Starting phenix.real_space_refine
on Thu Oct 22 20:58:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10ed_75104/10_2026/10ed_75104.map"
  }
  resolution = 1.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    3641      2.51       5
     N     828      2.21       5
     O     958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5448
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "X"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 439
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 3, 'TRANS': 47}
    Chain: "A"
      Number of atoms: 4641
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4618
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 29, 'TRANS': 566}
      Conformer: "B"
        Number of residues, atoms: 596, 4618
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 29, 'TRANS': 566}
          bond proxies already assigned to first conformer: 4712
    Chain: "X"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'R16': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 277
          Unusual residues: {'LMN': 2, 'R16': 14}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 12
    Chain: "X"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 66
          Classifications: {'water': 66}
          Link IDs: {None: 65}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AGLY A  70 " occ=0.56
      ... (6 atoms not shown)
      pdb=" O  BGLY A  70 " occ=0.44
    residue:
      pdb=" N  APHE A  71 " occ=0.56
      ... (20 atoms not shown)
      pdb=" CZ BPHE A  71 " occ=0.44
    residue:
      pdb=" N  ALEU A  72 " occ=0.56
      ... (14 atoms not shown)
      pdb=" CD2BLEU A  72 " occ=0.44
  Time building chain proxies: 1.79, per 1000 atoms: 0.33
  Number of scatterers: 5448
  At special positions: 0
  Unit cell: (81.872, 73.1, 90.644, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     958      8.00
     N     828      7.00
     C    3641      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 465.2 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 1 sheets defined
      83.0% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'X' and resid 2 through 18
    Processing helix  chain 'X' and resid 19 through 25
    Processing helix  chain 'X' and resid 33 through 52
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 40 through 48
    Processing helix  chain 'A' and resid 49 through 52
    Processing helix  chain 'A' and resid 53 through 58
    Processing helix  chain 'A' and resid 58 through 68
      removed outlier: 3.915A  pdb=" N   GLY A  62 " --> pdb=" O   TYR A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 84
      removed outlier: 3.937A  pdb=" N   TYR A  75 " --> pdb=" O  APHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 100
      removed outlier: 3.756A  pdb=" N   ILE A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 113
    Processing helix  chain 'A' and resid 114 through 149
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 153 through 173
      removed outlier: 3.816A  pdb=" N   ALA A 157 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 211
    Processing helix  chain 'A' and resid 214 through 225
    Processing helix  chain 'A' and resid 225 through 233
    Processing helix  chain 'A' and resid 237 through 255
      removed outlier: 3.946A  pdb=" N   ALA A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   ILE A 253 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
    Processing helix  chain 'A' and resid 270 through 301
      removed outlier: 3.709A  pdb=" N   SER A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TRP A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      removed outlier: 3.903A  pdb=" N   ALA A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   VAL A 290 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 308 through 317
      removed outlier: 4.425A  pdb=" N   GLY A 314 " --> pdb=" O   THR A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 353
      removed outlier: 3.560A  pdb=" N   LEU A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 392
    Processing helix  chain 'A' and resid 397 through 411
      removed outlier: 3.510A  pdb=" N   VAL A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 422
      removed outlier: 3.645A  pdb=" N   LEU A 420 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 445
    Processing helix  chain 'A' and resid 445 through 452
    Processing helix  chain 'A' and resid 470 through 494
      removed outlier: 4.294A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 507
    Processing helix  chain 'A' and resid 524 through 533
    Processing helix  chain 'A' and resid 537 through 553
    Processing helix  chain 'A' and resid 560 through 580
    Processing helix  chain 'A' and resid 580 through 592
    Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 458
      removed outlier: 3.665A  pdb=" N   TYR A 465 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 458 " --> pdb=" O   MET A 463 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET A 463 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1131 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: 0.86

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1556
        1.34 -     1.46: 1349
        1.46 -     1.58: 2564
        1.58 -     1.70: 0
        1.70 -     1.81: 39
  Bond restraints: 5508
  Sorted by residual:
  bond pdb=" C   LYS A 534 "
       pdb=" N   PRO A 535 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.11e+00
  bond pdb=" C41 R16 A 717 "
       pdb=" C42 R16 A 717 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.020 2.00e-02 2.50e+03 1.02e+00
  bond pdb=" CG1 ILE A 169 "
       pdb=" CD1 ILE A 169 "
    ideal  model  delta    sigma   weight residual
    1.513  1.477  0.036 3.90e-02 6.57e+02 8.52e-01
  bond pdb=" C41 R16 A 706 "
       pdb=" C42 R16 A 706 "
    ideal  model  delta    sigma   weight residual
    1.523  1.541 -0.018 2.00e-02 2.50e+03 8.52e-01
  bond pdb=" CB  GLU X  27 "
       pdb=" CG  GLU X  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.21e-01
  ... (remaining 5503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 7306
        1.79 -     3.58: 113
        3.58 -     5.37: 22
        5.37 -     7.16: 4
        7.16 -     8.95: 1
  Bond angle restraints: 7446
  Sorted by residual:
  angle pdb=" CA  LEU X  37 "
        pdb=" CB  LEU X  37 "
        pdb=" CG  LEU X  37 "
      ideal   model   delta    sigma   weight residual
     116.30  125.25   -8.95 3.50e+00 8.16e-02 6.53e+00
  angle pdb=" CB  MET A 474 "
        pdb=" CG  MET A 474 "
        pdb=" SD  MET A 474 "
      ideal   model   delta    sigma   weight residual
     112.70  119.68   -6.98 3.00e+00 1.11e-01 5.42e+00
  angle pdb=" N   SER X  18 "
        pdb=" CA  SER X  18 "
        pdb=" C   SER X  18 "
      ideal   model   delta    sigma   weight residual
     109.81  114.52   -4.71 2.21e+00 2.05e-01 4.53e+00
  angle pdb=" CB  MET A 258 "
        pdb=" CG  MET A 258 "
        pdb=" SD  MET A 258 "
      ideal   model   delta    sigma   weight residual
     112.70  119.05   -6.35 3.00e+00 1.11e-01 4.48e+00
  angle pdb=" CA  GLU X  27 "
        pdb=" CB  GLU X  27 "
        pdb=" CG  GLU X  27 "
      ideal   model   delta    sigma   weight residual
     114.10  118.07   -3.97 2.00e+00 2.50e-01 3.93e+00
  ... (remaining 7441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2942
       17.16 -    34.32: 297
       34.32 -    51.48: 82
       51.48 -    68.64: 25
       68.64 -    85.81: 10
  Dihedral angle restraints: 3356
    sinusoidal: 1467
      harmonic: 1889
  Sorted by residual:
  dihedral pdb=" CA BPHE A  71 "
           pdb=" C  BPHE A  71 "
           pdb=" N  BLEU A  72 "
           pdb=" CA BLEU A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.16   22.84     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASP A 468 "
           pdb=" CB  ASP A 468 "
           pdb=" CG  ASP A 468 "
           pdb=" OD1 ASP A 468 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.86   57.86     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  LEU A 420 "
           pdb=" C   LEU A 420 "
           pdb=" N   TYR A 421 "
           pdb=" CA  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.44  -16.56     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 3353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 547
       0.027 -    0.055: 192
       0.055 -    0.082: 90
       0.082 -    0.109: 30
       0.109 -    0.136: 9
  Chirality restraints: 868
  Sorted by residual:
  chirality pdb=" CA  ILE A  33 "
            pdb=" N   ILE A  33 "
            pdb=" C   ILE A  33 "
            pdb=" CB  ILE A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CG  LEU A 279 "
            pdb=" CB  LEU A 279 "
            pdb=" CD1 LEU A 279 "
            pdb=" CD2 LEU A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" C1  LMN A 702 "
            pdb=" C2  LMN A 702 "
            pdb=" O1  LMN A 702 "
            pdb=" O5  LMN A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.16   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 865 not shown)

  Planarity restraints: 875
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 239 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 240 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER X  18 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.07e+00
        pdb=" N   PRO X  19 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO X  19 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO X  19 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 248 "   -0.010 2.00e-02 2.50e+03   7.89e-03 1.09e+00
        pdb=" CG  PHE A 248 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 248 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 248 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 248 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 248 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 248 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 872 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 542
        2.74 -     3.28: 5587
        3.28 -     3.82: 10014
        3.82 -     4.36: 11809
        4.36 -     4.90: 19540
  Nonbonded interactions: 47492
  Sorted by model distance:
  nonbonded pdb=" O   TRP X  32 "
            pdb=" OH  TYR A  69 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   VAL A  87 "
            pdb=" OH  TYR A 421 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   ILE A 490 "
            pdb=" OG1 THR A 494 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLU A 180 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR A 367 "
            pdb=" OE2 GLU A 544 "
     model   vdw
     2.276 3.040
  ... (remaining 47487 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=0.44 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:             2.060
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
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   0.036   5508  Z= 0.121
  Angle     :  0.588   8.945   7446  Z= 0.272
  Chirality :  0.038   0.136    868
  Planarity :  0.004   0.041    875
  Dihedral  : 16.153  85.806   2146
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.37 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.33), residues: 648
  helix:  1.92 (0.22), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.72 (0.54), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 155 
 TYR   0.014   0.002   TYR A  17 
 PHE   0.018   0.002   PHE A 248 
 TRP   0.006   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 5508)
  covalent geometry    : angle       0.58769 /  0.27 ( 7446)
  hydrogen bonds       : bond        0.17079 / 11.05 (  382)
  hydrogen bonds       : angle       6.82402 /  5.14 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  223 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (mm)
REVERT: A  363 GLU cc_start: 0.7632 (pm20) cc_final: 0.7034 (pt0)
REVERT: A  463 MET cc_start: 0.3601 (tpt) cc_final: 0.2711 (ppp)
REVERT: A  526 GLN cc_start: 0.7698 (tp40) cc_final: 0.7306 (tp40)
REVERT: A  565 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7764 (mtp180)
  outliers start: 4
  outliers final: 2
  residues processed: 67
  average time/residue: 0.6331
  time to fit residues: 44.0683
Evaluate side-chains
  69 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  499 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [49, 53, 5, 33, 62, 51, 38, 61, 45, 27, 17]
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN
A 392 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.161479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117632 restraints weight = 6186.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.28
r_work: 0.3061 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.0630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5508  Z= 0.174
  Angle     :  0.637   6.296   7446  Z= 0.326
  Chirality :  0.041   0.157    868
  Planarity :  0.005   0.044    875
  Dihedral  : 12.129  84.006   1039
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.85 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.33), residues: 648
  helix:  2.05 (0.23), residues: 507
  sheet: -1.75 (1.81), residues: 12
  loop : -0.59 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 155 
 TYR   0.020   0.002   TYR A  17 
 PHE   0.022   0.002   PHE A 248 
 TRP   0.008   0.002   TRP X  25 
 HIS   0.006   0.002   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.17 ( 5508)
  covalent geometry    : angle       0.63725 /  0.33 ( 7446)
  hydrogen bonds       : bond        0.06074 /  3.94 (  382)
  hydrogen bonds       : angle       5.32870 /  4.02 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  363 GLU cc_start: 0.7490 (pm20) cc_final: 0.6845 (pt0)
REVERT: A  447 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: A  463 MET cc_start: 0.3469 (tpt) cc_final: 0.2593 (ppp)
REVERT: A  565 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7668 (mtp180)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 0.6696
  time to fit residues: 51.4450
Evaluate side-chains
  67 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue    3 ILE
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  498 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [28, 43, 33, 8, 57, 16, 4, 12, 56, 35, 42]
   chunk 28 optimal weight:    0.0070
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0970
   chunk 57 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0570
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.3114

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.166592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.126342 restraints weight = 4672.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.09
r_work: 0.3196 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5508  Z= 0.109
  Angle     :  0.539   8.427   7446  Z= 0.267
  Chirality :  0.037   0.132    868
  Planarity :  0.004   0.045    875
  Dihedral  : 11.121  86.183   1033
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.23 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.33), residues: 648
  helix:  2.41 (0.22), residues: 509
  sheet: -1.70 (1.79), residues: 12
  loop : -0.57 (0.57), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 155 
 TYR   0.012   0.001   TYR A  17 
 PHE   0.018   0.001   PHE A 487 
 TRP   0.008   0.001   TRP A 372 
 HIS   0.003   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.11 ( 5508)
  covalent geometry    : angle       0.53893 /  0.27 ( 7446)
  hydrogen bonds       : bond        0.04229 /  2.74 (  382)
  hydrogen bonds       : angle       4.83951 /  3.65 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.3620 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7497 (pm20) cc_final: 0.6888 (pt0)
REVERT: A  463 MET cc_start: 0.3532 (tpt) cc_final: 0.2786 (ppp)
REVERT: A  565 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7479 (mtp180)
  outliers start: 7
  outliers final: 1
  residues processed: 76
  average time/residue: 0.5687
  time to fit residues: 45.1099
Evaluate side-chains
  69 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue    3 ILE
Chi-restraints excluded: chain A residue  179 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [50, 60, 62, 25, 28, 47, 61, 46, 55, 37, 32]
   chunk 50 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117812 restraints weight = 8720.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.51
r_work: 0.3053 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5508  Z= 0.130
  Angle     :  0.565   6.259   7446  Z= 0.285
  Chirality :  0.038   0.133    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.338  87.513   1033
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.18 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.33), residues: 648
  helix:  2.32 (0.23), residues: 508
  sheet: -1.70 (1.80), residues: 12
  loop : -0.58 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 155 
 TYR   0.017   0.002   TYR A  17 
 PHE   0.020   0.002   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.13 ( 5508)
  covalent geometry    : angle       0.56464 /  0.29 ( 7446)
  hydrogen bonds       : bond        0.05013 /  3.26 (  382)
  hydrogen bonds       : angle       4.96196 /  3.75 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  363 GLU cc_start: 0.7464 (pm20) cc_final: 0.6839 (pt0)
REVERT: A  463 MET cc_start: 0.3630 (tpt) cc_final: 0.2720 (ppp)
REVERT: A  565 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7653 (mtp180)
  outliers start: 4
  outliers final: 0
  residues processed: 69
  average time/residue: 0.6206
  time to fit residues: 44.6479
Evaluate side-chains
  67 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [21, 50, 11, 14, 25, 53, 33, 18, 35, 63, 22]
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.162763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.118291 restraints weight = 7181.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.34
r_work: 0.3072 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2900
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5508  Z= 0.141
  Angle     :  0.594   7.974   7446  Z= 0.298
  Chirality :  0.039   0.133    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.579  87.080   1033
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.80 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.33), residues: 648
  helix:  2.21 (0.22), residues: 508
  sheet: -1.74 (1.80), residues: 12
  loop : -0.59 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 155 
 TYR   0.018   0.002   TYR A  17 
 PHE   0.021   0.002   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 5508)
  covalent geometry    : angle       0.59416 /  0.30 ( 7446)
  hydrogen bonds       : bond        0.05266 /  3.42 (  382)
  hydrogen bonds       : angle       5.02224 /  3.80 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.3457 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7363 (pm20) cc_final: 0.6758 (pt0)
REVERT: A  463 MET cc_start: 0.3556 (tpt) cc_final: 0.2777 (ppp)
REVERT: A  565 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7610 (mtp180)
  outliers start: 5
  outliers final: 1
  residues processed: 71
  average time/residue: 0.6248
  time to fit residues: 46.1457
Evaluate side-chains
  69 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain A residue  179 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [1, 29, 51, 0, 21, 6, 39, 17, 9, 53, 54]
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.120953 restraints weight = 5543.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.22
r_work: 0.3092 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5508  Z= 0.128
  Angle     :  0.566   7.317   7446  Z= 0.285
  Chirality :  0.038   0.132    868
  Planarity :  0.004   0.046    875
  Dihedral  : 11.457  87.264   1033
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.80 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.33), residues: 648
  helix:  2.26 (0.22), residues: 508
  sheet: -1.77 (1.83), residues: 12
  loop : -0.56 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 179 
 TYR   0.017   0.002   TYR A  17 
 PHE   0.020   0.002   PHE A 487 
 TRP   0.007   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.13 ( 5508)
  covalent geometry    : angle       0.56562 /  0.29 ( 7446)
  hydrogen bonds       : bond        0.04955 /  3.22 (  382)
  hydrogen bonds       : angle       4.95036 /  3.74 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.3472 (tpp-160)
REVERT: A  223 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8165 (mm)
REVERT: A  363 GLU cc_start: 0.7366 (pm20) cc_final: 0.6750 (pt0)
REVERT: A  463 MET cc_start: 0.3531 (tpt) cc_final: 0.2704 (ppp)
REVERT: A  565 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7591 (mtp180)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.6152
  time to fit residues: 46.7718
Evaluate side-chains
  72 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [38, 28, 6, 24, 46, 57, 18, 40, 32, 60, 54]
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0170
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0870
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.164820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.122861 restraints weight = 5346.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.19
r_work: 0.3132 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5508  Z= 0.116
  Angle     :  0.555   8.984   7446  Z= 0.275
  Chirality :  0.037   0.132    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.206  88.282   1033
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.80 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.33), residues: 648
  helix:  2.36 (0.22), residues: 508
  sheet: -1.80 (1.84), residues: 12
  loop : -0.51 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 368 
 TYR   0.015   0.001   TYR A  17 
 PHE   0.019   0.001   PHE A 487 
 TRP   0.007   0.001   TRP A 372 
 HIS   0.004   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 ( 5508)
  covalent geometry    : angle       0.55513 /  0.28 ( 7446)
  hydrogen bonds       : bond        0.04563 /  2.96 (  382)
  hydrogen bonds       : angle       4.85361 /  3.67 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.3559 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7418 (pm20) cc_final: 0.6816 (pt0)
REVERT: A  463 MET cc_start: 0.3506 (tpt) cc_final: 0.2659 (ppp)
REVERT: A  565 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7690 (mtp180)
  outliers start: 6
  outliers final: 4
  residues processed: 73
  average time/residue: 0.6301
  time to fit residues: 47.9294
Evaluate side-chains
  72 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [24, 4, 26, 49, 3, 63, 33, 11, 23, 35, 14]
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.164168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.121328 restraints weight = 5819.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.24
r_work: 0.3115 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5508  Z= 0.123
  Angle     :  0.563   6.650   7446  Z= 0.281
  Chirality :  0.038   0.132    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.246  88.096   1033
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.80 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.58 (0.33), residues: 648
  helix:  2.33 (0.22), residues: 508
  sheet: -1.87 (1.83), residues: 12
  loop : -0.50 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 179 
 TYR   0.017   0.001   TYR A 327 
 PHE   0.020   0.002   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 5508)
  covalent geometry    : angle       0.56290 /  0.28 ( 7446)
  hydrogen bonds       : bond        0.04781 /  3.11 (  382)
  hydrogen bonds       : angle       4.89230 /  3.70 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.3566 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7385 (pm20) cc_final: 0.6782 (pt0)
REVERT: A  463 MET cc_start: 0.3500 (tpt) cc_final: 0.2644 (ppp)
REVERT: A  565 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7557 (mtp180)
  outliers start: 7
  outliers final: 5
  residues processed: 72
  average time/residue: 0.6210
  time to fit residues: 46.5461
Evaluate side-chains
  74 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [9, 8, 12, 15, 18, 10, 41, 13, 55, 48, 61]
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.164768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122737 restraints weight = 5337.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.20
r_work: 0.3115 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5508  Z= 0.118
  Angle     :  0.563   9.563   7446  Z= 0.278
  Chirality :  0.038   0.132    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.155  88.413   1033
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.56 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.33), residues: 648
  helix:  2.36 (0.22), residues: 508
  sheet: -1.88 (1.84), residues: 12
  loop : -0.48 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.016   0.001   TYR A  17 
 PHE   0.020   0.002   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.004   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 ( 5508)
  covalent geometry    : angle       0.56303 /  0.28 ( 7446)
  hydrogen bonds       : bond        0.04624 /  3.01 (  382)
  hydrogen bonds       : angle       4.85162 /  3.67 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.3552 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7372 (pm20) cc_final: 0.6776 (pt0)
REVERT: A  463 MET cc_start: 0.3464 (tpt) cc_final: 0.2602 (ppp)
REVERT: A  565 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7562 (mtp180)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.6362
  time to fit residues: 46.9407
Evaluate side-chains
  72 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [26, 23, 18, 45, 53, 19, 54, 60, 25, 31, 1]
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 18 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 60 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.165176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.121535 restraints weight = 6697.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.33
r_work: 0.3118 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5508  Z= 0.115
  Angle     :  0.547   6.807   7446  Z= 0.274
  Chirality :  0.037   0.132    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.053  88.851   1033
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.37 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.33), residues: 648
  helix:  2.39 (0.22), residues: 509
  sheet: -1.89 (1.84), residues: 12
  loop : -0.46 (0.59), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 368 
 TYR   0.015   0.001   TYR A 327 
 PHE   0.019   0.001   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.004   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.12 ( 5508)
  covalent geometry    : angle       0.54694 /  0.27 ( 7446)
  hydrogen bonds       : bond        0.04531 /  2.95 (  382)
  hydrogen bonds       : angle       4.82791 /  3.65 ( 1131)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  179 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.3537 (tpp-160)
REVERT: A  363 GLU cc_start: 0.7459 (pm20) cc_final: 0.6824 (pt0)
REVERT: A  463 MET cc_start: 0.3485 (tpt) cc_final: 0.2572 (ppp)
REVERT: A  565 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7556 (mtp180)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 0.6248
  time to fit residues: 46.7796
Evaluate side-chains
  74 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   29 THR
Chi-restraints excluded: chain X residue   45 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks: [26, 14, 33, 39, 61, 8, 16, 49, 47, 53, 32]
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 47 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.164187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118118 restraints weight = 9317.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.57
r_work: 0.3044 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5508  Z= 0.124
  Angle     :  0.573   9.422   7446  Z= 0.285
  Chirality :  0.038   0.132    868
  Planarity :  0.004   0.047    875
  Dihedral  : 11.162  88.750   1033
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.37 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.33), residues: 648
  helix:  2.32 (0.22), residues: 508
  sheet: -1.89 (1.84), residues: 12
  loop : -0.49 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 368 
 TYR   0.017   0.001   TYR A  17 
 PHE   0.020   0.002   PHE A 487 
 TRP   0.006   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 352 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 5508)
  covalent geometry    : angle       0.57340 /  0.29 ( 7446)
  hydrogen bonds       : bond        0.04813 /  3.14 (  382)
  hydrogen bonds       : angle       4.88824 /  3.69 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3188.46 seconds
wall clock time: 54 minutes 54.10 seconds (3294.10 seconds total)