Starting phenix.real_space_refine
on Thu Jul  2 04:32:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z2r_73776/07_2026/9z2r_73776.cif"
  }
  resolution = 3.71
  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=   0.005
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      75      5.49       5
     S      31      5.16       5
     C    3811      2.51       5
     N    1125      2.21       5
     O    1407      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6449
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4822
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 555}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1600
          Classifications: {'RNA': 75}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 9, 'rna3p': 65}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.21
  Number of scatterers: 6449
  At special positions: 0
  Unit cell: (74.784, 93.48, 105.288, 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      31     16.00
     P      75     15.00
     O    1407      8.00
     N    1125      7.00
     C    3811      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: 0.56
  Conformation dependent library (CDL) restraints added in 247.7 milliseconds
  

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      42.7% alpha, 17.6% beta
      21 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 98 through 103
      removed outlier: 3.709A  pdb=" N   GLU A 103 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 124
      removed outlier: 3.676A  pdb=" N   GLU A 124 " --> pdb=" O   TYR A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 124'
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 142 through 155
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 3.549A  pdb=" N   LEU A 170 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASN A 173 " --> pdb=" O   PRO A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 4.039A  pdb=" N   GLN A 193 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 242 through 246
      removed outlier: 3.795A  pdb=" N   ILE A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 277
      removed outlier: 3.824A  pdb=" N   MET A 277 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 289 through 309
      removed outlier: 4.600A  pdb=" N   GLY A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LEU A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 340
      removed outlier: 4.042A  pdb=" N   ILE A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 381 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.711A  pdb=" N   HIS A 405 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 408
      No H-bonds generated for 'chain 'A' and resid 406 through 408'
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 4.459A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 538
      removed outlier: 3.706A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 546
      No H-bonds generated for 'chain 'A' and resid 544 through 546'
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 613 through 615
      No H-bonds generated for 'chain 'A' and resid 613 through 615'
    Processing helix  chain 'A' and resid 623 through 633
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 642 through 651
      removed outlier: 3.820A  pdb=" N   ASP A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 702
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117
      removed outlier: 8.222A  pdb=" N   TRP A 127 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ILE A  80 " --> pdb=" O   TRP A 127 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   LEU A  78 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   LEU A 131 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107
    Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345
    Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345
      removed outlier: 4.473A  pdb=" N   GLY A 314 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ASP A 263 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   LYS A 179 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   LEU A 266 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU A 181 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ILE A 236 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL A 238 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253
    Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522
      removed outlier: 6.726A  pdb=" N   LEU A 560 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 622

    195 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      56 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1810
        1.34 -     1.46: 1663
        1.46 -     1.58: 3085
        1.58 -     1.70: 149
        1.70 -     1.82: 50
  Bond restraints: 6757
  Sorted by residual:
  bond pdb=" N1    C B  48 "
       pdb=" C2    C B  48 "
    ideal  model  delta    sigma   weight residual
    1.397  1.419 -0.022 1.00e-02 1.00e+04 5.04e+00
  bond pdb=" CD  SFG A 801 "
       pdb=" NE  SFG A 801 "
    ideal  model  delta    sigma   weight residual
    1.471  1.496 -0.025 2.00e-02 2.50e+03 1.60e+00
  bond pdb=" C1'   C B  48 "
       pdb=" N1    C B  48 "
    ideal  model  delta    sigma   weight residual
    1.480  1.497 -0.017 1.50e-02 4.44e+03 1.34e+00
  bond pdb=" CA  SFG A 801 "
       pdb=" C   SFG A 801 "
    ideal  model  delta    sigma   weight residual
    1.553  1.532  0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" N1    C B  11 "
       pdb=" C2    C B  11 "
    ideal  model  delta    sigma   weight residual
    1.397  1.407 -0.010 1.00e-02 1.00e+04 9.70e-01
  ... (remaining 6752 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 9357
        1.27 -     2.55: 115
        2.55 -     3.82: 39
        3.82 -     5.09: 3
        5.09 -     6.36: 3
  Bond angle restraints: 9517
  Sorted by residual:
  angle pdb=" C1'   C B  11 "
        pdb=" N1    C B  11 "
        pdb=" C2    C B  11 "
      ideal   model   delta    sigma   weight residual
     118.80  122.35   -3.55 1.10e+00 8.26e-01 1.04e+01
  angle pdb=" C1'   C B  11 "
        pdb=" N1    C B  11 "
        pdb=" C6    C B  11 "
      ideal   model   delta    sigma   weight residual
     120.80  117.70    3.10 1.20e+00 6.94e-01 6.69e+00
  angle pdb=" C1'   G B  46 "
        pdb=" N9    G B  46 "
        pdb=" C4    G B  46 "
      ideal   model   delta    sigma   weight residual
     126.50  129.33   -2.83 1.30e+00 5.92e-01 4.72e+00
  angle pdb=" N2    G B  30 "
        pdb=" C2    G B  30 "
        pdb=" N3    G B  30 "
      ideal   model   delta    sigma   weight residual
     119.90  118.43    1.47 7.00e-01 2.04e+00 4.38e+00
  angle pdb=" N   PRO A 531 "
        pdb=" CA  PRO A 531 "
        pdb=" C   PRO A 531 "
      ideal   model   delta    sigma   weight residual
     110.70  113.21   -2.51 1.22e+00 6.72e-01 4.22e+00
  ... (remaining 9512 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.78: 4059
       35.78 -    71.57: 176
       71.57 -   107.35: 27
      107.35 -   143.13: 2
      143.13 -   178.92: 1
  Dihedral angle restraints: 4265
    sinusoidal: 2518
      harmonic: 1747
  Sorted by residual:
  dihedral pdb=" O4'   C B  48 "
           pdb=" C1'   C B  48 "
           pdb=" N1    C B  48 "
           pdb=" C2    C B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   72.81  127.19     1      1.50e+01 4.44e-03 6.85e+01
  dihedral pdb=" O4'   U B  20 "
           pdb=" C1'   U B  20 "
           pdb=" N1    U B  20 "
           pdb=" C2    U B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.92 -178.92     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   G B  15 "
           pdb=" C1'   G B  15 "
           pdb=" N9    G B  15 "
           pdb=" C4    G B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -20.55  -69.45     1      2.00e+01 2.50e-03 1.56e+01
  ... (remaining 4262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 942
       0.047 -    0.093: 113
       0.093 -    0.140: 54
       0.140 -    0.187: 0
       0.187 -    0.234: 1
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" P     C B  48 "
            pdb=" OP1   C B  48 "
            pdb=" OP2   C B  48 "
            pdb=" O5'   C B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.64   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  VAL A  58 "
            pdb=" N   VAL A  58 "
            pdb=" C   VAL A  58 "
            pdb=" CB  VAL A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  VAL A 114 "
            pdb=" N   VAL A 114 "
            pdb=" C   VAL A 114 "
            pdb=" CB  VAL A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 531 "    0.025 5.00e-02 4.00e+02   3.73e-02 2.22e+00
        pdb=" N   PRO A 532 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 532 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 532 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 167 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 168 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 168 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 168 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 530 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO A 531 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 531 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 531 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 935 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1124
        2.77 -     3.30: 5865
        3.30 -     3.83: 11617
        3.83 -     4.37: 13416
        4.37 -     4.90: 20974
  Nonbonded interactions: 52996
  Sorted by model distance:
  nonbonded pdb=" OP2   U B  50 "
            pdb=" N2    G B  59 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OG  SER A 151 "
            pdb=" NH1 ARG A 700 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" N2    G B  29 "
            pdb=" O2    C B  41 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG A 438 "
            pdb=" OP2   U B  33 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OD1 ASN A 569 "
            pdb=" ND2 ASN A 573 "
     model   vdw
     2.284 3.120
  ... (remaining 52991 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
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      :  0.002   0.026   6757  Z= 0.119
  Angle     :  0.423   6.363   9517  Z= 0.285
  Chirality :  0.036   0.234   1110
  Planarity :  0.004   0.037    938
  Dihedral  : 17.258 178.918   3129
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  2.34 (0.36), residues: 593
  helix:  2.40 (0.42), residues: 192
  sheet:  0.47 (0.51), residues: 104
  loop :  1.62 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 248 
 TYR   0.008   0.001   TYR A  38 
 PHE   0.007   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.000   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.12 ( 6757)
  covalent geometry    : angle       0.42311 /  0.28 ( 9517)
  hydrogen bonds       : bond        0.16819 / 11.44 (  249)
  hydrogen bonds       : angle       5.60212 /  3.80 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0924
  time to fit residues: 7.1211
Evaluate side-chains
  31 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:   30.0000
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 416 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.081508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.055182 restraints weight = 26710.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.056585 restraints weight = 16155.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.057147 restraints weight = 10342.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.057516 restraints weight = 9413.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.057721 restraints weight = 8760.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6757  Z= 0.167
  Angle     :  0.556   9.386   9517  Z= 0.285
  Chirality :  0.039   0.287   1110
  Planarity :  0.005   0.037    938
  Dihedral  : 20.943 178.705   1881
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.46 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  2.08 (0.36), residues: 593
  helix:  2.12 (0.41), residues: 198
  sheet: -0.01 (0.47), residues: 113
  loop :  1.71 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 639 
 TYR   0.014   0.001   TYR A  51 
 PHE   0.011   0.001   PHE A 597 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.004   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.17 ( 6757)
  covalent geometry    : angle       0.55566 /  0.28 ( 9517)
  hydrogen bonds       : bond        0.04638 /  3.14 (  249)
  hydrogen bonds       : angle       4.83150 /  3.34 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 MET cc_start: 0.8522 (mtp) cc_final: 0.8177 (mtp)
  outliers start: 4
  outliers final: 1
  residues processed: 33
  average time/residue: 0.0467
  time to fit residues: 2.4950
Evaluate side-chains
  28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 64 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 62 optimal weight:   40.0000
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.080284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053946 restraints weight = 26563.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.055438 restraints weight = 16007.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.056018 restraints weight = 10477.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.056559 restraints weight = 9589.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.056645 restraints weight = 9125.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6757  Z= 0.172
  Angle     :  0.523   9.059   9517  Z= 0.268
  Chirality :  0.038   0.293   1110
  Planarity :  0.004   0.040    938
  Dihedral  : 20.904 178.602   1881
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  5.58 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.90 (0.36), residues: 593
  helix:  1.81 (0.40), residues: 199
  sheet:  0.11 (0.49), residues: 103
  loop :  1.58 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 695 
 TYR   0.011   0.001   TYR A  52 
 PHE   0.009   0.001   PHE A  48 
 TRP   0.012   0.001   TRP A 435 
 HIS   0.004   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 ( 6757)
  covalent geometry    : angle       0.52295 /  0.27 ( 9517)
  hydrogen bonds       : bond        0.04293 /  2.86 (  249)
  hydrogen bonds       : angle       4.57468 /  3.20 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9280 (mmm) cc_final: 0.8274 (mmm)
REVERT: A  202 MET cc_start: 0.8458 (tpp) cc_final: 0.8047 (tpp)
REVERT: A  277 MET cc_start: 0.8479 (mtp) cc_final: 0.8274 (mtp)
REVERT: A  701 MET cc_start: 0.8507 (mmp) cc_final: 0.8218 (mmp)
  outliers start: 6
  outliers final: 2
  residues processed: 34
  average time/residue: 0.0488
  time to fit residues: 2.7008
Evaluate side-chains
  25 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 63 optimal weight:   20.0000
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:   30.0000
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.081366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.055206 restraints weight = 26780.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.056815 restraints weight = 15421.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.057381 restraints weight = 10018.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.057810 restraints weight = 9281.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.057882 restraints weight = 8925.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6757  Z= 0.106
  Angle     :  0.486   8.094   9517  Z= 0.246
  Chirality :  0.037   0.301   1110
  Planarity :  0.004   0.040    938
  Dihedral  : 20.852 178.182   1881
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  7.43 %
    Favored  : 92.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.96 (0.36), residues: 593
  helix:  1.90 (0.40), residues: 198
  sheet:  0.10 (0.49), residues: 103
  loop :  1.59 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.008   0.001   PHE A  48 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.002   0.001   HIS A 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 6757)
  covalent geometry    : angle       0.48577 /  0.25 ( 9517)
  hydrogen bonds       : bond        0.03680 /  2.46 (  249)
  hydrogen bonds       : angle       4.28288 /  3.01 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.8451 (tpp) cc_final: 0.7963 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0559
  time to fit residues: 2.4537
Evaluate side-chains
  25 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 9 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.081050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.054216 restraints weight = 26982.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.056153 restraints weight = 13901.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.057401 restraints weight = 9769.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.058035 restraints weight = 8119.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.058191 restraints weight = 7436.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6757  Z= 0.097
  Angle     :  0.467   8.136   9517  Z= 0.237
  Chirality :  0.037   0.302   1110
  Planarity :  0.004   0.038    938
  Dihedral  : 20.789 177.885   1881
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  7.43 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  2.03 (0.36), residues: 593
  helix:  2.06 (0.40), residues: 192
  sheet: -0.01 (0.49), residues: 106
  loop :  1.65 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 639 
 TYR   0.008   0.001   TYR A  51 
 PHE   0.016   0.001   PHE A 145 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 697 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00216 /  0.10 ( 6757)
  covalent geometry    : angle       0.46678 /  0.24 ( 9517)
  hydrogen bonds       : bond        0.03533 /  2.35 (  249)
  hydrogen bonds       : angle       4.13898 /  2.92 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  702 MET cc_start: 0.8149 (tpp) cc_final: 0.7809 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.0578
  time to fit residues: 2.7662
Evaluate side-chains
  27 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:   40.0000
   chunk 14 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 63 optimal weight:   20.0000
   chunk 8 optimal weight:    0.3980
   chunk 34 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.4586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.082083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.055463 restraints weight = 27263.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.057430 restraints weight = 14252.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.058632 restraints weight = 10215.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.059292 restraints weight = 8609.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.059499 restraints weight = 7909.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6757  Z= 0.133
  Angle     :  0.500   9.556   9517  Z= 0.249
  Chirality :  0.037   0.302   1110
  Planarity :  0.004   0.039    938
  Dihedral  : 20.766 177.951   1881
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.62 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.96 (0.36), residues: 593
  helix:  2.03 (0.40), residues: 192
  sheet: -0.06 (0.49), residues: 103
  loop :  1.57 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 545 
 TYR   0.011   0.001   TYR A  51 
 PHE   0.014   0.001   PHE A 145 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 6757)
  covalent geometry    : angle       0.49977 /  0.25 ( 9517)
  hydrogen bonds       : bond        0.03698 /  2.48 (  249)
  hydrogen bonds       : angle       4.15499 /  2.94 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  702 MET cc_start: 0.7967 (tpp) cc_final: 0.7684 (tpp)
  outliers start: 5
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0652
  time to fit residues: 3.0937
Evaluate side-chains
  28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0010
   chunk 16 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.080824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.054142 restraints weight = 26399.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.056037 restraints weight = 13670.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.057192 restraints weight = 9702.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.057791 restraints weight = 8132.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.058207 restraints weight = 7473.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6757  Z= 0.094
  Angle     :  0.465   7.991   9517  Z= 0.235
  Chirality :  0.037   0.308   1110
  Planarity :  0.004   0.038    938
  Dihedral  : 20.729 177.819   1881
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.18 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.97 (0.36), residues: 593
  helix:  2.05 (0.41), residues: 192
  sheet: -0.07 (0.49), residues: 103
  loop :  1.57 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 639 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.013   0.001   PHE A 145 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.002   0.000   HIS A 697 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00207 /  0.09 ( 6757)
  covalent geometry    : angle       0.46510 /  0.24 ( 9517)
  hydrogen bonds       : bond        0.03378 /  2.25 (  249)
  hydrogen bonds       : angle       4.00802 /  2.84 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  702 MET cc_start: 0.8079 (tpp) cc_final: 0.7834 (tpp)
  outliers start: 3
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0532
  time to fit residues: 2.4152
Evaluate side-chains
  28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 CYS
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.2582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.081655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.055527 restraints weight = 26426.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.057367 restraints weight = 14584.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.057606 restraints weight = 9465.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.057830 restraints weight = 9740.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.058010 restraints weight = 8932.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6757  Z= 0.122
  Angle     :  0.493  11.869   9517  Z= 0.243
  Chirality :  0.037   0.307   1110
  Planarity :  0.004   0.039    938
  Dihedral  : 20.709 177.855   1881
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.11 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.92 (0.36), residues: 593
  helix:  2.00 (0.40), residues: 192
  sheet: -0.02 (0.49), residues: 103
  loop :  1.51 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 264 
 TYR   0.011   0.001   TYR A  51 
 PHE   0.011   0.001   PHE A 145 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.002   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 6757)
  covalent geometry    : angle       0.49298 /  0.24 ( 9517)
  hydrogen bonds       : bond        0.03602 /  2.41 (  249)
  hydrogen bonds       : angle       4.07126 /  2.88 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0540
  time to fit residues: 2.5426
Evaluate side-chains
  26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 62 optimal weight:   30.0000
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.3588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.080299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.053859 restraints weight = 27248.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.055719 restraints weight = 14081.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.056887 restraints weight = 10005.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.057242 restraints weight = 8373.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.057836 restraints weight = 7793.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6757  Z= 0.195
  Angle     :  0.581   9.995   9517  Z= 0.286
  Chirality :  0.039   0.307   1110
  Planarity :  0.004   0.038    938
  Dihedral  : 20.766 178.495   1881
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  8.92 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.76 (0.36), residues: 593
  helix:  1.83 (0.39), residues: 192
  sheet: -0.09 (0.50), residues: 105
  loop :  1.46 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.014   0.002   TYR A  51 
 PHE   0.014   0.001   PHE A 145 
 TRP   0.014   0.002   TRP A 127 
 HIS   0.005   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.19 ( 6757)
  covalent geometry    : angle       0.58060 /  0.29 ( 9517)
  hydrogen bonds       : bond        0.04233 /  2.88 (  249)
  hydrogen bonds       : angle       4.28600 /  3.04 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0505
  time to fit residues: 2.3617
Evaluate side-chains
  27 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:   30.0000
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.081248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.055076 restraints weight = 26613.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.056635 restraints weight = 15782.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.057182 restraints weight = 10297.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.057467 restraints weight = 9615.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.057642 restraints weight = 9091.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6757  Z= 0.123
  Angle     :  0.522   9.690   9517  Z= 0.255
  Chirality :  0.038   0.315   1110
  Planarity :  0.004   0.038    938
  Dihedral  : 20.776 178.392   1881
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.29 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.80 (0.36), residues: 593
  helix:  1.83 (0.40), residues: 194
  sheet: -0.13 (0.49), residues: 105
  loop :  1.52 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 315 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.014   0.001   PHE A 145 
 TRP   0.013   0.001   TRP A 435 
 HIS   0.002   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6757)
  covalent geometry    : angle       0.52168 /  0.25 ( 9517)
  hydrogen bonds       : bond        0.03696 /  2.51 (  249)
  hydrogen bonds       : angle       4.09584 /  2.92 (  613)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9250 (mmm) cc_final: 0.8016 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0535
  time to fit residues: 2.3857
Evaluate side-chains
  26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  587 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 61 optimal weight:   40.0000
   chunk 28 optimal weight:    0.7980
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.9784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.081193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.054635 restraints weight = 26757.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.056523 restraints weight = 14078.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057675 restraints weight = 10088.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.058032 restraints weight = 8524.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.058605 restraints weight = 7947.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6757  Z= 0.110
  Angle     :  0.529   9.573   9517  Z= 0.256
  Chirality :  0.037   0.316   1110
  Planarity :  0.004   0.038    938
  Dihedral  : 20.763 178.156   1881
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.29 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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:  1.84 (0.36), residues: 593
  helix:  1.87 (0.40), residues: 194
  sheet: -0.12 (0.50), residues: 105
  loop :  1.55 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 278 
 TYR   0.010   0.001   TYR A  51 
 PHE   0.014   0.001   PHE A 145 
 TRP   0.013   0.001   TRP A 435 
 HIS   0.002   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6757)
  covalent geometry    : angle       0.52942 /  0.26 ( 9517)
  hydrogen bonds       : bond        0.03588 /  2.43 (  249)
  hydrogen bonds       : angle       4.03099 /  2.88 (  613)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1023.61 seconds
wall clock time: 18 minutes 29.31 seconds (1109.31 seconds total)