Starting phenix.real_space_refine
on Sat Jun 14 20:16:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pso_17858/06_2025/8pso_17858_trim.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 8
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      31      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    5046      2.51       5
     N    1459      2.21       5
     O    1681      1.98       5
     H    7937      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16201
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 5036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 5036
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 18, 'TRANS': 297}
    Chain: "B"
      Number of atoms: 7974
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 515, 7973
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
      Conformer: "B"
        Number of residues, atoms: 515, 7973
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
          bond proxies already assigned to first conformer: 8044
    Chain: "C"
      Number of atoms: 2233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 2233
          Classifications: {'peptide': 140}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
    Chain: "V"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 406
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 4, 'rna3p': 8}
    Chain: "S"
      Number of atoms: 476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 476
          Classifications: {'RNA': 15}
          Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 6, 'rna3p': 8}
    Chain: "F"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'CTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 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}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 27
          Classifications: {'water': 27}
          Link IDs: {None: 26}
    Chain: "V"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "S"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    969  SG  CYS A 161      47.014  44.089  83.490  1.00 27.60           S
  ATOM   2857  SG  CYS A 282      45.317  46.416  86.158  1.00 26.75           S

  Time building chain proxies: 11.04, per 1000 atoms: 0.68
  Number of scatterers: 16201
  At special positions: 0
  Unit cell: (88.2, 94.92, 102.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     S      44     16.00
     P      31     15.00
     Mg      2     11.99
     O    1681      8.00
     N    1459      7.00
     C    5046      6.00
     H    7937      1.00
    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: 4.52
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      Number of angles added : 2


  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      48.1% alpha, 12.8% beta
      7 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 8.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.657A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.540A  pdb=" N   GLY A 168 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 236
      removed outlier: 3.585A  pdb=" N   THR A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   THR A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 322
      removed outlier: 3.626A  pdb=" N   LEU A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.511A  pdb=" N   VAL A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.930A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.579A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 40
      removed outlier: 3.563A  pdb=" N   GLY B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 92 through 104
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 130 through 137
    Processing helix  chain 'B' and resid 161 through 183
    Processing helix  chain 'B' and resid 184 through 187
    Processing helix  chain 'B' and resid 191 through 204
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 3.737A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.809A  pdb=" N   LEU B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 356 through 372
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.979A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
    Processing helix  chain 'B' and resid 479 through 496
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 2 through 8
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.677A  pdb=" N   HIS C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 42 through 55
      removed outlier: 3.687A  pdb=" N   ASP C  53 " --> pdb=" O   ASN C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 87 through 98
    Processing helix  chain 'C' and resid 100 through 107
    Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.234A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.234A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159
      removed outlier: 3.726A  pdb=" N   ARG B 155 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287
    Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 83
      removed outlier: 7.242A  pdb=" N   LYS C  75 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   TYR C 119 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 6.29

  Time building geometry restraints manager: 5.46 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7915
        1.03 -     1.23: 32
        1.23 -     1.42: 3521
        1.42 -     1.61: 4838
        1.61 -     1.81: 64
  Bond restraints: 16370
  Sorted by residual:
  bond pdb=" CB  PRO B 470 "
       pdb=" CG  PRO B 470 "
    ideal  model  delta    sigma   weight residual
    1.492  1.614 -0.122 5.00e-02 4.00e+02 5.94e+00
  bond pdb=" C5  CTP F   1 "
       pdb=" C6  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.342  0.048 2.00e-02 2.50e+03 5.82e+00
  bond pdb=" C4' CTP F   1 "
       pdb=" O4' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.452 -0.042 2.00e-02 2.50e+03 4.41e+00
  bond pdb=" C4  CTP F   1 "
       pdb=" N3  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.380  1.339  0.041 2.00e-02 2.50e+03 4.24e+00
  bond pdb=" C5' CTP F   1 "
       pdb=" O5' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.449 -0.039 2.00e-02 2.50e+03 3.71e+00
  ... (remaining 16365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 29524
        3.10 -     6.19: 39
        6.19 -     9.29: 3
        9.29 -    12.38: 4
       12.38 -    15.48: 1
  Bond angle restraints: 29571
  Sorted by residual:
  angle pdb=" CA  PRO B 470 "
        pdb=" N   PRO B 470 "
        pdb=" CD  PRO B 470 "
      ideal   model   delta    sigma   weight residual
     112.00  103.06    8.94 1.40e+00 5.10e-01 4.08e+01
  angle pdb=" PA  CTP F   1 "
        pdb=" O3A CTP F   1 "
        pdb=" PB  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  135.98  -15.48 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
        pdb=" C4' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.47   11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C1' CTP F   1 "
        pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.93   11.07 3.00e+00 1.11e-01 1.36e+01
  angle pdb=" PB  CTP F   1 "
        pdb=" O3B CTP F   1 "
        pdb=" PG  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  130.57  -10.07 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 29566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.72: 7377
       34.72 -    69.44: 317
       69.44 -   104.16: 20
      104.16 -   138.88: 2
      138.88 -   173.61: 2
  Dihedral angle restraints: 7718
    sinusoidal: 4475
      harmonic: 3243
  Sorted by residual:
  dihedral pdb=" O3B CTP F   1 "
           pdb=" O3A CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PA  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     320.71  153.36  167.34     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" O1G CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PG  CTP F   1 "
           pdb=" PB  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.72  -47.94  130.65     1      2.00e+01 2.50e-03 3.96e+01
  dihedral pdb=" O3A CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PG  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -155.50  -47.76 -107.74     1      2.00e+01 2.50e-03 3.13e+01
  ... (remaining 7715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1164
       0.050 -    0.100: 129
       0.100 -    0.151: 33
       0.151 -    0.201: 0
       0.201 -    0.251: 1
  Chirality restraints: 1327
  Sorted by residual:
  chirality pdb=" C2' CTP F   1 "
            pdb=" C1' CTP F   1 "
            pdb=" C3' CTP F   1 "
            pdb=" O2' CTP F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.72    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" C3'   G S   1 "
            pdb=" C4'   G S   1 "
            pdb=" O3'   G S   1 "
            pdb=" C2'   G S   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  ILE A 199 "
            pdb=" N   ILE A 199 "
            pdb=" C   ILE A 199 "
            pdb=" CB  ILE A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 1324 not shown)

  Planarity restraints: 2320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 469 "   -0.057 5.00e-02 4.00e+02   8.16e-02 1.07e+01
        pdb=" N   PRO B 470 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO B 162 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A S   8 "   -0.022 2.00e-02 2.50e+03   9.61e-03 3.00e+00
        pdb=" N9    A S   8 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A S   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A S   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A S   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A S   8 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A S   8 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" H8    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" H2    A S   8 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2317 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 537
        2.15 -     2.76: 29691
        2.76 -     3.37: 46745
        3.37 -     3.99: 62048
        3.99 -     4.60: 95312
  Nonbonded interactions: 234333
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" H   GLU C  89 "
     model   vdw
     1.532 2.450
  nonbonded pdb=" OD2 ASP B 222 "
            pdb="HH22 ARG B 247 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASP B 444 "
            pdb=" H   ASP B 444 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" HZ3 LYS B 249 "
            pdb=" O   CYS B 260 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" HH  TYR B 186 "
            pdb=" O   SER B 286 "
     model   vdw
     1.639 2.450
  ... (remaining 234328 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=0.40 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:             1.990
  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:             0.300
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     54.930
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.080
  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:14.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.122   8437  Z= 0.115
  Angle     :  0.562  15.480  11535  Z= 0.274
  Chirality :  0.036   0.251   1327
  Planarity :  0.005   0.082   1377
  Dihedral  : 18.686 173.606   3344
  Min Nonbonded Distance : 1.693

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.90 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.27), residues: 965
  helix:  2.12 (0.25), residues: 421
  sheet:  0.72 (0.52), residues: 93
  loop : -0.03 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 296 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.008   0.001   TYR A 403 
 ARG   0.010   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12060 (  389)
  hydrogen bonds       : angle       4.95017 ( 1060)
  metal coordination   : bond        0.00502 (    4)
  metal coordination   : angle       0.60854 (    2)
  covalent geometry    : bond        0.00267 ( 8433)
  covalent geometry    : angle       0.56206 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 3.1354
  time to fit residues: 415.1832
Evaluate side-chains
  123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.094424 restraints weight = 22637.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.30
r_work: 0.2844 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.0502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8437  Z= 0.145
  Angle     :  0.540   8.093  11535  Z= 0.282
  Chirality :  0.038   0.158   1327
  Planarity :  0.004   0.045   1377
  Dihedral  : 14.082 166.516   1505
  Min Nonbonded Distance : 1.790

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.59 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.43 (0.27), residues: 965
  helix:  2.04 (0.25), residues: 428
  sheet:  0.61 (0.52), residues: 95
  loop : -0.01 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.006   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.006   0.000   ARG B 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05099 (  389)
  hydrogen bonds       : angle       4.25431 ( 1060)
  metal coordination   : bond        0.00817 (    4)
  metal coordination   : angle       0.09386 (    2)
  covalent geometry    : bond        0.00323 ( 8433)
  covalent geometry    : angle       0.54020 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 128
  average time/residue: 3.6034
  time to fit residues: 486.2511
Evaluate side-chains
  123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   94 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.093294 restraints weight = 22545.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.29
r_work: 0.2833 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.0696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8437  Z= 0.161
  Angle     :  0.555   8.465  11535  Z= 0.290
  Chirality :  0.038   0.156   1327
  Planarity :  0.004   0.050   1377
  Dihedral  : 13.615 165.244   1499
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.88 %
    Favored  : 80.10 %
  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:  1.22 (0.27), residues: 965
  helix:  1.86 (0.25), residues: 428
  sheet:  0.54 (0.51), residues: 95
  loop : -0.12 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.017   0.002   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05291 (  389)
  hydrogen bonds       : angle       4.24678 ( 1060)
  metal coordination   : bond        0.00830 (    4)
  metal coordination   : angle       0.06782 (    2)
  covalent geometry    : bond        0.00359 ( 8433)
  covalent geometry    : angle       0.55532 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.298 
Fit side-chains
REVERT: A  189 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7979 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8332 (ttp80)
REVERT: A  347 ASP cc_start: 0.8608 (m-30) cc_final: 0.8400 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 128
  average time/residue: 3.2357
  time to fit residues: 435.2905
Evaluate side-chains
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.093748 restraints weight = 22581.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.29
r_work: 0.2839 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.0801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8437  Z= 0.142
  Angle     :  0.533   7.653  11535  Z= 0.279
  Chirality :  0.038   0.148   1327
  Planarity :  0.004   0.051   1377
  Dihedral  : 13.454 164.315   1498
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.00 %
    Favored  : 80.57 %
  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:  1.18 (0.27), residues: 965
  helix:  1.83 (0.25), residues: 429
  sheet:  0.55 (0.51), residues: 95
  loop : -0.16 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.006   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04961 (  389)
  hydrogen bonds       : angle       4.19613 ( 1060)
  metal coordination   : bond        0.00837 (    4)
  metal coordination   : angle       0.21245 (    2)
  covalent geometry    : bond        0.00317 ( 8433)
  covalent geometry    : angle       0.53354 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.230 
Fit side-chains
REVERT: A  189 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8315 (ttp80)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 3.2170
  time to fit residues: 422.7959
Evaluate side-chains
  125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.119098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.093016 restraints weight = 22793.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.30
r_work: 0.2824 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8437  Z= 0.158
  Angle     :  0.552   8.232  11535  Z= 0.289
  Chirality :  0.038   0.152   1327
  Planarity :  0.004   0.052   1377
  Dihedral  : 13.501 164.226   1498
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.88 %
    Favored  : 80.69 %
  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:  1.10 (0.26), residues: 965
  helix:  1.76 (0.25), residues: 428
  sheet:  0.49 (0.50), residues: 95
  loop : -0.19 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 432 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.016   0.002   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.006   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05211 (  389)
  hydrogen bonds       : angle       4.22521 ( 1060)
  metal coordination   : bond        0.00891 (    4)
  metal coordination   : angle       0.17178 (    2)
  covalent geometry    : bond        0.00353 ( 8433)
  covalent geometry    : angle       0.55160 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8337 (ttp80)
  outliers start: 12
  outliers final: 6
  residues processed: 121
  average time/residue: 3.2615
  time to fit residues: 415.8402
Evaluate side-chains
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.118646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.092711 restraints weight = 22516.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.29
r_work: 0.2821 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8437  Z= 0.165
  Angle     :  0.560   8.284  11535  Z= 0.294
  Chirality :  0.039   0.150   1327
  Planarity :  0.005   0.076   1377
  Dihedral  : 13.568 164.020   1497
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.88 %
    Favored  : 80.57 %
  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:  1.03 (0.26), residues: 965
  helix:  1.70 (0.25), residues: 428
  sheet:  0.44 (0.50), residues: 95
  loop : -0.22 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.017   0.002   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.009   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05321 (  389)
  hydrogen bonds       : angle       4.25514 ( 1060)
  metal coordination   : bond        0.00903 (    4)
  metal coordination   : angle       0.22746 (    2)
  covalent geometry    : bond        0.00369 ( 8433)
  covalent geometry    : angle       0.55999 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8357 (ttp80)
REVERT: B  486 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7033 (mt)
  outliers start: 13
  outliers final: 7
  residues processed: 123
  average time/residue: 3.2822
  time to fit residues: 424.5866
Evaluate side-chains
  122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain C residue   17 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.118243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.092076 restraints weight = 22776.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 1.31
r_work: 0.2811 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.1012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8437  Z= 0.180
  Angle     :  0.579   8.665  11535  Z= 0.304
  Chirality :  0.039   0.155   1327
  Planarity :  0.004   0.046   1377
  Dihedral  : 13.619 163.915   1497
  Min Nonbonded Distance : 1.787

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.24 %
    Favored  : 80.10 %
  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:  0.93 (0.26), residues: 965
  helix:  1.62 (0.25), residues: 428
  sheet:  0.37 (0.50), residues: 95
  loop : -0.27 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.018   0.002   PHE C  44 
 TYR   0.013   0.002   TYR A 403 
 ARG   0.006   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05515 (  389)
  hydrogen bonds       : angle       4.29205 ( 1060)
  metal coordination   : bond        0.00984 (    4)
  metal coordination   : angle       0.21310 (    2)
  covalent geometry    : bond        0.00404 ( 8433)
  covalent geometry    : angle       0.57870 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 1.873 
Fit side-chains
REVERT: A  189 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7963 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8371 (ttp80)
  outliers start: 14
  outliers final: 8
  residues processed: 122
  average time/residue: 3.3728
  time to fit residues: 432.9518
Evaluate side-chains
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.094540 restraints weight = 22829.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.26
r_work: 0.2850 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8437  Z= 0.112
  Angle     :  0.514   6.910  11535  Z= 0.270
  Chirality :  0.037   0.143   1327
  Planarity :  0.004   0.052   1377
  Dihedral  : 13.342 163.360   1497
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.47 %
    Favored  : 80.33 %
  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:  1.17 (0.27), residues: 965
  helix:  1.86 (0.25), residues: 429
  sheet:  0.46 (0.51), residues: 95
  loop : -0.20 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.012   0.001   PHE C  44 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.006   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04512 (  389)
  hydrogen bonds       : angle       4.13607 ( 1060)
  metal coordination   : bond        0.00714 (    4)
  metal coordination   : angle       0.51765 (    2)
  covalent geometry    : bond        0.00246 ( 8433)
  covalent geometry    : angle       0.51429 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 1.331 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 118
  average time/residue: 3.2087
  time to fit residues: 402.1648
Evaluate side-chains
  114 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.120490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.094592 restraints weight = 22552.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.27
r_work: 0.2848 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8437  Z= 0.118
  Angle     :  0.515   7.010  11535  Z= 0.270
  Chirality :  0.037   0.144   1327
  Planarity :  0.004   0.065   1377
  Dihedral  : 13.321 163.841   1497
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.59 %
    Favored  : 80.10 %
  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:  1.21 (0.27), residues: 965
  helix:  1.90 (0.25), residues: 429
  sheet:  0.53 (0.51), residues: 93
  loop : -0.19 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.017   0.001   PHE C  82 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.009   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04558 (  389)
  hydrogen bonds       : angle       4.09168 ( 1060)
  metal coordination   : bond        0.00779 (    4)
  metal coordination   : angle       0.29689 (    2)
  covalent geometry    : bond        0.00260 ( 8433)
  covalent geometry    : angle       0.51526 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 3.1761
  time to fit residues: 391.3228
Evaluate side-chains
  110 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
C 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.092322 restraints weight = 22529.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.32
r_work: 0.2821 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8437  Z= 0.164
  Angle     :  0.563   8.573  11535  Z= 0.296
  Chirality :  0.039   0.155   1327
  Planarity :  0.004   0.061   1377
  Dihedral  : 13.593 164.061   1497
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 18.71 %
    Favored  : 80.21 %
  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:  1.03 (0.26), residues: 965
  helix:  1.73 (0.25), residues: 428
  sheet:  0.37 (0.50), residues: 95
  loop : -0.23 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.017   0.002   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.008   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05282 (  389)
  hydrogen bonds       : angle       4.22075 ( 1060)
  metal coordination   : bond        0.00995 (    4)
  metal coordination   : angle       0.30368 (    2)
  covalent geometry    : bond        0.00368 ( 8433)
  covalent geometry    : angle       0.56270 (11533)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 113
  average time/residue: 3.3074
  time to fit residues: 392.8817
Evaluate side-chains
  110 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN
C 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.093307 restraints weight = 22730.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.28
r_work: 0.2836 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8437  Z= 0.141
  Angle     :  0.538   7.717  11535  Z= 0.282
  Chirality :  0.038   0.146   1327
  Planarity :  0.004   0.062   1377
  Dihedral  : 13.504 163.606   1497
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 19.07 %
    Favored  : 80.10 %
  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:  1.08 (0.26), residues: 965
  helix:  1.77 (0.25), residues: 428
  sheet:  0.42 (0.51), residues: 95
  loop : -0.22 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 432 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.014   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.008   0.000   ARG B 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04951 (  389)
  hydrogen bonds       : angle       4.17750 ( 1060)
  metal coordination   : bond        0.00820 (    4)
  metal coordination   : angle       0.20456 (    2)
  covalent geometry    : bond        0.00313 ( 8433)
  covalent geometry    : angle       0.53772 (11533)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14154.29 seconds
wall clock time: 244 minutes 2.39 seconds (14642.39 seconds total)