Starting phenix.real_space_refine
on Fri Feb 14 01:51:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tmi_10522/02_2025/6tmi_10522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tmi_10522/02_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_10522/02_2025/6tmi_10522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tmi_10522/02_2025/6tmi_10522.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tmi_10522/02_2025/6tmi_10522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tmi_10522/02_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-5592/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: 7.48, per 1000 atoms: 0.78
  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: 2.56
  Conformation dependent library (CDL) restraints added in 820.3 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: 0.71
  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: 3.22

  Time building geometry restraints manager: 3.03 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:             9.460
  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:             0.180
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.280
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.490
-------------------------------------------------------------------------------
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  : 0.660 
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: 0.4765
  time to fit residues: 81.0794
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  : 0.856 
-------------------------------------------------------------------------------
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 = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.079165 restraints weight = 38324.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.082884 restraints weight = 14454.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.085068 restraints weight = 7521.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
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   5.572   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  : 0.764 
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: 0.8128 (m-30) cc_final: 0.7016 (t70)
REVERT: A   51 GLU cc_start: 0.8071 (pp20) cc_final: 0.7660 (pp20)
REVERT: R  113 ASP cc_start: 0.8741 (t0) cc_final: 0.8092 (t0)
REVERT: R  119 GLN cc_start: 0.7925 (tp40) cc_final: 0.7477 (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: 0.3260
  time to fit residues: 45.1398
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  : 0.782 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 43 optimal weight:    5.9990
   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:    0.0980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.100951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.078509 restraints weight = 37437.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.082194 restraints weight = 14360.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.084392 restraints weight = 7524.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.4259

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= 0.215
  Angle     :  0.566   5.038   6510  Z= 0.305
  Chirality :  0.035   0.138    748
  Planarity :  0.004   0.067    837
  Dihedral  :  5.233  39.804    646
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.15 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.36), residues: 591
  helix:  0.35 (0.26), residues: 427
  sheet: -3.43 (0.90), residues: 16
  loop : -3.77 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   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   0.003   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
  104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.816 
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: 0.8088 (m-30) cc_final: 0.7076 (t70)
REVERT: G  242 ASP cc_start: 0.8364 (t70) cc_final: 0.8097 (t0)
REVERT: A   51 GLU cc_start: 0.8119 (pp20) cc_final: 0.7916 (pp20)
REVERT: R  113 ASP cc_start: 0.8736 (t0) cc_final: 0.8176 (t0)
REVERT: R  119 GLN cc_start: 0.7918 (tp40) cc_final: 0.7615 (tp40)
REVERT: B  323 LYS cc_start: 0.4449 (mttp) cc_final: 0.3930 (mttt)
REVERT: B  547 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 100
  average time/residue: 0.3085
  time to fit residues: 41.6037
Evaluate side-chains
  96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.100717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.077898 restraints weight = 38116.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.081574 restraints weight = 14526.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.083794 restraints weight = 7622.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4883

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= 0.200
  Angle     :  0.553   5.142   6510  Z= 0.298
  Chirality :  0.035   0.140    748
  Planarity :  0.004   0.068    837
  Dihedral  :  4.959  39.899    646
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.29 %
    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: -0.55 (0.36), residues: 591
  helix:  0.84 (0.26), residues: 427
  sheet: -2.76 (1.02), residues: 16
  loop : -3.72 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  67 
 HIS   0.003   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
  102 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.679 
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: C   57 SER cc_start: 0.9002 (p) cc_final: 0.8694 (p)
REVERT: G  109 ASP cc_start: 0.8029 (m-30) cc_final: 0.7006 (t70)
REVERT: G  242 ASP cc_start: 0.8427 (t70) cc_final: 0.8148 (t0)
REVERT: R  113 ASP cc_start: 0.8824 (t0) cc_final: 0.8271 (t0)
REVERT: R  119 GLN cc_start: 0.7968 (tp40) cc_final: 0.7717 (tp40)
REVERT: B  367 GLU cc_start: 0.8441 (tp30) cc_final: 0.8142 (tp30)
REVERT: B  547 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7982 (t)
  outliers start: 14
  outliers final: 12
  residues processed: 99
  average time/residue: 0.3153
  time to fit residues: 41.2415
Evaluate side-chains
  94 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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  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:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.100606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.077710 restraints weight = 38176.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.081448 restraints weight = 14301.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.083714 restraints weight = 7432.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.5276

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= 0.177
  Angle     :  0.534   5.325   6510  Z= 0.283
  Chirality :  0.033   0.137    748
  Planarity :  0.004   0.065    837
  Dihedral  :  4.778  39.554    646
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.48 %
    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: -0.16 (0.37), residues: 591
  helix:  1.15 (0.26), residues: 426
  sheet: -2.46 (1.18), residues: 16
  loop : -3.66 (0.49), residues: 149

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   0.004   0.001   TYR B 513 
 ARG   0.003   0.000   ARG B 519 

*********************** 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
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.814 
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: 0.7965 (m-30) cc_final: 0.7039 (t70)
REVERT: G  242 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (t0)
REVERT: A   53 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6473 (tm-30)
REVERT: R  113 ASP cc_start: 0.8841 (t0) cc_final: 0.8300 (t0)
REVERT: B  367 GLU cc_start: 0.8501 (tp30) cc_final: 0.8208 (tp30)
  outliers start: 13
  outliers final: 12
  residues processed: 96
  average time/residue: 0.2829
  time to fit residues: 36.8915
Evaluate side-chains
  97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.098699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.075795 restraints weight = 38602.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.079453 restraints weight = 14582.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.081646 restraints weight = 7641.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.5672

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= 0.218
  Angle     :  0.557   5.299   6510  Z= 0.296
  Chirality :  0.034   0.137    748
  Planarity :  0.004   0.066    837
  Dihedral  :  4.738  39.299    646
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.87 %
    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:  0.04 (0.37), residues: 591
  helix:  1.33 (0.26), residues: 423
  sheet: -2.17 (1.24), residues: 16
  loop : -3.64 (0.47), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.009   0.001   PHE A 117 
 TYR   0.005   0.001   TYR B 349 
 ARG   0.002   0.000   ARG B 508 

*********************** 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
  102 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.755 
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: C   65 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8650 (mm-30)
REVERT: G  109 ASP cc_start: 0.7691 (m-30) cc_final: 0.6992 (t70)
REVERT: G  242 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (t0)
REVERT: R  113 ASP cc_start: 0.8874 (t0) cc_final: 0.8330 (t0)
REVERT: B  367 GLU cc_start: 0.8584 (tp30) cc_final: 0.8283 (tp30)
REVERT: B  547 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7917 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 98
  average time/residue: 0.2941
  time to fit residues: 38.9527
Evaluate side-chains
  96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.098272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.075897 restraints weight = 37465.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.079459 restraints weight = 14121.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.081633 restraints weight = 7382.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.5911

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= 0.181
  Angle     :  0.536   5.327   6510  Z= 0.283
  Chirality :  0.033   0.136    748
  Planarity :  0.004   0.064    837
  Dihedral  :  4.622  38.974    646
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  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:  0.38 (0.38), residues: 591
  helix:  1.51 (0.26), residues: 426
  sheet: -2.15 (1.21), residues: 21
  loop : -3.36 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  64 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.004   0.001   TYR B 399 
 ARG   0.002   0.000   ARG G 203 

*********************** 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
  100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.786 
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: 0.7570 (m-30) cc_final: 0.6907 (t70)
REVERT: G  242 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8213 (t0)
REVERT: A   53 GLN cc_start: 0.7381 (tp40) cc_final: 0.7140 (mm-40)
REVERT: R  113 ASP cc_start: 0.8842 (t0) cc_final: 0.8303 (t0)
REVERT: B  367 GLU cc_start: 0.8576 (tp30) cc_final: 0.8301 (tp30)
REVERT: B  547 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 96
  average time/residue: 0.3028
  time to fit residues: 38.7245
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  : 0.822 
-------------------------------------------------------------------------------
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 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  449 ASP
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:    0.9980
   chunk 28 optimal weight:    0.0670
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.099630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.076550 restraints weight = 38745.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.080313 restraints weight = 14530.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.082546 restraints weight = 7537.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.6052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4831  Z= 0.158
  Angle     :  0.530   5.681   6510  Z= 0.277
  Chirality :  0.033   0.134    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.509  38.733    646
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.04 %
    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:  0.73 (0.38), residues: 591
  helix:  1.74 (0.27), residues: 424
  sheet: -2.10 (1.23), residues: 21
  loop : -3.05 (0.52), residues: 146

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   0.003   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
  98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.748 
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  109 ASP cc_start: 0.7575 (m-30) cc_final: 0.6805 (t0)
REVERT: G  136 ASN cc_start: 0.8915 (m110) cc_final: 0.8589 (p0)
REVERT: G  242 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8224 (t0)
REVERT: A   53 GLN cc_start: 0.7356 (tp40) cc_final: 0.7143 (mm-40)
REVERT: R  113 ASP cc_start: 0.8844 (t0) cc_final: 0.8310 (t0)
REVERT: B  367 GLU cc_start: 0.8570 (tp30) cc_final: 0.8286 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 94
  average time/residue: 0.3109
  time to fit residues: 38.7655
Evaluate side-chains
  91 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4976

-------------------------------------------------------------------------------
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 = 0.100208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.077344 restraints weight = 38118.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.081039 restraints weight = 14519.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.083208 restraints weight = 7598.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.6216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4831  Z= 0.147
  Angle     :  0.529   5.913   6510  Z= 0.277
  Chirality :  0.033   0.136    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.391  38.376    646
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.62 %
    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:  0.90 (0.38), residues: 591
  helix:  1.92 (0.27), residues: 421
  sheet: -2.19 (1.21), residues: 21
  loop : -3.04 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.003   0.001   HIS B 406 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.010   0.001   TYR G  79 
 ARG   0.003   0.000   ARG C  61 

*********************** 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
  96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.808 
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: 0.8966 (m110) cc_final: 0.8666 (p0)
REVERT: G  242 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (t0)
REVERT: A   53 GLN cc_start: 0.7299 (tp40) cc_final: 0.7097 (mm-40)
REVERT: R  113 ASP cc_start: 0.8812 (t0) cc_final: 0.8275 (t0)
REVERT: B  367 GLU cc_start: 0.8532 (tp30) cc_final: 0.8283 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 92
  average time/residue: 0.3382
  time to fit residues: 40.5033
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  : 0.926 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    0.0040
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0060
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.3208

-------------------------------------------------------------------------------
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 = 0.100063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.077631 restraints weight = 36972.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.081317 restraints weight = 13757.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.083496 restraints weight = 7112.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.6384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4831  Z= 0.145
  Angle     :  0.536   7.509   6510  Z= 0.279
  Chirality :  0.033   0.130    748
  Planarity :  0.004   0.062    837
  Dihedral  :  4.253  38.801    646
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 21.21 %
    Favored  : 77.04 %
  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:  1.13 (0.38), residues: 591
  helix:  2.06 (0.27), residues: 421
  sheet: -2.44 (1.12), residues: 21
  loop : -2.77 (0.53), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  67 
 HIS   0.003   0.001   HIS B 406 
 PHE   0.011   0.001   PHE A 117 
 TYR   0.003   0.001   TYR B 325 
 ARG   0.003   0.000   ARG G 209 

********************** 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
  93 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.647 
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  136 ASN cc_start: 0.8989 (m110) cc_final: 0.8692 (p0)
REVERT: G  242 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8199 (t0)
REVERT: R  113 ASP cc_start: 0.8814 (t0) cc_final: 0.8299 (t0)
REVERT: B  367 GLU cc_start: 0.8559 (tp30) cc_final: 0.8285 (tp30)
  outliers start: 9
  outliers final: 8
  residues processed: 89
  average time/residue: 0.3156
  time to fit residues: 37.6487
Evaluate side-chains
  89 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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 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  449 ASP
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:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.098262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.075453 restraints weight = 38495.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.079049 restraints weight = 14868.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.081202 restraints weight = 7872.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6538

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= 0.214
  Angle     :  0.563   6.087   6510  Z= 0.300
  Chirality :  0.034   0.130    748
  Planarity :  0.004   0.063    837
  Dihedral  :  4.334  38.539    646
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 21.40 %
    Favored  : 76.46 %
  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:  0.91 (0.38), residues: 591
  helix:  1.86 (0.27), residues: 426
  sheet: -2.40 (1.10), residues: 21
  loop : -2.93 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  64 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.008   0.001   PHE A 117 
 TYR   0.009   0.001   TYR G  79 
 ARG   0.002   0.000   ARG B 508 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4184.08 seconds
wall clock time: 74 minutes 47.17 seconds (4487.17 seconds total)