Starting phenix.real_space_refine
on Fri Mar 14 05:59:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2025/6tmi_10522.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    3004      2.51       5
     N     837      2.21       5
     O     904      1.98       5
     H    4842      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9606
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 327
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 1, 'TRANS': 18}
    Chain: "G"
      Number of atoms: 2901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 2901
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 6, 'TRANS': 173}
    Chain: "A"
      Number of atoms: 1688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 1688
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 4, 'TRANS': 104}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 754
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "B"
      Number of atoms: 3936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 3936
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 5, 'TRANS': 240}
          Chain breaks: 1
  Time building chain proxies: 7.78, per 1000 atoms: 0.81
  Number of scatterers: 9606
  At special positions: 0
  Unit cell: (100.43, 129.48, 135.29, 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      19     16.00
     O     904      8.00
     N     837      7.00
     C    3004      6.00
     H    4842      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 728.5 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 1 sheets defined
      72.9% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'C' and resid 54 through 67
      removed outlier: 3.727A  pdb=" N   GLU C  58 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   SER C  60 " --> pdb=" O   PRO C  56 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ARG C  61 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 74 through 88
    Processing helix  chain 'G' and resid 92 through 111
      removed outlier: 3.730A  pdb=" N   VAL G  96 " --> pdb=" O   GLN G  92 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   SER G 111 " --> pdb=" O   LEU G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 119
    Processing helix  chain 'G' and resid 123 through 136
      removed outlier: 3.869A  pdb=" N   ASN G 136 " --> pdb=" O   ARG G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 141 through 154
    Processing helix  chain 'G' and resid 159 through 175
    Processing helix  chain 'G' and resid 188 through 204
    Processing helix  chain 'G' and resid 236 through 249
      removed outlier: 3.866A  pdb=" N   ARG G 240 " --> pdb=" O   SER G 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.542A  pdb=" N   LEU A  24 " --> pdb=" O   TRP A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 53
      removed outlier: 3.799A  pdb=" N   TRP A  36 " --> pdb=" O   ASN A  32 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 71
      removed outlier: 4.063A  pdb=" N   TRP A  67 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 99
      removed outlier: 4.285A  pdb=" N   CYS A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN A  89 " --> pdb=" O   THR A  85 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE A  90 " --> pdb=" O   ASN A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 131
      removed outlier: 4.376A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS A 130 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 95 through 115
      removed outlier: 3.997A  pdb=" N   LEU R  99 " --> pdb=" O   TRP R  95 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA R 115 " --> pdb=" O   GLU R 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 330
      removed outlier: 3.572A  pdb=" N   THR B 327 " --> pdb=" O   LYS B 324 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 329 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 346
      removed outlier: 3.672A  pdb=" N   SER B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLU B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ASP B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 402
      removed outlier: 4.211A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ALA B 352 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE B 391 " --> pdb=" O   MET B 387 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 417
      removed outlier: 4.059A  pdb=" N   ASP B 407 " --> pdb=" O   PRO B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 439
    Processing helix  chain 'B' and resid 453 through 471
      removed outlier: 4.111A  pdb=" N   ALA B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL B 461 " --> pdb=" O   ARG B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 487
      removed outlier: 3.502A  pdb=" N   ILE B 483 " --> pdb=" O   GLU B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 492
      removed outlier: 3.864A  pdb=" N   HIS B 491 " --> pdb=" O   VAL B 487 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS B 492 " --> pdb=" O   ASP B 488 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 487 through 492'
    Processing helix  chain 'B' and resid 505 through 521
      removed outlier: 3.973A  pdb=" N   ASN B 518 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 530
    Processing helix  chain 'B' and resid 537 through 539
      No H-bonds generated for 'chain 'B' and resid 537 through 539'
    Processing helix  chain 'B' and resid 540 through 569
      removed outlier: 3.629A  pdb=" N   GLU B 545 " --> pdb=" O   LYS B 541 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   PHE B 546 " --> pdb=" O   GLY B 542 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LYS B 557 " --> pdb=" O   ILE B 553 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ALA B 565 " --> pdb=" O   ALA B 561 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 207 through 210
      removed outlier: 6.512A  pdb=" N   GLU G 177 " --> pdb=" O   ARG G 209 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    876 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: 2.96

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4836
        1.03 -     1.23: 7
        1.23 -     1.42: 1947
        1.42 -     1.62: 2851
        1.62 -     1.81: 32
  Bond restraints: 9673
  Sorted by residual:
  bond pdb=" CG  LEU A  24 "
       pdb=" CD1 LEU A  24 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.04e+00
  bond pdb=" CG  LEU A  91 "
       pdb=" CD2 LEU A  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.49e+00
  bond pdb=" CB  VAL B 342 "
       pdb=" CG2 VAL B 342 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  bond pdb=" CB  VAL R 114 "
       pdb=" CG2 VAL R 114 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" CB  ILE A  90 "
       pdb=" CG2 ILE A  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  ... (remaining 9668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 15779
        0.98 -     1.96: 1614
        1.96 -     2.94: 88
        2.94 -     3.92: 26
        3.92 -     4.90: 15
  Bond angle restraints: 17522
  Sorted by residual:
  angle pdb=" N   GLU G 177 "
        pdb=" CA  GLU G 177 "
        pdb=" C   GLU G 177 "
      ideal   model   delta    sigma   weight residual
     110.48  113.81   -3.33 1.48e+00 4.57e-01 5.08e+00
  angle pdb=" N   ILE G 220 "
        pdb=" CA  ILE G 220 "
        pdb=" C   ILE G 220 "
      ideal   model   delta    sigma   weight residual
     109.34  113.75   -4.41 2.08e+00 2.31e-01 4.50e+00
  angle pdb=" N   PRO G 218 "
        pdb=" CA  PRO G 218 "
        pdb=" C   PRO G 218 "
      ideal   model   delta    sigma   weight residual
     112.47  108.26    4.21 2.06e+00 2.36e-01 4.18e+00
  angle pdb=" N   GLY G 222 "
        pdb=" CA  GLY G 222 "
        pdb=" C   GLY G 222 "
      ideal   model   delta    sigma   weight residual
     113.18  117.67   -4.49 2.37e+00 1.78e-01 3.59e+00
  angle pdb=" N   LEU G 157 "
        pdb=" CA  LEU G 157 "
        pdb=" C   LEU G 157 "
      ideal   model   delta    sigma   weight residual
     109.81  113.87   -4.06 2.21e+00 2.05e-01 3.38e+00
  ... (remaining 17517 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3975
       17.86 -    35.72: 397
       35.72 -    53.57: 90
       53.57 -    71.43: 21
       71.43 -    89.29: 9
  Dihedral angle restraints: 4492
    sinusoidal: 2491
      harmonic: 2001
  Sorted by residual:
  dihedral pdb=" CA  PRO G 218 "
           pdb=" C   PRO G 218 "
           pdb=" N   GLN G 219 "
           pdb=" CA  GLN G 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.46  -29.54     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  VAL A  49 "
           pdb=" C   VAL A  49 "
           pdb=" N   ILE A  50 "
           pdb=" CA  ILE A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.43  -26.57     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  LYS B 324 "
           pdb=" C   LYS B 324 "
           pdb=" N   TYR B 325 "
           pdb=" CA  TYR B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.00  -25.00     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 4489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 438
       0.027 -    0.054: 192
       0.054 -    0.081: 80
       0.081 -    0.107: 33
       0.107 -    0.134: 5
  Chirality restraints: 748
  Sorted by residual:
  chirality pdb=" CA  VAL G 178 "
            pdb=" N   VAL G 178 "
            pdb=" C   VAL G 178 "
            pdb=" CB  VAL G 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  ILE G 211 "
            pdb=" N   ILE G 211 "
            pdb=" C   ILE G 211 "
            pdb=" CB  ILE G 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CB  THR R 108 "
            pdb=" CA  THR R 108 "
            pdb=" OG1 THR R 108 "
            pdb=" CG2 THR R 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.44    0.12 2.00e-01 2.50e+01 3.38e-01
  ... (remaining 745 not shown)

  Planarity restraints: 1418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  55 "   -0.049 5.00e-02 4.00e+02   7.34e-02 8.62e+00
        pdb=" N   PRO C  56 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO C  56 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C  56 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 402 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO B 403 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 403 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 403 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  42 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   GLY A  42 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLY A  42 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A  43 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1415 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.20: 725
        2.20 -     2.80: 20923
        2.80 -     3.40: 24981
        3.40 -     4.00: 31047
        4.00 -     4.60: 48715
  Nonbonded interactions: 126391
  Sorted by model distance:
  nonbonded pdb=" HH  TYR R 126 "
            pdb=" OD1 ASN B 517 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" O   ARG G 172 "
            pdb=" H   GLY G 176 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" O   ASN G  91 "
            pdb="HD22 ASN G  91 "
     model   vdw
     1.663 2.450
  nonbonded pdb=" O   SER G 110 "
            pdb=" HG  SER G 111 "
     model   vdw
     1.670 2.450
  nonbonded pdb=" O   GLN G  92 "
            pdb=" H   LYS G  95 "
     model   vdw
     1.674 2.450
  ... (remaining 126386 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:             142.060
  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:             0.150
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     25.750
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  171.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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      :  0.006   0.047   4831  Z= 0.389
  Angle     :  0.637   4.905   6510  Z= 0.359
  Chirality :  0.038   0.134    748
  Planarity :  0.005   0.073    837
  Dihedral  : 16.160  89.290   1825
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.00 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.29), residues: 591
  helix: -2.20 (0.21), residues: 423
  sheet: -3.67 (1.00), residues: 16
  loop : -4.49 (0.43), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  95 
 HIS   0.007   0.002   HIS B 499 
 PHE   0.018   0.002   PHE B 469 
 TYR   0.011   0.002   TYR B 513 
 ARG   0.014   0.001   ARG B 508 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.8047 (m-30) cc_final: 0.7162 (t70)
REVERT: R  113 ASP cc_start: 0.8394 (t0) cc_final: 0.7766 (t0)
REVERT: B  323 LYS cc_start: 0.4109 (mttp) cc_final: 0.3484 (mttt)
REVERT: B  518 ASN cc_start: 0.8346 (m110) cc_final: 0.8139 (m-40)
  outliers start: 3
  outliers final: 1
  residues processed: 142
  average time/residue: 0.4776
  time to fit residues: 81.6884
Evaluate side-chains
  80 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0050
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.7800

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

Flipped N/Q/H residues before XYZ refinement:
G 105 ASN
G 202 ASN
B 518 ASN
B 526 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.101575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.079165 restraints weight = 38324.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.082885 restraints weight = 14455.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.085073 restraints weight = 7521.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4831  Z= 0.291
  Angle     :  0.656   5.573   6510  Z= 0.357
  Chirality :  0.038   0.153    748
  Planarity :  0.005   0.074    837
  Dihedral  :  5.724  40.070    646
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.95 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.40 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.34), residues: 591
  helix: -0.61 (0.24), residues: 429
  sheet: -3.30 (0.90), residues: 16
  loop : -3.96 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  64 
 HIS   0.005   0.001   HIS B 499 
 PHE   0.012   0.002   PHE G 116 
 TYR   0.007   0.001   TYR G 138 
 ARG   0.008   0.001   ARG G 137 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.8129 (m-30) cc_final: 0.7016 (t70)
REVERT: A   51 GLU cc_start: 0.8069 (pp20) cc_final: 0.7658 (pp20)
REVERT: R  113 ASP cc_start: 0.8742 (t0) cc_final: 0.8092 (t0)
REVERT: R  119 GLN cc_start: 0.7924 (tp40) cc_final: 0.7476 (tp40)
REVERT: B  323 LYS cc_start: 0.4302 (mttp) cc_final: 0.3732 (mttt)
REVERT: B  547 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7996 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 106
  average time/residue: 0.3188
  time to fit residues: 44.2758
Evaluate side-chains
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  202 ASN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.100358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.077545 restraints weight = 39002.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.081291 restraints weight = 14807.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.083514 restraints weight = 7746.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4831  Z= 0.251
  Angle     :  0.585   4.919   6510  Z= 0.316
  Chirality :  0.036   0.139    748
  Planarity :  0.004   0.068    837
  Dihedral  :  5.275  39.965    646
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.34 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.36), residues: 591
  helix:  0.32 (0.26), residues: 427
  sheet: -3.44 (0.89), residues: 16
  loop : -3.81 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.011   0.001   PHE G 167 
 TYR   0.005   0.001   TYR G 171 
 ARG   0.004   0.000   ARG G 203 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.8094 (m-30) cc_final: 0.7058 (t70)
REVERT: G  242 ASP cc_start: 0.8398 (t70) cc_final: 0.8142 (t0)
REVERT: R  113 ASP cc_start: 0.8771 (t0) cc_final: 0.8186 (t0)
REVERT: B  323 LYS cc_start: 0.4464 (mttp) cc_final: 0.3948 (mttt)
REVERT: B  547 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7971 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 102
  average time/residue: 0.2866
  time to fit residues: 39.8584
Evaluate side-chains
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  177 GLU
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 463 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.098902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.076447 restraints weight = 37139.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.080008 restraints weight = 14189.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.082166 restraints weight = 7473.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4831  Z= 0.225
  Angle     :  0.574   5.046   6510  Z= 0.311
  Chirality :  0.035   0.138    748
  Planarity :  0.004   0.069    837
  Dihedral  :  5.015  39.926    646
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.90 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.36), residues: 591
  helix:  0.69 (0.26), residues: 428
  sheet: -2.92 (1.00), residues: 16
  loop : -3.84 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  67 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.006   0.001   TYR G  79 
 ARG   0.003   0.000   ARG B 508 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.7962 (m-30) cc_final: 0.7012 (t70)
REVERT: G  153 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8233 (pp20)
REVERT: G  242 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8203 (t0)
REVERT: R  113 ASP cc_start: 0.8869 (t0) cc_final: 0.8311 (t0)
REVERT: B  367 GLU cc_start: 0.8528 (tp30) cc_final: 0.8243 (tp30)
REVERT: B  547 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7946 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 101
  average time/residue: 0.3292
  time to fit residues: 44.1860
Evaluate side-chains
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain G residue  242 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    0.2980
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.100319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.077491 restraints weight = 38256.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.081156 restraints weight = 14525.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.083349 restraints weight = 7610.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4831  Z= 0.167
  Angle     :  0.539   5.636   6510  Z= 0.284
  Chirality :  0.033   0.138    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.800  39.322    646
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.87 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.37), residues: 591
  helix:  1.17 (0.26), residues: 424
  sheet: -2.39 (1.17), residues: 16
  loop : -3.70 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.012   0.001   PHE A 117 
 TYR   0.004   0.001   TYR G  79 
 ARG   0.003   0.000   ARG G 203 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.7898 (m-30) cc_final: 0.7016 (t70)
REVERT: G  242 ASP cc_start: 0.8473 (t70) cc_final: 0.8201 (t0)
REVERT: A   53 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6450 (tm-30)
REVERT: R  113 ASP cc_start: 0.8811 (t0) cc_final: 0.8259 (t0)
REVERT: R  119 GLN cc_start: 0.8583 (tp40) cc_final: 0.8155 (tp40)
REVERT: B  367 GLU cc_start: 0.8496 (tp30) cc_final: 0.8245 (tp30)
  outliers start: 14
  outliers final: 13
  residues processed: 101
  average time/residue: 0.2822
  time to fit residues: 38.3539
Evaluate side-chains
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.098976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.075891 restraints weight = 38526.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.079575 restraints weight = 14620.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.081787 restraints weight = 7660.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.5783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4831  Z= 0.194
  Angle     :  0.546   5.555   6510  Z= 0.290
  Chirality :  0.034   0.138    748
  Planarity :  0.004   0.066    837
  Dihedral  :  4.698  38.952    646
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.46 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.37), residues: 591
  helix:  1.31 (0.26), residues: 427
  sheet: -2.46 (1.14), residues: 21
  loop : -3.50 (0.51), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.010   0.001   PHE A 117 
 TYR   0.004   0.001   TYR B 399 
 ARG   0.003   0.000   ARG G 209 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.7706 (m-30) cc_final: 0.7009 (t70)
REVERT: G  242 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8227 (t0)
REVERT: R  113 ASP cc_start: 0.8866 (t0) cc_final: 0.8313 (t0)
REVERT: B  367 GLU cc_start: 0.8593 (tp30) cc_final: 0.8297 (tp30)
REVERT: B  547 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 100
  average time/residue: 0.3023
  time to fit residues: 40.8450
Evaluate side-chains
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain G residue  242 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0070
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.099585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.076626 restraints weight = 38626.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.080303 restraints weight = 14703.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.082492 restraints weight = 7705.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.5972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4831  Z= 0.163
  Angle     :  0.530   5.400   6510  Z= 0.278
  Chirality :  0.033   0.137    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.579  38.475    646
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.65 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.37), residues: 591
  helix:  1.65 (0.26), residues: 419
  sheet: -2.20 (1.24), residues: 21
  loop : -3.17 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.003   0.001   TYR B 399 
 ARG   0.002   0.000   ARG G 209 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  109 ASP cc_start: 0.7605 (m-30) cc_final: 0.6872 (t0)
REVERT: G  242 ASP cc_start: 0.8493 (t70) cc_final: 0.8232 (t0)
REVERT: A   53 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6267 (tm-30)
REVERT: R  113 ASP cc_start: 0.8830 (t0) cc_final: 0.8287 (t0)
REVERT: B  367 GLU cc_start: 0.8547 (tp30) cc_final: 0.8304 (tp30)
REVERT: B  547 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7939 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 99
  average time/residue: 0.3582
  time to fit residues: 47.1134
Evaluate side-chains
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
G 191 GLN
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.098364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.075300 restraints weight = 38978.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.078953 restraints weight = 15010.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.081120 restraints weight = 7947.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4831  Z= 0.193
  Angle     :  0.549   5.784   6510  Z= 0.289
  Chirality :  0.034   0.137    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.516  38.304    646
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.68 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.37), residues: 591
  helix:  1.79 (0.26), residues: 419
  sheet: -2.11 (1.24), residues: 21
  loop : -3.14 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.010   0.001   PHE A 117 
 TYR   0.012   0.001   TYR G  79 
 ARG   0.002   0.000   ARG G 209 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  136 ASN cc_start: 0.8975 (m110) cc_final: 0.8657 (p0)
REVERT: G  242 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8277 (t0)
REVERT: A   89 GLN cc_start: 0.8066 (tt0) cc_final: 0.7738 (tm-30)
REVERT: A   99 GLU cc_start: 0.8238 (tt0) cc_final: 0.7947 (tm-30)
REVERT: R  113 ASP cc_start: 0.8870 (t0) cc_final: 0.8326 (t0)
REVERT: B  547 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7974 (t)
  outliers start: 20
  outliers final: 14
  residues processed: 104
  average time/residue: 0.2997
  time to fit residues: 41.4590
Evaluate side-chains
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  191 GLN
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain G residue  242 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** R 119 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 = 0.3792 r_free = 0.3792 target = 0.097850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.074740 restraints weight = 38594.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.078357 restraints weight = 14784.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.080519 restraints weight = 7836.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.6453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4831  Z= 0.211
  Angle     :  0.562   5.750   6510  Z= 0.297
  Chirality :  0.034   0.136    748
  Planarity :  0.004   0.064    837
  Dihedral  :  4.517  37.932    646
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.23 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.37), residues: 591
  helix:  1.74 (0.26), residues: 422
  sheet: -2.14 (1.21), residues: 21
  loop : -3.08 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 
 PHE   0.010   0.001   PHE A 117 
 TYR   0.005   0.001   TYR B 349 
 ARG   0.001   0.000   ARG B 508 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  242 ASP cc_start: 0.8564 (t70) cc_final: 0.8309 (t0)
REVERT: A   53 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6593 (tm-30)
REVERT: A   89 GLN cc_start: 0.8087 (tt0) cc_final: 0.7731 (tm-30)
REVERT: A   99 GLU cc_start: 0.8267 (tt0) cc_final: 0.7998 (tm-30)
REVERT: R  113 ASP cc_start: 0.8865 (t0) cc_final: 0.8326 (t0)
REVERT: B  547 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7927 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 95
  average time/residue: 0.2858
  time to fit residues: 37.0915
Evaluate side-chains
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** R 119 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 = 0.3801 r_free = 0.3801 target = 0.098399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.075434 restraints weight = 38777.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.079037 restraints weight = 14881.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.081194 restraints weight = 7881.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.6605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4831  Z= 0.170
  Angle     :  0.548   5.941   6510  Z= 0.288
  Chirality :  0.033   0.130    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.425  38.413    646
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.84 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.37), residues: 591
  helix:  1.87 (0.26), residues: 423
  sheet: -2.28 (1.16), residues: 21
  loop : -3.04 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.004   0.001   TYR B 399 
 ARG   0.001   0.000   ARG G 240 

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  136 ASN cc_start: 0.9031 (m110) cc_final: 0.8723 (p0)
REVERT: G  242 ASP cc_start: 0.8563 (t70) cc_final: 0.8298 (t0)
REVERT: A   53 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6795 (tm-30)
REVERT: A   89 GLN cc_start: 0.8059 (tt0) cc_final: 0.7747 (tm-30)
REVERT: A   99 GLU cc_start: 0.8185 (tt0) cc_final: 0.7976 (tm-30)
REVERT: R  113 ASP cc_start: 0.8846 (t0) cc_final: 0.8322 (t0)
REVERT: B  363 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: B  547 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7961 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 96
  average time/residue: 0.3114
  time to fit residues: 40.1040
Evaluate side-chains
  96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  101 GLU
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  201 GLN
Chi-restraints excluded: chain G residue  211 ILE
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  547 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** R 119 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 = 0.3785 r_free = 0.3785 target = 0.097153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.074752 restraints weight = 37066.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.078276 restraints weight = 14195.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.080391 restraints weight = 7468.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.6780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4831  Z= 0.183
  Angle     :  0.550   5.937   6510  Z= 0.290
  Chirality :  0.033   0.126    748
  Planarity :  0.004   0.064    837
  Dihedral  :  4.393  38.422    646
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.65 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.37), residues: 591
  helix:  1.87 (0.26), residues: 424
  sheet: -2.41 (1.09), residues: 21
  loop : -3.00 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.004   0.001   HIS B 406 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.005   0.001   TYR B 349 
 ARG   0.001   0.000   ARG B 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4542.45 seconds
wall clock time: 79 minutes 13.36 seconds (4753.36 seconds total)