Starting phenix.real_space_refine
on Fri Jun  6 06:17:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/06_2025/8tzp_41765.cif"
  }
  resolution = 3.23
  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=   0.002 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      75      5.16       5
     C    4470      2.51       5
     N    1170      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 6920
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2342
          Classifications: {'peptide': 301}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 289}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 4037
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 21, 'TRANS': 474}
    Chain: "C"
      Number of atoms: 484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 484
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 4.62, per 1000 atoms: 0.67
  Number of scatterers: 6920
  At special positions: 0
  Unit cell: (87.98, 92.96, 129.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      75     16.00
     P       1     15.00
     O    1204      8.00
     N    1170      7.00
     C    4470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  73 " - pdb=" SG  CYS A  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 123 " - pdb=" SG  CYS A 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 202 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 294 " - pdb=" SG  CYS A 304 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 216 " - pdb=" SG  CYS C 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 217 " - pdb=" SG  CYS C 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 225 " - pdb=" SG  CYS C 250 " distance=2.04

  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: 1.63
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      52.7% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 41
      removed outlier: 4.293A  pdb=" N   LYS A  40 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 55 through 77
      removed outlier: 3.637A  pdb=" N   ILE A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 125
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 4.000A  pdb=" N   TYR A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 195
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.583A  pdb=" N   LEU A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 3.835A  pdb=" N   GLY B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 121 through 125
      removed outlier: 4.142A  pdb=" N   GLN B 125 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 227 through 258
      Proline residue:  B 243  - end of helix
    Processing helix  chain 'B' and resid 264 through 282
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 295 through 322
      removed outlier: 3.584A  pdb=" N   ILE B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 334
    Processing helix  chain 'B' and resid 335 through 357
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 358 through 362
    Processing helix  chain 'B' and resid 367 through 370
    Processing helix  chain 'B' and resid 371 through 414
      removed outlier: 3.820A  pdb=" N   SER B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B 413 " --> pdb=" O   GLY B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 456
    Processing helix  chain 'B' and resid 469 through 492
    Processing helix  chain 'C' and resid 210 through 219
      removed outlier: 4.797A  pdb=" N   TYR C 215 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS C 217 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 236
    Processing helix  chain 'C' and resid 238 through 250
    Processing helix  chain 'C' and resid 258 through 270
      removed outlier: 3.823A  pdb=" N   GLN C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER C 270 " --> pdb=" O   GLU C 266 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202
    Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 254
      removed outlier: 5.852A  pdb=" N   VAL A 236 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294
      removed outlier: 4.193A  pdb=" N   TYR A 346 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46
      removed outlier: 6.870A  pdb=" N   ASP B 117 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ILE B 219 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU B 111 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   LEU B 114 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51
      removed outlier: 3.504A  pdb=" N   ALA B 152 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   TYR B 140 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   GLU B 150 " --> pdb=" O   TYR B 140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462
      removed outlier: 3.619A  pdb=" N   VAL B 465 " --> pdb=" O   TRP B 462 " (cutoff:3.500A)

    375 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.69

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1085
        1.31 -     1.44: 1983
        1.44 -     1.57: 3918
        1.57 -     1.69: 3
        1.69 -     1.82: 108
  Bond restraints: 7097
  Sorted by residual:
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.418 -0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C21 POV B 601 "
       pdb=" O21 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.420 -0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb="C210 POV B 601 "
       pdb="C211 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.558 -0.061 2.00e-02 2.50e+03 9.42e+00
  bond pdb=" N   POV B 601 "
       pdb=" C14 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.436  0.054 2.00e-02 2.50e+03 7.23e+00
  bond pdb=" C28 POV B 601 "
       pdb=" C29 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.548 -0.051 2.00e-02 2.50e+03 6.44e+00
  ... (remaining 7092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 9420
        2.35 -     4.71: 128
        4.71 -     7.06: 26
        7.06 -     9.41: 9
        9.41 -    11.76: 2
  Bond angle restraints: 9585
  Sorted by residual:
  angle pdb=" CA  PRO A  56 "
        pdb=" N   PRO A  56 "
        pdb=" CD  PRO A  56 "
      ideal   model   delta    sigma   weight residual
     112.00  103.61    8.39 1.40e+00 5.10e-01 3.60e+01
  angle pdb=" C   THR A 297 "
        pdb=" N   ALA A 298 "
        pdb=" CA  ALA A 298 "
      ideal   model   delta    sigma   weight residual
     120.09  125.66   -5.57 1.25e+00 6.40e-01 1.99e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.35   11.76 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" O11 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O12 POV B 601 "
      ideal   model   delta    sigma   weight residual
      97.67  109.26  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" CA  LYS B 208 "
        pdb=" CB  LYS B 208 "
        pdb=" CG  LYS B 208 "
      ideal   model   delta    sigma   weight residual
     114.10  121.79   -7.69 2.00e+00 2.50e-01 1.48e+01
  ... (remaining 9580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.02: 3786
       18.02 -    36.04: 355
       36.04 -    54.05: 83
       54.05 -    72.07: 21
       72.07 -    90.09: 9
  Dihedral angle restraints: 4254
    sinusoidal: 1775
      harmonic: 2479
  Sorted by residual:
  dihedral pdb=" CB  CYS C 217 "
           pdb=" SG  CYS C 217 "
           pdb=" SG  CYS C 229 "
           pdb=" CB  CYS C 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.07   77.07     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS A 324 "
           pdb=" SG  CYS A 324 "
           pdb=" SG  CYS A 339 "
           pdb=" CB  CYS A 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.26  -62.26     1      1.00e+01 1.00e-02 5.13e+01
  dihedral pdb=" CB  CYS A  38 "
           pdb=" SG  CYS A  38 "
           pdb=" SG  CYS A  52 "
           pdb=" CB  CYS A  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.52   60.52     1      1.00e+01 1.00e-02 4.87e+01
  ... (remaining 4251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 599
       0.029 -    0.058: 283
       0.058 -    0.087: 99
       0.087 -    0.116: 38
       0.116 -    0.146: 10
  Chirality restraints: 1029
  Sorted by residual:
  chirality pdb=" CA  CYS C 250 "
            pdb=" N   CYS C 250 "
            pdb=" C   CYS C 250 "
            pdb=" CB  CYS C 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CB  THR A 343 "
            pdb=" CA  THR A 343 "
            pdb=" OG1 THR A 343 "
            pdb=" CG2 THR A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  ILE A  41 "
            pdb=" N   ILE A  41 "
            pdb=" C   ILE A  41 "
            pdb=" CB  ILE A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1026 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  55 "    0.100 5.00e-02 4.00e+02   1.46e-01 3.42e+01
        pdb=" N   PRO A  56 "   -0.253 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "    0.077 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "    0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  67 "    0.063 5.00e-02 4.00e+02   9.46e-02 1.43e+01
        pdb=" N   PRO B  68 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO B  68 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B  68 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 208 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" C   LYS B 208 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LYS B 208 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE B 209 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 2
        2.05 -     2.76: 1128
        2.76 -     3.48: 9683
        3.48 -     4.19: 15535
        4.19 -     4.90: 28735
  Nonbonded interactions: 55083
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 206 "
            pdb=" O1  PAM A 601 "
     model   vdw
     1.341 3.040
  nonbonded pdb=" OG  SER A 206 "
            pdb=" C1  PAM A 601 "
     model   vdw
     1.375 3.270
  nonbonded pdb=" O   ASN A 181 "
            pdb=" ND2 ASN A 185 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   LEU B 312 "
            pdb=" OH  TYR B 392 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   ARG C 231 "
            pdb=" OG  SER C 235 "
     model   vdw
     2.314 3.040
  ... (remaining 55078 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:             2.440
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.310
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   7114  Z= 0.203
  Angle     :  0.734  11.763   9619  Z= 0.378
  Chirality :  0.041   0.146   1029
  Planarity :  0.006   0.146   1206
  Dihedral  : 15.231  90.091   2605
  Min Nonbonded Distance : 1.341

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 12.52 %
    Favored  : 87.21 %
  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:  1.16 (0.28), residues: 851
  helix:  2.20 (0.25), residues: 387
  sheet:  0.14 (0.53), residues: 92
  loop : -0.60 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 432 
 TYR   0.011   0.001   TYR B 308 
 ARG   0.003   0.000   ARG A 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13130 (  375)
  hydrogen bonds       : angle       5.53280 ( 1050)
  SS BOND              : bond        0.00286 (   17)
  SS BOND              : angle       1.16007 (   34)
  covalent geometry    : bond        0.00443 ( 7097)
  covalent geometry    : angle       0.73176 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 1.351 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2480
  time to fit residues: 35.3141
Evaluate side-chains
  88 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.183117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140605 restraints weight = 8181.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.18
r_work: 0.3520 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.0763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7114  Z= 0.143
  Angle     :  0.552   8.675   9619  Z= 0.287
  Chirality :  0.041   0.164   1029
  Planarity :  0.005   0.090   1206
  Dihedral  :  8.210  88.703    968
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 11.84 %
    Favored  : 85.20 %
  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 (0.28), residues: 851
  helix:  2.24 (0.25), residues: 394
  sheet:  0.07 (0.51), residues: 109
  loop : -0.63 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.012   0.001   TYR B 484 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  375)
  hydrogen bonds       : angle       4.36508 ( 1050)
  SS BOND              : bond        0.00369 (   17)
  SS BOND              : angle       1.22413 (   34)
  covalent geometry    : bond        0.00336 ( 7097)
  covalent geometry    : angle       0.54833 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7680 (p90) cc_final: 0.7453 (p90)
REVERT: B  423 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (mm)
  outliers start: 22
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1772
  time to fit residues: 25.7465
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 25 optimal weight:    0.0270
   chunk 62 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    1.1244

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
B  25 GLN
B 470 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.176517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.133457 restraints weight = 8294.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.26
r_work: 0.3483 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7114  Z= 0.167
  Angle     :  0.549   6.905   9619  Z= 0.285
  Chirality :  0.042   0.214   1029
  Planarity :  0.005   0.071   1206
  Dihedral  :  7.801  89.313    968
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.52 %
    Favored  : 84.39 %
  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 (0.28), residues: 851
  helix:  2.09 (0.25), residues: 403
  sheet: -0.07 (0.51), residues: 109
  loop : -0.70 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 481 
 HIS   0.003   0.001   HIS A 117 
 PHE   0.011   0.001   PHE B 432 
 TYR   0.014   0.002   TYR A 318 
 ARG   0.003   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  375)
  hydrogen bonds       : angle       4.19409 ( 1050)
  SS BOND              : bond        0.00355 (   17)
  SS BOND              : angle       1.11425 (   34)
  covalent geometry    : bond        0.00396 ( 7097)
  covalent geometry    : angle       0.54631 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 TYR cc_start: 0.7761 (p90) cc_final: 0.7503 (p90)
REVERT: A  346 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6538 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1795
  time to fit residues: 25.3927
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0770
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.180892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.138830 restraints weight = 8318.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.15
r_work: 0.3561 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7114  Z= 0.153
  Angle     :  0.534   7.064   9619  Z= 0.277
  Chirality :  0.041   0.166   1029
  Planarity :  0.004   0.061   1206
  Dihedral  :  7.589  86.499    968
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 11.17 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 851
  helix:  2.24 (0.25), residues: 394
  sheet: -0.00 (0.52), residues: 109
  loop : -0.56 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.019   0.002   TYR A 318 
 ARG   0.002   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03845 (  375)
  hydrogen bonds       : angle       4.10787 ( 1050)
  SS BOND              : bond        0.00311 (   17)
  SS BOND              : angle       1.12121 (   34)
  covalent geometry    : bond        0.00362 ( 7097)
  covalent geometry    : angle       0.53114 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7798 (p90) cc_final: 0.7570 (p90)
REVERT: A  346 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6561 (m-10)
REVERT: B  423 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (mm)
REVERT: C  261 TRP cc_start: 0.8340 (m100) cc_final: 0.8138 (m-90)
  outliers start: 29
  outliers final: 22
  residues processed: 114
  average time/residue: 0.1619
  time to fit residues: 26.5221
Evaluate side-chains
  114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
B 198 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.173788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130395 restraints weight = 8402.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.24
r_work: 0.3410 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   7114  Z= 0.324
  Angle     :  0.684   9.222   9619  Z= 0.350
  Chirality :  0.046   0.159   1029
  Planarity :  0.005   0.056   1206
  Dihedral  :  8.015  89.423    968
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 12.65 %
    Favored  : 83.31 %
  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:  0.69 (0.28), residues: 851
  helix:  1.72 (0.25), residues: 396
  sheet: -0.28 (0.51), residues: 110
  loop : -0.75 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 147 
 HIS   0.007   0.001   HIS A 117 
 PHE   0.018   0.002   PHE B 318 
 TYR   0.021   0.002   TYR A 318 
 ARG   0.002   0.000   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04761 (  375)
  hydrogen bonds       : angle       4.43702 ( 1050)
  SS BOND              : bond        0.00432 (   17)
  SS BOND              : angle       1.31371 (   34)
  covalent geometry    : bond        0.00790 ( 7097)
  covalent geometry    : angle       0.68026 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7678 (pp30)
REVERT: B  377 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7122 (mp)
  outliers start: 30
  outliers final: 21
  residues processed: 112
  average time/residue: 0.2948
  time to fit residues: 47.6181
Evaluate side-chains
  108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 1.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0670
   chunk 54 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.181482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.139208 restraints weight = 8281.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.21
r_work: 0.3506 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7114  Z= 0.129
  Angle     :  0.536   7.266   9619  Z= 0.279
  Chirality :  0.041   0.177   1029
  Planarity :  0.004   0.051   1206
  Dihedral  :  7.590  86.775    968
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.94 %
    Favored  : 81.97 %
  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 (0.29), residues: 851
  helix:  2.15 (0.24), residues: 395
  sheet: -0.19 (0.52), residues: 110
  loop : -0.63 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 432 
 TYR   0.023   0.002   TYR A 313 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  375)
  hydrogen bonds       : angle       4.06893 ( 1050)
  SS BOND              : bond        0.00294 (   17)
  SS BOND              : angle       1.12071 (   34)
  covalent geometry    : bond        0.00297 ( 7097)
  covalent geometry    : angle       0.53327 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7659 (pp30)
REVERT: A  346 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6591 (m-10)
REVERT: B  377 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7120 (mp)
REVERT: C  261 TRP cc_start: 0.8315 (m100) cc_final: 0.8081 (m-90)
  outliers start: 23
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1841
  time to fit residues: 28.0182
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0770
   overall best weight:    1.1344

-------------------------------------------------------------------------------
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 = 0.4124 r_free = 0.4124 target = 0.175859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134367 restraints weight = 8297.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.11
r_work: 0.3493 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7114  Z= 0.171
  Angle     :  0.558   7.790   9619  Z= 0.288
  Chirality :  0.042   0.161   1029
  Planarity :  0.004   0.050   1206
  Dihedral  :  7.561  88.917    968
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.21 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.29), residues: 851
  helix:  2.07 (0.24), residues: 402
  sheet: -0.44 (0.50), residues: 116
  loop : -0.67 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.003   0.001   HIS A 117 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.020   0.002   TYR A 318 
 ARG   0.007   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  375)
  hydrogen bonds       : angle       4.03339 ( 1050)
  SS BOND              : bond        0.00309 (   17)
  SS BOND              : angle       1.07496 (   34)
  covalent geometry    : bond        0.00408 ( 7097)
  covalent geometry    : angle       0.55543 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7683 (pp30)
REVERT: A  346 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6612 (m-10)
REVERT: B  220 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7959 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7110 (mp)
  outliers start: 24
  outliers final: 18
  residues processed: 103
  average time/residue: 0.2455
  time to fit residues: 35.1432
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 21 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:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.180107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138127 restraints weight = 8418.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.17
r_work: 0.3499 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7114  Z= 0.165
  Angle     :  0.559   7.389   9619  Z= 0.288
  Chirality :  0.041   0.157   1029
  Planarity :  0.004   0.049   1206
  Dihedral  :  7.474  89.955    968
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.80 %
    Favored  : 82.10 %
  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:  1.02 (0.29), residues: 851
  helix:  2.05 (0.24), residues: 403
  sheet: -0.40 (0.50), residues: 116
  loop : -0.62 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   0.001   HIS A 117 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.022   0.002   TYR A 318 
 ARG   0.006   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  375)
  hydrogen bonds       : angle       4.00951 ( 1050)
  SS BOND              : bond        0.00296 (   17)
  SS BOND              : angle       1.04401 (   34)
  covalent geometry    : bond        0.00391 ( 7097)
  covalent geometry    : angle       0.55627 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (pp30)
REVERT: A  346 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6679 (m-10)
REVERT: B  220 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7963 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7099 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 103
  average time/residue: 0.2244
  time to fit residues: 32.6555
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.177535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136083 restraints weight = 8409.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.16
r_work: 0.3551 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7114  Z= 0.136
  Angle     :  0.547   6.925   9619  Z= 0.283
  Chirality :  0.041   0.158   1029
  Planarity :  0.004   0.049   1206
  Dihedral  :  7.255  89.291    968
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.34 %
    Favored  : 81.70 %
  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:  1.12 (0.29), residues: 851
  helix:  2.17 (0.24), residues: 402
  sheet: -0.41 (0.50), residues: 118
  loop : -0.58 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 291 
 TYR   0.023   0.002   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  375)
  hydrogen bonds       : angle       3.93548 ( 1050)
  SS BOND              : bond        0.00248 (   17)
  SS BOND              : angle       1.03737 (   34)
  covalent geometry    : bond        0.00315 ( 7097)
  covalent geometry    : angle       0.54484 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7752 (pp30)
REVERT: A  346 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6648 (m-10)
REVERT: B  220 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7959 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7056 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1888
  time to fit residues: 27.9543
Evaluate side-chains
  106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.183330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.142294 restraints weight = 8349.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.19
r_work: 0.3564 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7114  Z= 0.138
  Angle     :  0.551   6.651   9619  Z= 0.284
  Chirality :  0.041   0.182   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  7.123  87.909    968
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.34 %
    Favored  : 81.70 %
  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:  1.16 (0.29), residues: 851
  helix:  2.22 (0.24), residues: 402
  sheet: -0.46 (0.50), residues: 118
  loop : -0.55 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 291 
 TYR   0.023   0.002   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  375)
  hydrogen bonds       : angle       3.92372 ( 1050)
  SS BOND              : bond        0.00259 (   17)
  SS BOND              : angle       1.00281 (   34)
  covalent geometry    : bond        0.00322 ( 7097)
  covalent geometry    : angle       0.54919 ( 9585)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7752 (pp30)
REVERT: A  346 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6714 (m-10)
REVERT: B  220 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7939 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7047 (mp)
  outliers start: 22
  outliers final: 18
  residues processed: 102
  average time/residue: 0.1684
  time to fit residues: 24.0899
Evaluate side-chains
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.183097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.142111 restraints weight = 8273.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.19
r_work: 0.3565 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7114  Z= 0.144
  Angle     :  0.549   6.612   9619  Z= 0.284
  Chirality :  0.041   0.152   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  7.031  86.838    968
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.94 %
    Favored  : 81.70 %
  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:  1.15 (0.29), residues: 851
  helix:  2.22 (0.24), residues: 402
  sheet: -0.52 (0.50), residues: 118
  loop : -0.56 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 291 
 TYR   0.023   0.002   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  375)
  hydrogen bonds       : angle       3.91241 ( 1050)
  SS BOND              : bond        0.00263 (   17)
  SS BOND              : angle       0.97705 (   34)
  covalent geometry    : bond        0.00337 ( 7097)
  covalent geometry    : angle       0.54736 ( 9585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5302.19 seconds
wall clock time: 95 minutes 47.80 seconds (5747.80 seconds total)