3.66e+00
        pdb=" N9    G B -33 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G B -33 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G B -33 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B -33 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B -33 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B -33 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G B -33 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B -33 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G B -33 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G B -33 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B -33 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.024 2.00e-02 2.50e+03   1.07e-02 3.15e+00
        pdb=" N9    A B   7 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 28
        2.57 -     3.15: 5448
        3.15 -     3.73: 11763
        3.73 -     4.32: 17565
        4.32 -     4.90: 25896
  Nonbonded interactions: 60700
  Sorted by model distance:
  nonbonded pdb=" OP1   G B -30 "
            pdb="MG    MG A 801 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" OD1 ASP A 499 "
            pdb="MG    MG A 801 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" O4    U B -23 "
            pdb="MG    MG B 102 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" O2'   C B  -1 "
            pdb=" OP1   G B   1 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A 437 "
            pdb=" O   PHE A 602 "
     model   vdw
     2.251 3.040
  ... (remaining 60695 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.100
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.230
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:13.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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   0.058   7510  Z= 0.216
  Angle     :  0.554   5.713  10530  Z= 0.317
  Chirality :  0.041   0.163   1198
  Planarity :  0.003   0.042   1005
  Dihedral  : 18.573  90.329   3303
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.17 (0.33), residues: 624
  helix:  0.51 (0.29), residues: 322
  sheet:  1.16 (0.84), residues: 41
  loop : -1.06 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.002   PHE A 382 
 TYR   0.021   0.002   TYR A  92 
 ARG   0.010   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15475 (  357)
  hydrogen bonds       : angle       6.06837 (  951)
  covalent geometry    : bond        0.00483 ( 7510)
  covalent geometry    : angle       0.55443 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7742 (mttt) cc_final: 0.7461 (mtpp)
REVERT: A   88 ASP cc_start: 0.8338 (m-30) cc_final: 0.8087 (m-30)
REVERT: A  242 LYS cc_start: 0.8832 (tptt) cc_final: 0.8592 (tppp)
REVERT: A  323 LEU cc_start: 0.8325 (mt) cc_final: 0.8019 (tp)
REVERT: A  324 ASP cc_start: 0.7779 (t0) cc_final: 0.7152 (m-30)
REVERT: A  413 LYS cc_start: 0.8255 (tttt) cc_final: 0.8021 (ttpp)
REVERT: A  447 TYR cc_start: 0.8842 (t80) cc_final: 0.8629 (t80)
REVERT: A  471 MET cc_start: 0.6247 (mtm) cc_final: 0.5723 (mtp)
REVERT: A  512 TYR cc_start: 0.8236 (t80) cc_final: 0.7990 (t80)
REVERT: A  545 LEU cc_start: 0.8002 (tp) cc_final: 0.7735 (tp)
REVERT: A  612 PHE cc_start: 0.8328 (m-80) cc_final: 0.8043 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 1.2277
  time to fit residues: 144.9449
Evaluate side-chains
  77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 167 ASN
A 255 ASN
A 498 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.178492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141643 restraints weight = 8436.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 1.61
r_work: 0.3374 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7510  Z= 0.163
  Angle     :  0.530   5.092  10530  Z= 0.303
  Chirality :  0.038   0.149   1198
  Planarity :  0.003   0.040   1005
  Dihedral  : 21.089  91.487   1937
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.82 %
    Favored  : 91.16 %
  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:  0.44 (0.33), residues: 624
  helix:  1.10 (0.29), residues: 330
  sheet:  1.14 (0.70), residues: 54
  loop : -1.01 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.019   0.002   PHE A 478 
 TYR   0.017   0.002   TYR A 437 
 ARG   0.003   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  357)
  hydrogen bonds       : angle       4.44243 (  951)
  covalent geometry    : bond        0.00355 ( 7510)
  covalent geometry    : angle       0.53010 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7893 (mttt) cc_final: 0.7672 (mtpp)
REVERT: A   88 ASP cc_start: 0.8123 (m-30) cc_final: 0.7861 (m-30)
REVERT: A  242 LYS cc_start: 0.8631 (tptt) cc_final: 0.8307 (tptp)
REVERT: A  324 ASP cc_start: 0.7596 (t0) cc_final: 0.7131 (m-30)
REVERT: A  385 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7722 (mp10)
REVERT: A  413 LYS cc_start: 0.8374 (tttt) cc_final: 0.7960 (ttpp)
REVERT: A  437 TYR cc_start: 0.8010 (t80) cc_final: 0.7704 (t80)
REVERT: A  455 ASP cc_start: 0.8001 (m-30) cc_final: 0.7628 (m-30)
REVERT: A  471 MET cc_start: 0.6182 (mtm) cc_final: 0.5726 (mtp)
REVERT: A  525 LEU cc_start: 0.8178 (tp) cc_final: 0.7972 (mm)
REVERT: A  526 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6650 (tp30)
REVERT: A  537 GLN cc_start: 0.7426 (pm20) cc_final: 0.7215 (pm20)
REVERT: A  618 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7715 (mm-30)
  outliers start: 6
  outliers final: 0
  residues processed: 87
  average time/residue: 1.2400
  time to fit residues: 114.1864
Evaluate side-chains
  79 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.172610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.135236 restraints weight = 8466.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.64
r_work: 0.3281 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.069   7510  Z= 0.390
  Angle     :  0.703   7.468  10530  Z= 0.389
  Chirality :  0.049   0.199   1198
  Planarity :  0.004   0.041   1005
  Dihedral  : 21.441  93.001   1937
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.69 %
    Favored  : 88.10 %
  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: -0.02 (0.33), residues: 624
  helix:  0.69 (0.28), residues: 328
  sheet:  0.57 (0.72), residues: 52
  loop : -1.04 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 268 
 HIS   0.004   0.002   HIS A 549 
 PHE   0.019   0.003   PHE A 382 
 TYR   0.029   0.003   TYR A 437 
 ARG   0.003   0.001   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06084 (  357)
  hydrogen bonds       : angle       4.68605 (  951)
  covalent geometry    : bond        0.00876 ( 7510)
  covalent geometry    : angle       0.70329 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7947 (t0)
REVERT: A  242 LYS cc_start: 0.8586 (tptt) cc_final: 0.8278 (tptp)
REVERT: A  324 ASP cc_start: 0.7705 (t0) cc_final: 0.7248 (m-30)
REVERT: A  385 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7931 (mp10)
REVERT: A  413 LYS cc_start: 0.8420 (tttt) cc_final: 0.8043 (ttpp)
REVERT: A  471 MET cc_start: 0.6204 (mtm) cc_final: 0.5912 (mtm)
REVERT: A  490 LEU cc_start: 0.9098 (mt) cc_final: 0.8874 (mt)
REVERT: A  526 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6857 (tp30)
REVERT: A  537 GLN cc_start: 0.7564 (pm20) cc_final: 0.7339 (pm20)
REVERT: A  618 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7554 (mm-30)
  outliers start: 13
  outliers final: 3
  residues processed: 86
  average time/residue: 1.2332
  time to fit residues: 111.9850
Evaluate side-chains
  77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  541 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:   20.0000
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7878

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
A 156 GLN
A 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.181150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144928 restraints weight = 8570.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.61
r_work: 0.3412 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7510  Z= 0.122
  Angle     :  0.487   4.965  10530  Z= 0.282
  Chirality :  0.036   0.138   1198
  Planarity :  0.003   0.041   1005
  Dihedral  : 21.131  92.678   1937
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.24 %
    Favored  : 86.05 %
  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:  0.61 (0.34), residues: 624
  helix:  1.27 (0.29), residues: 332
  sheet:  0.66 (0.70), residues: 54
  loop : -0.87 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  33 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.013   0.001   PHE A 382 
 TYR   0.016   0.002   TYR A 589 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  357)
  hydrogen bonds       : angle       4.14081 (  951)
  covalent geometry    : bond        0.00258 ( 7510)
  covalent geometry    : angle       0.48740 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 ASP cc_start: 0.7380 (t0) cc_final: 0.7068 (m-30)
REVERT: A  385 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7836 (mp10)
REVERT: A  413 LYS cc_start: 0.8373 (tttt) cc_final: 0.7950 (ttpp)
REVERT: A  455 ASP cc_start: 0.7957 (m-30) cc_final: 0.7572 (m-30)
REVERT: A  471 MET cc_start: 0.6129 (mtm) cc_final: 0.5554 (mtp)
REVERT: A  526 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6561 (tp30)
REVERT: A  571 ASN cc_start: 0.6761 (m110) cc_final: 0.6458 (m-40)
REVERT: A  586 ASP cc_start: 0.8209 (t0) cc_final: 0.7505 (m-30)
REVERT: A  618 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: A  625 ASN cc_start: 0.7460 (t0) cc_final: 0.7204 (t0)
  outliers start: 10
  outliers final: 2
  residues processed: 90
  average time/residue: 1.1558
  time to fit residues: 110.5860
Evaluate side-chains
  83 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   overall best weight:    3.3986

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.176402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.139502 restraints weight = 8329.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.56
r_work: 0.3341 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7510  Z= 0.230
  Angle     :  0.573   5.349  10530  Z= 0.323
  Chirality :  0.041   0.165   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.159  93.104   1937
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.78 %
    Favored  : 84.01 %
  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:  0.42 (0.33), residues: 624
  helix:  1.15 (0.28), residues: 331
  sheet:  0.47 (0.69), residues: 54
  loop : -0.97 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  33 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.016   0.002   PHE A 382 
 TYR   0.020   0.002   TYR A  60 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04702 (  357)
  hydrogen bonds       : angle       4.23541 (  951)
  covalent geometry    : bond        0.00512 ( 7510)
  covalent geometry    : angle       0.57290 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 ASP cc_start: 0.7520 (t0) cc_final: 0.7179 (m-30)
REVERT: A  385 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7928 (mp10)
REVERT: A  413 LYS cc_start: 0.8388 (tttt) cc_final: 0.7996 (ttpp)
REVERT: A  455 ASP cc_start: 0.7956 (m-30) cc_final: 0.7591 (m-30)
REVERT: A  471 MET cc_start: 0.6157 (mtm) cc_final: 0.5637 (mtp)
REVERT: A  526 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6669 (tp30)
REVERT: A  625 ASN cc_start: 0.7570 (t0) cc_final: 0.7299 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 84
  average time/residue: 1.2044
  time to fit residues: 106.9785
Evaluate side-chains
  78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.177972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141328 restraints weight = 8403.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.56
r_work: 0.3370 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7510  Z= 0.177
  Angle     :  0.532   5.607  10530  Z= 0.303
  Chirality :  0.039   0.151   1198
  Planarity :  0.003   0.039   1005
  Dihedral  : 21.125  93.758   1937
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.29 %
    Favored  : 83.84 %
  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:  0.51 (0.33), residues: 624
  helix:  1.25 (0.28), residues: 332
  sheet:  0.43 (0.69), residues: 54
  loop : -0.97 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  33 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.014   0.001   PHE A 382 
 TYR   0.018   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  357)
  hydrogen bonds       : angle       4.13038 (  951)
  covalent geometry    : bond        0.00390 ( 7510)
  covalent geometry    : angle       0.53217 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.8012 (m-30) cc_final: 0.7718 (m-30)
REVERT: A  247 GLU cc_start: 0.7416 (mp0) cc_final: 0.6925 (mp0)
REVERT: A  324 ASP cc_start: 0.7531 (t0) cc_final: 0.7182 (m-30)
REVERT: A  385 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7952 (mp10)
REVERT: A  413 LYS cc_start: 0.8394 (tttt) cc_final: 0.7971 (ttpp)
REVERT: A  455 ASP cc_start: 0.7834 (m-30) cc_final: 0.7504 (m-30)
REVERT: A  471 MET cc_start: 0.6122 (mtm) cc_final: 0.5577 (mtp)
REVERT: A  526 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6695 (tp30)
REVERT: A  586 ASP cc_start: 0.8166 (t0) cc_final: 0.7574 (m-30)
REVERT: A  588 LYS cc_start: 0.8937 (mtmp) cc_final: 0.8657 (mtmm)
REVERT: A  618 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7587 (mm-30)
  outliers start: 11
  outliers final: 4
  residues processed: 82
  average time/residue: 1.7463
  time to fit residues: 151.6701
Evaluate side-chains
  78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 2 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.177890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141029 restraints weight = 8421.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.55
r_work: 0.3358 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7510  Z= 0.187
  Angle     :  0.549   6.166  10530  Z= 0.311
  Chirality :  0.039   0.153   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.123  94.022   1937
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.46 %
    Favored  : 83.33 %
  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:  0.52 (0.33), residues: 624
  helix:  1.26 (0.28), residues: 332
  sheet:  0.48 (0.69), residues: 54
  loop : -0.97 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  33 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.014   0.001   PHE A 382 
 TYR   0.020   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  357)
  hydrogen bonds       : angle       4.11346 (  951)
  covalent geometry    : bond        0.00412 ( 7510)
  covalent geometry    : angle       0.54854 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7947 (m-30) cc_final: 0.7631 (m-30)
REVERT: A  247 GLU cc_start: 0.7368 (mp0) cc_final: 0.6920 (mp0)
REVERT: A  324 ASP cc_start: 0.7517 (t0) cc_final: 0.7149 (m-30)
REVERT: A  385 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7908 (mp10)
REVERT: A  413 LYS cc_start: 0.8395 (tttt) cc_final: 0.7982 (ttpp)
REVERT: A  455 ASP cc_start: 0.7808 (m-30) cc_final: 0.7500 (m-30)
REVERT: A  471 MET cc_start: 0.6120 (mtm) cc_final: 0.5575 (mtp)
REVERT: A  526 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6740 (tp30)
REVERT: A  566 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8052 (mmtt)
REVERT: A  588 LYS cc_start: 0.8952 (mtmp) cc_final: 0.8658 (mtmm)
REVERT: A  618 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7562 (mm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 81
  average time/residue: 1.9889
  time to fit residues: 170.3529
Evaluate side-chains
  80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 16 optimal weight:   40.0000
   chunk 64 optimal weight:   10.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.176157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138893 restraints weight = 8455.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.58
r_work: 0.3329 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   7510  Z= 0.251
  Angle     :  0.609   6.405  10530  Z= 0.342
  Chirality :  0.042   0.173   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.219  94.634   1937
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.80 %
    Favored  : 83.16 %
  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:  0.42 (0.33), residues: 624
  helix:  1.16 (0.28), residues: 331
  sheet:  0.37 (0.69), residues: 54
  loop : -0.97 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 268 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.014   0.002   PHE A 382 
 TYR   0.022   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04880 (  357)
  hydrogen bonds       : angle       4.23744 (  951)
  covalent geometry    : bond        0.00563 ( 7510)
  covalent geometry    : angle       0.60937 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.7249 (pp-130) cc_final: 0.6864 (ppp)
REVERT: A  220 LYS cc_start: 0.7397 (mppt) cc_final: 0.6803 (tppt)
REVERT: A  247 GLU cc_start: 0.7199 (mp0) cc_final: 0.6811 (mp0)
REVERT: A  296 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8373 (m-40)
REVERT: A  324 ASP cc_start: 0.7545 (t0) cc_final: 0.7160 (m-30)
REVERT: A  385 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7874 (mp10)
REVERT: A  413 LYS cc_start: 0.8398 (tttt) cc_final: 0.7981 (ttpp)
REVERT: A  455 ASP cc_start: 0.7826 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  471 MET cc_start: 0.6260 (mtm) cc_final: 0.5676 (mtp)
REVERT: A  526 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6721 (tp30)
REVERT: A  588 LYS cc_start: 0.8969 (mtmp) cc_final: 0.8654 (mtmm)
REVERT: A  618 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7575 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 84
  average time/residue: 1.1577
  time to fit residues: 103.0998
Evaluate side-chains
  84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    3.3986

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.176613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.139628 restraints weight = 8415.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.57
r_work: 0.3342 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110   7510  Z= 0.231
  Angle     :  0.593   6.837  10530  Z= 0.335
  Chirality :  0.042   0.168   1198
  Planarity :  0.004   0.038   1005
  Dihedral  : 21.213  94.668   1937
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.99 %
    Favored  : 82.14 %
  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:  0.39 (0.33), residues: 624
  helix:  1.13 (0.28), residues: 331
  sheet:  0.30 (0.69), residues: 54
  loop : -0.95 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 268 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.014   0.002   PHE A 382 
 TYR   0.022   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04696 (  357)
  hydrogen bonds       : angle       4.25015 (  951)
  covalent geometry    : bond        0.00526 ( 7510)
  covalent geometry    : angle       0.59265 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.7886 (ptpp) cc_final: 0.7686 (pptt)
REVERT: A  247 GLU cc_start: 0.7183 (mp0) cc_final: 0.6817 (mp0)
REVERT: A  296 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8364 (m-40)
REVERT: A  324 ASP cc_start: 0.7530 (t0) cc_final: 0.7182 (m-30)
REVERT: A  385 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7862 (mp10)
REVERT: A  413 LYS cc_start: 0.8379 (tttt) cc_final: 0.7974 (ttpp)
REVERT: A  447 TYR cc_start: 0.8673 (t80) cc_final: 0.8432 (t80)
REVERT: A  455 ASP cc_start: 0.7791 (m-30) cc_final: 0.7480 (m-30)
REVERT: A  471 MET cc_start: 0.6288 (mtm) cc_final: 0.5728 (mtp)
REVERT: A  526 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6758 (tp30)
REVERT: A  588 LYS cc_start: 0.8981 (mtmp) cc_final: 0.8679 (mtmm)
REVERT: A  618 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7582 (mm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 80
  average time/residue: 1.2031
  time to fit residues: 102.0691
Evaluate side-chains
  82 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  526 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:   30.0000
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.181132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144792 restraints weight = 8626.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.58
r_work: 0.3407 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7510  Z= 0.141
  Angle     :  0.533   7.130  10530  Z= 0.305
  Chirality :  0.037   0.146   1198
  Planarity :  0.003   0.040   1005
  Dihedral  : 21.029  94.195   1937
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.82 %
    Favored  : 82.65 %
  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:  0.78 (0.34), residues: 624
  helix:  1.43 (0.28), residues: 331
  sheet:  0.60 (0.72), residues: 54
  loop : -0.77 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  33 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.011   0.001   PHE A 382 
 TYR   0.018   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  357)
  hydrogen bonds       : angle       4.08504 (  951)
  covalent geometry    : bond        0.00312 ( 7510)
  covalent geometry    : angle       0.53314 (10530)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7971 (m-30) cc_final: 0.7658 (m-30)
REVERT: A  155 MET cc_start: 0.7250 (pp-130) cc_final: 0.6864 (ppp)
REVERT: A  220 LYS cc_start: 0.7299 (mppt) cc_final: 0.6757 (tppt)
REVERT: A  296 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8383 (m-40)
REVERT: A  385 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7983 (mp10)
REVERT: A  413 LYS cc_start: 0.8366 (tttt) cc_final: 0.7959 (ttpp)
REVERT: A  455 ASP cc_start: 0.7642 (m-30) cc_final: 0.7258 (m-30)
REVERT: A  471 MET cc_start: 0.6123 (mtm) cc_final: 0.5597 (mtp)
REVERT: A  566 LYS cc_start: 0.8470 (mmtm) cc_final: 0.7887 (mmtt)
REVERT: A  586 ASP cc_start: 0.8153 (t0) cc_final: 0.7427 (m-30)
REVERT: A  588 LYS cc_start: 0.8984 (mtmp) cc_final: 0.8694 (mtmm)
REVERT: A  618 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7477 (mm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 82
  average time/residue: 1.1801
  time to fit residues: 102.5523
Evaluate side-chains
  80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** A 232 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 = 0.4070 r_free = 0.4070 target = 0.179391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.142599 restraints weight = 8472.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.56
r_work: 0.3376 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   7510  Z= 0.175
  Angle     :  0.558   6.818  10530  Z= 0.317
  Chirality :  0.039   0.155   1198
  Planarity :  0.003   0.038   1005
  Dihedral  : 21.025  94.461   1937
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.67 %
    Favored  : 82.31 %
  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:  0.79 (0.34), residues: 624
  helix:  1.43 (0.28), residues: 331
  sheet:  0.59 (0.72), residues: 54
  loop : -0.74 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  33 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.013   0.001   PHE A 478 
 TYR   0.020   0.002   TYR A 437 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  357)
  hydrogen bonds       : angle       4.11540 (  951)
  covalent geometry    : bond        0.00393 ( 7510)
  covalent geometry    : angle       0.55762 (10530)

===============================================================================
Job complete
usr+sys time: 5842.31 seconds
wall clock time: 104 minutes 27.15 seconds (6267.15 seconds total)