Starting phenix.real_space_refine
on Wed Mar  4 00:45:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tmi_10522/03_2026/6tmi_10522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tmi_10522/03_2026/6tmi_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_2026/6tmi_10522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2026/6tmi_10522.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2026/6tmi_10522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tmi_10522/03_2026/6tmi_10522.cif"
  }
  resolution = 3.5
  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=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.17
  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: 0.63
  Conformation dependent library (CDL) restraints added in 185.1 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: 0.12
  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: 1.88

  Time building geometry restraints manager: 0.89 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:             12.100
  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:             0.050
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.480
-------------------------------------------------------------------------------
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= 0.251
  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 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: -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
 ARG   0.014   0.001   ARG B 508 
 TYR   0.011   0.002   TYR B 513 
 PHE   0.018   0.002   PHE B 469 
 TRP   0.010   0.001   TRP R  95 
 HIS   0.007   0.002   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 4831)
  covalent geometry    : angle       0.63694 ( 6510)
  hydrogen bonds       : bond        0.15441 (  297)
  hydrogen bonds       : angle       6.91565 (  876)

*********************** 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  : 0.323 
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: G  109 ASP cc_start: 0.8047 (m-30) cc_final: 0.7161 (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: 0.2279
  time to fit residues: 38.6659
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  : 0.252 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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
R 132 ASN
B 518 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.105461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.083516 restraints weight = 37867.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.087428 restraints weight = 13615.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.089666 restraints weight = 6869.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.090966 restraints weight = 4285.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.091653 restraints weight = 3128.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4831  Z= 0.140
  Angle     :  0.597   4.845   6510  Z= 0.321
  Chirality :  0.035   0.151    748
  Planarity :  0.005   0.072    837
  Dihedral  :  5.761  38.495    646
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.42 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.33), residues: 591
  helix: -0.67 (0.24), residues: 424
  sheet: -3.31 (0.88), residues: 16
  loop : -3.76 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 137 
 TYR   0.006   0.001   TYR G 171 
 PHE   0.013   0.002   PHE G 116 
 TRP   0.004   0.001   TRP R  95 
 HIS   0.003   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4831)
  covalent geometry    : angle       0.59674 ( 6510)
  hydrogen bonds       : bond        0.05093 (  297)
  hydrogen bonds       : angle       4.79497 (  876)

*********************** 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
  101 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.249 
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: 0.8172 (m-30) cc_final: 0.7123 (t70)
REVERT: A   51 GLU cc_start: 0.7843 (pp20) cc_final: 0.7640 (pp20)
REVERT: A   66 LYS cc_start: 0.8842 (tttt) cc_final: 0.8614 (tttt)
REVERT: R  113 ASP cc_start: 0.8651 (t0) cc_final: 0.8044 (t0)
REVERT: R  119 GLN cc_start: 0.7838 (tp40) cc_final: 0.7384 (tp40)
REVERT: B  323 LYS cc_start: 0.4134 (mttp) cc_final: 0.3597 (mttt)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1611
  time to fit residues: 20.5806
Evaluate side-chains
  89 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
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  379 ILE
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  497 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 33 optimal weight:    0.2980
   chunk 45 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.104545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.082006 restraints weight = 38232.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.085888 restraints weight = 13960.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.088141 restraints weight = 7123.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.089470 restraints weight = 4462.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.090261 restraints weight = 3254.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3779

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= 0.126
  Angle     :  0.548   5.133   6510  Z= 0.293
  Chirality :  0.034   0.146    748
  Planarity :  0.004   0.067    837
  Dihedral  :  5.218  39.723    646
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.95 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.36), residues: 591
  helix:  0.22 (0.26), residues: 427
  sheet: -3.42 (0.87), residues: 16
  loop : -3.58 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 203 
 TYR   0.005   0.001   TYR G 171 
 PHE   0.010   0.001   PHE G 167 
 TRP   0.004   0.001   TRP R  95 
 HIS   0.003   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4831)
  covalent geometry    : angle       0.54800 ( 6510)
  hydrogen bonds       : bond        0.04509 (  297)
  hydrogen bonds       : angle       4.24365 (  876)

*********************** 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
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.279 
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: 0.8099 (m-30) cc_final: 0.7059 (t70)
REVERT: A   51 GLU cc_start: 0.7956 (pp20) cc_final: 0.7594 (pp20)
REVERT: R  113 ASP cc_start: 0.8737 (t0) cc_final: 0.8247 (t0)
REVERT: R  119 GLN cc_start: 0.7815 (tp40) cc_final: 0.7607 (tp40)
REVERT: B  323 LYS cc_start: 0.4355 (mttp) cc_final: 0.3909 (mttt)
  outliers start: 11
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1450
  time to fit residues: 17.5200
Evaluate side-chains
  86 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  211 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.103250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.080455 restraints weight = 38281.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.084271 restraints weight = 14218.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.086514 restraints weight = 7328.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.087804 restraints weight = 4621.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.088545 restraints weight = 3423.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4831  Z= 0.129
  Angle     :  0.541   5.127   6510  Z= 0.291
  Chirality :  0.034   0.144    748
  Planarity :  0.004   0.067    837
  Dihedral  :  4.932  40.292    646
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.93 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.47 (0.37), residues: 591
  helix:  0.85 (0.26), residues: 424
  sheet: -3.08 (0.89), residues: 16
  loop : -3.41 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 508 
 TYR   0.004   0.001   TYR G 171 
 PHE   0.009   0.001   PHE A 117 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4831)
  covalent geometry    : angle       0.54086 ( 6510)
  hydrogen bonds       : bond        0.04260 (  297)
  hydrogen bonds       : angle       3.96783 (  876)

*********************** 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
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.290 
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: 0.8038 (m-30) cc_final: 0.7037 (t70)
REVERT: R  113 ASP cc_start: 0.8780 (t0) cc_final: 0.8285 (t0)
REVERT: R  119 GLN cc_start: 0.7890 (tp40) cc_final: 0.7633 (tp40)
  outliers start: 11
  outliers final: 10
  residues processed: 93
  average time/residue: 0.1213
  time to fit residues: 15.4172
Evaluate side-chains
  89 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
G 191 GLN
G 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.102332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.079497 restraints weight = 37815.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.083282 restraints weight = 14059.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.085524 restraints weight = 7237.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.086848 restraints weight = 4573.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.087618 restraints weight = 3357.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4831  Z= 0.115
  Angle     :  0.521   5.690   6510  Z= 0.275
  Chirality :  0.033   0.141    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.767  39.872    646
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.90 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.37), residues: 591
  helix:  1.16 (0.26), residues: 427
  sheet: -2.66 (1.00), residues: 16
  loop : -3.46 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 508 
 TYR   0.003   0.001   TYR B 513 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4831)
  covalent geometry    : angle       0.52060 ( 6510)
  hydrogen bonds       : bond        0.04007 (  297)
  hydrogen bonds       : angle       3.78545 (  876)

*********************** 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
  99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.317 
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: 0.7976 (m-30) cc_final: 0.6975 (t70)
REVERT: R  113 ASP cc_start: 0.8809 (t0) cc_final: 0.8280 (t0)
REVERT: R  119 GLN cc_start: 0.7915 (tp40) cc_final: 0.7662 (tp40)
  outliers start: 12
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1235
  time to fit residues: 16.1716
Evaluate side-chains
  92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
Chi-restraints excluded: chain G residue  191 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  449 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0980
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0270
   chunk 12 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.8244

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

Flipped N/Q/H residues before XYZ refinement:
B 380 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.101826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.078843 restraints weight = 37970.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.082610 restraints weight = 14239.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.084856 restraints weight = 7390.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.086191 restraints weight = 4683.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.086969 restraints weight = 3434.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4831  Z= 0.124
  Angle     :  0.529   5.547   6510  Z= 0.281
  Chirality :  0.034   0.140    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.690  39.483    646
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.09 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.06 (0.37), residues: 591
  helix:  1.26 (0.26), residues: 427
  sheet: -2.58 (1.06), residues: 16
  loop : -3.41 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 508 
 TYR   0.007   0.001   TYR G  79 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.006   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4831)
  covalent geometry    : angle       0.52868 ( 6510)
  hydrogen bonds       : bond        0.04025 (  297)
  hydrogen bonds       : angle       3.76243 (  876)

*********************** 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
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.272 
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  109 ASP cc_start: 0.7945 (m-30) cc_final: 0.6959 (t70)
REVERT: G  213 ASP cc_start: 0.8075 (t70) cc_final: 0.7781 (t70)
REVERT: G  242 ASP cc_start: 0.8376 (t70) cc_final: 0.8118 (t0)
REVERT: R  113 ASP cc_start: 0.8803 (t0) cc_final: 0.8253 (t0)
REVERT: R  119 GLN cc_start: 0.8013 (tp40) cc_final: 0.7772 (tp40)
  outliers start: 12
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1207
  time to fit residues: 15.7930
Evaluate side-chains
  92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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  449 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.100678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.078257 restraints weight = 39056.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.081831 restraints weight = 14797.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.083971 restraints weight = 7756.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.085265 restraints weight = 4958.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.086030 restraints weight = 3652.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5474

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= 0.143
  Angle     :  0.552   5.607   6510  Z= 0.293
  Chirality :  0.034   0.136    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.670  39.138    646
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.32 %
    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 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:  0.24 (0.37), residues: 591
  helix:  1.42 (0.27), residues: 424
  sheet: -2.55 (1.03), residues: 21
  loop : -3.32 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 508 
 TYR   0.004   0.001   TYR B 349 
 PHE   0.015   0.001   PHE B 473 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.004   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4831)
  covalent geometry    : angle       0.55248 ( 6510)
  hydrogen bonds       : bond        0.04169 (  297)
  hydrogen bonds       : angle       3.76613 (  876)

*********************** 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
  99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.182 
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: C   53 LYS cc_start: 0.8821 (pttt) cc_final: 0.8531 (ptpp)
REVERT: G  109 ASP cc_start: 0.7632 (m-30) cc_final: 0.6912 (t70)
REVERT: G  242 ASP cc_start: 0.8446 (t70) cc_final: 0.8180 (t0)
REVERT: A   53 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7056 (mt0)
REVERT: R  113 ASP cc_start: 0.8891 (t0) cc_final: 0.8331 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1253
  time to fit residues: 16.1848
Evaluate side-chains
  96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0970
   chunk 17 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7778

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.099798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.077340 restraints weight = 37083.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.080940 restraints weight = 13833.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.083129 restraints weight = 7205.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.084416 restraints weight = 4581.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.085227 restraints weight = 3379.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4831  Z= 0.116
  Angle     :  0.529   5.379   6510  Z= 0.278
  Chirality :  0.033   0.137    748
  Planarity :  0.004   0.062    837
  Dihedral  :  4.546  38.706    646
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.29 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.38), residues: 591
  helix:  1.61 (0.27), residues: 424
  sheet: -2.45 (1.11), residues: 21
  loop : -3.13 (0.52), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 203 
 TYR   0.014   0.001   TYR G  79 
 PHE   0.011   0.001   PHE A 117 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4831)
  covalent geometry    : angle       0.52923 ( 6510)
  hydrogen bonds       : bond        0.03938 (  297)
  hydrogen bonds       : angle       3.68355 (  876)

*********************** 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
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.217 
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: C   53 LYS cc_start: 0.8829 (pttt) cc_final: 0.8546 (ptpp)
REVERT: G  109 ASP cc_start: 0.7490 (m-30) cc_final: 0.6790 (t70)
REVERT: G  242 ASP cc_start: 0.8451 (t70) cc_final: 0.8177 (t0)
REVERT: A   53 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7086 (mt0)
REVERT: R  113 ASP cc_start: 0.8863 (t0) cc_final: 0.8328 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.1195
  time to fit residues: 15.4881
Evaluate side-chains
  93 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.100326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.077218 restraints weight = 38153.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.080931 restraints weight = 14245.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.083120 restraints weight = 7430.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.084443 restraints weight = 4744.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.085169 restraints weight = 3501.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4831  Z= 0.118
  Angle     :  0.529   5.387   6510  Z= 0.278
  Chirality :  0.033   0.137    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.482  38.544    646
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.68 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.38), residues: 591
  helix:  1.77 (0.27), residues: 424
  sheet: -2.25 (1.18), residues: 21
  loop : -3.12 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 209 
 TYR   0.004   0.001   TYR B 325 
 PHE   0.011   0.001   PHE A 117 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4831)
  covalent geometry    : angle       0.52887 ( 6510)
  hydrogen bonds       : bond        0.03901 (  297)
  hydrogen bonds       : angle       3.63403 (  876)

*********************** 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
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.269 
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: C   53 LYS cc_start: 0.8866 (pttt) cc_final: 0.8566 (ptpp)
REVERT: C   57 SER cc_start: 0.8945 (p) cc_final: 0.8717 (p)
REVERT: G  242 ASP cc_start: 0.8454 (t70) cc_final: 0.8186 (t0)
REVERT: A   53 GLN cc_start: 0.7303 (mm-40) cc_final: 0.7000 (mt0)
REVERT: R  113 ASP cc_start: 0.8915 (t0) cc_final: 0.8372 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.1168
  time to fit residues: 15.2933
Evaluate side-chains
  92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0980
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0970
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.3978

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.101214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.078430 restraints weight = 37828.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.082125 restraints weight = 14234.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.084305 restraints weight = 7431.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.085626 restraints weight = 4754.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.086365 restraints weight = 3504.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4831  Z= 0.104
  Angle     :  0.526   5.813   6510  Z= 0.275
  Chirality :  0.033   0.136    748
  Planarity :  0.004   0.062    837
  Dihedral  :  4.423  38.716    646
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.23 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.89 (0.38), residues: 591
  helix:  1.93 (0.27), residues: 421
  sheet: -2.29 (1.17), residues: 21
  loop : -3.08 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 240 
 TYR   0.011   0.001   TYR G  79 
 PHE   0.012   0.001   PHE B 395 
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 4831)
  covalent geometry    : angle       0.52604 ( 6510)
  hydrogen bonds       : bond        0.03748 (  297)
  hydrogen bonds       : angle       3.55454 (  876)

********************** 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
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.286 
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: C   53 LYS cc_start: 0.8826 (pttt) cc_final: 0.8566 (ptpp)
REVERT: C   57 SER cc_start: 0.8922 (p) cc_final: 0.8700 (p)
REVERT: G  242 ASP cc_start: 0.8436 (t70) cc_final: 0.8158 (t0)
REVERT: A   53 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7125 (mt0)
REVERT: R  113 ASP cc_start: 0.8867 (t0) cc_final: 0.8345 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1520
  time to fit residues: 18.6591
Evaluate side-chains
  91 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain G residue  140 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0870
   chunk 2 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6760

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.100604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.077734 restraints weight = 37877.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.081392 restraints weight = 14353.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.083577 restraints weight = 7519.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.084889 restraints weight = 4803.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.085684 restraints weight = 3550.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4831  Z= 0.118
  Angle     :  0.557   7.206   6510  Z= 0.292
  Chirality :  0.033   0.134    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.367  38.469    646
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 20.04 %
    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 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:  0.91 (0.38), residues: 591
  helix:  1.88 (0.27), residues: 423
  sheet: -2.32 (1.15), residues: 21
  loop : -2.90 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 209 
 TYR   0.004   0.001   TYR B 399 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4831)
  covalent geometry    : angle       0.55723 ( 6510)
  hydrogen bonds       : bond        0.03813 (  297)
  hydrogen bonds       : angle       3.55867 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2395.71 seconds
wall clock time: 41 minutes 24.80 seconds (2484.80 seconds total)