Starting phenix.real_space_refine
on Thu Sep 18 01:20:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tdw_10469/09_2025/6tdw_10469.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      10      5.16       5
     C    4087      2.51       5
     N    1105      2.21       5
     O    1234      1.98       5
     H    6561      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12997
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 398
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 3, 'TRANS': 21}
    Chain: "H"
      Number of atoms: 4014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 4014
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 22, 'TRANS': 226}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 4830
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 15, 'TRANS': 311}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 2463
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 5, 'TRANS': 151}
    Chain: "M"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 639
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 6, 'TRANS': 36}
    Chain: "N"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 509
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 28}
    Chain: "T"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 144
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 2.32, per 1000 atoms: 0.18
  Number of scatterers: 12997
  At special positions: 0
  Unit cell: (113.4, 72.45, 107.1, 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      10     16.00
     O    1234      8.00
     N    1105      7.00
     C    4087      6.00
     H    6561      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: 1.25
  Conformation dependent library (CDL) restraints added in 334.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1614

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 2 sheets defined
      67.9% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 474 through 487
      removed outlier: 5.596A  pdb=" N   LYS A 480 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   GLU A 481 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LYS A 487 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 40 through 58
      removed outlier: 4.020A  pdb=" N   LYS H  56 " --> pdb=" O   LYS H  52 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR H  57 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 59 through 79
    Processing helix  chain 'H' and resid 81 through 103
      Proline residue:  H 100  - end of helix
    Processing helix  chain 'H' and resid 111 through 125
      removed outlier: 4.378A  pdb=" N   GLU H 115 " --> pdb=" O   GLU H 111 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 267 through 279
      removed outlier: 3.950A  pdb=" N   MET H 271 " --> pdb=" O   VAL H 267 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LYS H 274 " --> pdb=" O   PRO H 270 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU H 277 " --> pdb=" O   GLU H 273 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 280 through 291
      removed outlier: 3.782A  pdb=" N   LYS H 284 " --> pdb=" O   ASN H 280 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU H 291 " --> pdb=" O   PHE H 287 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 293 through 297
      removed outlier: 3.679A  pdb=" N   LYS H 296 " --> pdb=" O   GLN H 293 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 299 through 307
    Processing helix  chain 'H' and resid 309 through 330
      removed outlier: 4.382A  pdb=" N   VAL H 313 " --> pdb=" O   ASP H 309 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 338 through 358
      removed outlier: 3.694A  pdb=" N   GLU H 345 " --> pdb=" O   GLN H 341 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE H 354 " --> pdb=" O   LYS H 350 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASP H 355 " --> pdb=" O   GLY H 351 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 444 through 455
      removed outlier: 4.838A  pdb=" N   GLN H 450 " --> pdb=" O   ALA H 446 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA H 453 " --> pdb=" O   ALA H 449 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 456 through 476
      removed outlier: 3.860A  pdb=" N   SER H 460 " --> pdb=" O   PRO H 456 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG H 464 " --> pdb=" O   SER H 460 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA H 471 " --> pdb=" O   THR H 467 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR H 472 " --> pdb=" O   GLU H 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 30
    Processing helix  chain 'B' and resid 56 through 68
    Processing helix  chain 'B' and resid 98 through 103
    Processing helix  chain 'B' and resid 104 through 107
      removed outlier: 4.364A  pdb=" N   SER B 107 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 104 through 107'
    Processing helix  chain 'B' and resid 121 through 164
    Processing helix  chain 'B' and resid 180 through 197
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 216 through 223
    Processing helix  chain 'B' and resid 235 through 249
    Processing helix  chain 'B' and resid 277 through 292
    Processing helix  chain 'B' and resid 293 through 310
    Processing helix  chain 'B' and resid 324 through 337
    Processing helix  chain 'C' and resid 13 through 25
    Processing helix  chain 'C' and resid 36 through 42
    Processing helix  chain 'C' and resid 47 through 60
    Processing helix  chain 'C' and resid 65 through 87
    Processing helix  chain 'C' and resid 89 through 95
    Processing helix  chain 'C' and resid 102 through 104
      No H-bonds generated for 'chain 'C' and resid 102 through 104'
    Processing helix  chain 'C' and resid 105 through 130
    Processing helix  chain 'C' and resid 131 through 150
    Processing helix  chain 'C' and resid 153 through 168
    Processing helix  chain 'M' and resid 239 through 246
    Processing helix  chain 'M' and resid 249 through 263
    Processing helix  chain 'N' and resid 84 through 112
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 9
      removed outlier: 5.916A  pdb=" N   LYS B   4 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL B  36 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE B   6 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   THR B  38 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   PHE B   8 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 6.822A  pdb=" N   LEU B  50 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 9.053A  pdb=" N   SER B 268 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.73 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: 6556
        1.03 -     1.23: 9
        1.23 -     1.42: 2561
        1.42 -     1.62: 3969
        1.62 -     1.81: 15
  Bond restraints: 13110
  Sorted by residual:
  bond pdb=" C   LYS C  36 "
       pdb=" N   ASP C  37 "
    ideal  model  delta    sigma   weight residual
    1.334  1.175  0.159 1.27e-02 6.20e+03 1.58e+02
  bond pdb=" C   ASP C  57 "
       pdb=" N   SER C  58 "
    ideal  model  delta    sigma   weight residual
    1.333  1.231  0.102 1.26e-02 6.30e+03 6.56e+01
  bond pdb=" N   VAL H 313 "
       pdb=" CA  VAL H 313 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.24e+00
  bond pdb=" N   VAL H 302 "
       pdb=" CA  VAL H 302 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.22e+00
  bond pdb=" N   VAL H 312 "
       pdb=" CA  VAL H 312 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.85e+00
  ... (remaining 13105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.24: 23859
        5.24 -    10.48: 22
       10.48 -    15.72: 2
       15.72 -    20.96: 0
       20.96 -    26.20: 6
  Bond angle restraints: 23889
  Sorted by residual:
  angle pdb=" CG2 VAL B 119 "
        pdb=" CB  VAL B 119 "
        pdb=" HB  VAL B 119 "
      ideal   model   delta    sigma   weight residual
     108.00   81.80   26.20 3.00e+00 1.11e-01 7.63e+01
  angle pdb=" CG1 VAL B 119 "
        pdb=" CB  VAL B 119 "
        pdb=" HB  VAL B 119 "
      ideal   model   delta    sigma   weight residual
     108.00   82.86   25.14 3.00e+00 1.11e-01 7.02e+01
  angle pdb=" CD2 LEU M 246 "
        pdb=" CG  LEU M 246 "
        pdb=" HG  LEU M 246 "
      ideal   model   delta    sigma   weight residual
     108.00   83.69   24.31 3.00e+00 1.11e-01 6.56e+01
  angle pdb=" CD1 LEU M 246 "
        pdb=" CG  LEU M 246 "
        pdb=" HG  LEU M 246 "
      ideal   model   delta    sigma   weight residual
     108.00   84.44   23.56 3.00e+00 1.11e-01 6.17e+01
  angle pdb=" CA  VAL B 119 "
        pdb=" CB  VAL B 119 "
        pdb=" HB  VAL B 119 "
      ideal   model   delta    sigma   weight residual
     109.00   85.48   23.52 3.00e+00 1.11e-01 6.15e+01
  ... (remaining 23884 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.27: 5182
       14.27 -    28.55: 702
       28.55 -    42.82: 189
       42.82 -    57.10: 72
       57.10 -    71.37: 12
  Dihedral angle restraints: 6157
    sinusoidal: 3416
      harmonic: 2741
  Sorted by residual:
  dihedral pdb=" CA  LEU C  29 "
           pdb=" C   LEU C  29 "
           pdb=" N   LYS C  30 "
           pdb=" CA  LYS C  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  SER C  58 "
           pdb=" C   SER C  58 "
           pdb=" N   GLU C  59 "
           pdb=" CA  GLU C  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  GLY B 179 "
           pdb=" C   GLY B 179 "
           pdb=" N   ASP B 180 "
           pdb=" CA  ASP B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.57  -18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 6154 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.343: 1048
       0.343 -    0.685: 0
       0.685 -    1.028: 0
       1.028 -    1.370: 0
       1.370 -    1.713: 2
  Chirality restraints: 1050
  Sorted by residual:
  chirality pdb=" CG  LEU M 246 "
            pdb=" CB  LEU M 246 "
            pdb=" CD1 LEU M 246 "
            pdb=" CD2 LEU M 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.88   -1.71 2.00e-01 2.50e+01 7.33e+01
  chirality pdb=" CB  VAL B 119 "
            pdb=" CA  VAL B 119 "
            pdb=" CG1 VAL B 119 "
            pdb=" CG2 VAL B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.10   -1.53 2.00e-01 2.50e+01 5.82e+01
  chirality pdb=" CA  VAL B  73 "
            pdb=" N   VAL B  73 "
            pdb=" C   VAL B  73 "
            pdb=" CB  VAL B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.18e-01
  ... (remaining 1047 not shown)

  Planarity restraints: 1929
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 217 "    0.039 5.00e-02 4.00e+02   5.84e-02 5.47e+00
        pdb=" N   PRO B 218 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 218 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 218 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C  57 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.68e+00
        pdb=" C   ASP C  57 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASP C  57 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER C  58 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 314 "   -0.012 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" N   ALA H 315 "    0.037 2.00e-02 2.50e+03
        pdb=" CA  ALA H 315 "   -0.010 2.00e-02 2.50e+03
        pdb=" H   ALA H 315 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1926 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 1812
        2.26 -     2.85: 29645
        2.85 -     3.43: 32052
        3.43 -     4.02: 41178
        4.02 -     4.60: 65451
  Nonbonded interactions: 170138
  Sorted by model distance:
  nonbonded pdb=" HG2 GLU H 311 "
            pdb="HG23 THR C  89 "
     model   vdw
     1.678 2.440
  nonbonded pdb=" O   PRO B  44 "
            pdb=" HH  TYR B  67 "
     model   vdw
     1.725 2.450
  nonbonded pdb="HH21 ARG H 319 "
            pdb=" OD1 ASP M 257 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" O   ALA B 305 "
            pdb=" HG1 THR B 309 "
     model   vdw
     1.736 2.450
  nonbonded pdb=" OE1 GLN B 240 "
            pdb="HH11 ARG C  90 "
     model   vdw
     1.748 2.450
  ... (remaining 170133 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:             8.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.650
  Find NCS groups from input model:        0.040
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
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      :  0.007   0.159   6549  Z= 0.362
  Angle     :  0.839  11.010   8899  Z= 0.465
  Chirality :  0.083   1.713   1050
  Planarity :  0.005   0.058   1150
  Dihedral  : 13.713  71.372   2442
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.22 %
    Favored  : 95.64 %
  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 aren not related in a simple way.
  whole: -1.91 (0.27), residues: 821
  helix: -0.17 (0.20), residues: 523
  sheet: -3.60 (0.56), residues: 59
  loop : -2.97 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  41 
 TYR   0.011   0.002   TYR H  25 
 PHE   0.016   0.002   PHE B 223 
 TRP   0.015   0.002   TRP C 152 
 HIS   0.006   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 ( 6549)
  covalent geometry    : angle       0.83853 ( 8899)
  hydrogen bonds       : bond        0.12677 (  422)
  hydrogen bonds       : angle       5.73342 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.348 
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: B  276 ASN cc_start: 0.7669 (t0) cc_final: 0.7302 (t0)
REVERT: C  148 LYS cc_start: 0.8632 (tttt) cc_final: 0.8253 (ttpt)
REVERT: N  106 LEU cc_start: 0.8104 (mt) cc_final: 0.7819 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 185
  average time/residue: 0.2268
  time to fit residues: 52.7092
Evaluate side-chains
  94 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0370
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
C  28 HIS
C  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.117695 restraints weight = 32671.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.122809 restraints weight = 14861.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.126097 restraints weight = 8672.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.128234 restraints weight = 5884.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129686 restraints weight = 4380.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6549  Z= 0.140
  Angle     :  0.624  10.907   8899  Z= 0.313
  Chirality :  0.078   1.687   1050
  Planarity :  0.005   0.046   1150
  Dihedral  :  4.599  35.605    887
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.79 %
    Favored  : 85.76 %
  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 aren not related in a simple way.
  whole: -0.42 (0.29), residues: 821
  helix:  1.11 (0.22), residues: 535
  sheet: -3.38 (0.58), residues: 57
  loop : -2.80 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 464 
 TYR   0.010   0.001   TYR H  25 
 PHE   0.018   0.001   PHE B  19 
 TRP   0.012   0.002   TRP B 217 
 HIS   0.005   0.002   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6549)
  covalent geometry    : angle       0.62362 ( 8899)
  hydrogen bonds       : bond        0.04271 (  422)
  hydrogen bonds       : angle       4.66424 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.337 
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: A  467 HIS cc_start: 0.7870 (m170) cc_final: 0.7609 (m170)
REVERT: B   23 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7497 (tp-100)
REVERT: B  276 ASN cc_start: 0.7606 (t0) cc_final: 0.7204 (t0)
REVERT: C  148 LYS cc_start: 0.8522 (tttt) cc_final: 0.8301 (ttpt)
  outliers start: 10
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1969
  time to fit residues: 28.0869
Evaluate side-chains
  93 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  298 LEU
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain C residue  152 TRP
Chi-restraints excluded: chain C residue  157 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0970
   chunk 36 optimal weight:    0.0370
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
B 335 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.142818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124349 restraints weight = 33314.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.129466 restraints weight = 15433.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.132644 restraints weight = 9182.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.134697 restraints weight = 6280.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136045 restraints weight = 4688.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6549  Z= 0.134
  Angle     :  0.579  10.973   8899  Z= 0.287
  Chirality :  0.078   1.701   1050
  Planarity :  0.004   0.045   1150
  Dihedral  :  4.376  38.880    887
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.81 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.31), residues: 821
  helix:  1.84 (0.22), residues: 535
  sheet: -3.11 (0.61), residues: 57
  loop : -2.42 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 464 
 TYR   0.009   0.001   TYR T  51 
 PHE   0.017   0.001   PHE B  19 
 TRP   0.010   0.001   TRP B 217 
 HIS   0.003   0.001   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6549)
  covalent geometry    : angle       0.57912 ( 8899)
  hydrogen bonds       : bond        0.03763 (  422)
  hydrogen bonds       : angle       4.41771 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.339 
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: A  467 HIS cc_start: 0.7900 (m170) cc_final: 0.7671 (m170)
REVERT: H   62 GLU cc_start: 0.7274 (mp0) cc_final: 0.6996 (mt-10)
REVERT: B   23 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7544 (tp-100)
REVERT: B  276 ASN cc_start: 0.7598 (t0) cc_final: 0.7382 (t0)
REVERT: B  326 GLU cc_start: 0.7789 (mp0) cc_final: 0.7484 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 102
  average time/residue: 0.2021
  time to fit residues: 26.4928
Evaluate side-chains
  97 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0060
   chunk 62 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 74 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
B 257 GLN
C  28 HIS
C  53 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.140519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.121762 restraints weight = 31709.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127003 restraints weight = 14535.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.130244 restraints weight = 8495.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.132249 restraints weight = 5767.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.133637 restraints weight = 4307.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6549  Z= 0.147
  Angle     :  0.574  11.018   8899  Z= 0.287
  Chirality :  0.078   1.700   1050
  Planarity :  0.004   0.045   1150
  Dihedral  :  4.338  40.866    887
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.95 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.31), residues: 821
  helix:  2.11 (0.22), residues: 535
  sheet: -2.95 (0.62), residues: 57
  loop : -2.26 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 317 
 TYR   0.009   0.001   TYR B  99 
 PHE   0.017   0.001   PHE B 245 
 TRP   0.010   0.001   TRP B 217 
 HIS   0.002   0.001   HIS H 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6549)
  covalent geometry    : angle       0.57397 ( 8899)
  hydrogen bonds       : bond        0.03586 (  422)
  hydrogen bonds       : angle       4.38904 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.358 
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: H   25 TYR cc_start: 0.8946 (t80) cc_final: 0.8641 (t80)
REVERT: B   74 THR cc_start: 0.8085 (p) cc_final: 0.7876 (p)
REVERT: B  326 GLU cc_start: 0.7836 (mp0) cc_final: 0.7560 (tm-30)
  outliers start: 8
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2284
  time to fit residues: 29.1760
Evaluate side-chains
  101 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  273 GLU
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 335 HIS
C  28 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.137082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.118082 restraints weight = 32191.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.123286 restraints weight = 14782.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.126572 restraints weight = 8700.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128599 restraints weight = 5900.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129994 restraints weight = 4415.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6549  Z= 0.179
  Angle     :  0.597  11.031   8899  Z= 0.301
  Chirality :  0.078   1.712   1050
  Planarity :  0.004   0.043   1150
  Dihedral  :  4.433  44.317    887
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.83 %
    Favored  : 83.28 %
  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 aren not related in a simple way.
  whole:  0.94 (0.31), residues: 821
  helix:  2.14 (0.23), residues: 535
  sheet: -3.14 (0.56), residues: 62
  loop : -2.10 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 233 
 TYR   0.009   0.001   TYR B  99 
 PHE   0.018   0.001   PHE B  19 
 TRP   0.011   0.002   TRP B 217 
 HIS   0.006   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6549)
  covalent geometry    : angle       0.59720 ( 8899)
  hydrogen bonds       : bond        0.03673 (  422)
  hydrogen bonds       : angle       4.50140 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.278 
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: H   91 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8213 (t70)
REVERT: B   74 THR cc_start: 0.8215 (p) cc_final: 0.8014 (p)
REVERT: B  326 GLU cc_start: 0.7943 (mp0) cc_final: 0.7697 (tm-30)
REVERT: C  112 LYS cc_start: 0.7646 (mttt) cc_final: 0.7225 (ttmt)
  outliers start: 13
  outliers final: 9
  residues processed: 113
  average time/residue: 0.2008
  time to fit residues: 29.2185
Evaluate side-chains
  105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0770
   chunk 72 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
B  37 GLN
B 235 ASN
C  28 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.136321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.117575 restraints weight = 31726.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122700 restraints weight = 14613.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.125864 restraints weight = 8646.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.127877 restraints weight = 5902.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.129254 restraints weight = 4426.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6549  Z= 0.145
  Angle     :  0.582  11.005   8899  Z= 0.291
  Chirality :  0.078   1.705   1050
  Planarity :  0.004   0.044   1150
  Dihedral  :  4.401  42.830    887
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.68 %
    Favored  : 83.14 %
  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 aren not related in a simple way.
  whole:  1.05 (0.31), residues: 821
  helix:  2.20 (0.22), residues: 535
  sheet: -3.13 (0.55), residues: 62
  loop : -1.96 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  41 
 TYR   0.012   0.001   TYR T  51 
 PHE   0.015   0.001   PHE B 245 
 TRP   0.010   0.001   TRP B 217 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6549)
  covalent geometry    : angle       0.58192 ( 8899)
  hydrogen bonds       : bond        0.03550 (  422)
  hydrogen bonds       : angle       4.41871 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.365 
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: B   74 THR cc_start: 0.8210 (p) cc_final: 0.7973 (p)
REVERT: C  112 LYS cc_start: 0.7637 (mttt) cc_final: 0.7222 (ttmt)
  outliers start: 15
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1956
  time to fit residues: 28.1250
Evaluate side-chains
  108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0010
   chunk 35 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 50 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
C  28 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.136069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.117285 restraints weight = 32034.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122423 restraints weight = 14801.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.125565 restraints weight = 8740.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.127621 restraints weight = 5972.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128990 restraints weight = 4463.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6549  Z= 0.141
  Angle     :  0.581  11.001   8899  Z= 0.290
  Chirality :  0.078   1.711   1050
  Planarity :  0.004   0.043   1150
  Dihedral  :  4.362  44.410    887
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.12 %
    Favored  : 82.70 %
  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 aren not related in a simple way.
  whole:  1.15 (0.31), residues: 821
  helix:  2.26 (0.22), residues: 536
  sheet: -3.09 (0.56), residues: 62
  loop : -1.88 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 317 
 TYR   0.008   0.001   TYR B  99 
 PHE   0.014   0.001   PHE B 245 
 TRP   0.010   0.001   TRP B 217 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6549)
  covalent geometry    : angle       0.58148 ( 8899)
  hydrogen bonds       : bond        0.03471 (  422)
  hydrogen bonds       : angle       4.37341 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.349 
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: H   25 TYR cc_start: 0.9055 (t80) cc_final: 0.8741 (t80)
REVERT: B   74 THR cc_start: 0.8229 (p) cc_final: 0.7981 (p)
REVERT: C   91 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8072 (mm-30)
REVERT: C  112 LYS cc_start: 0.7639 (mttt) cc_final: 0.7238 (ttmt)
  outliers start: 15
  outliers final: 13
  residues processed: 108
  average time/residue: 0.2189
  time to fit residues: 30.1860
Evaluate side-chains
  106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain H residue  348 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0870
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
C  28 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.139089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119556 restraints weight = 32042.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124843 restraints weight = 14350.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.128149 restraints weight = 8300.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.130258 restraints weight = 5603.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.131655 restraints weight = 4168.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6549  Z= 0.122
  Angle     :  0.570  11.008   8899  Z= 0.284
  Chirality :  0.078   1.709   1050
  Planarity :  0.004   0.043   1150
  Dihedral  :  4.272  45.635    887
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.84 %
    Favored  : 82.27 %
  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 aren not related in a simple way.
  whole:  1.35 (0.31), residues: 821
  helix:  2.39 (0.22), residues: 536
  sheet: -3.02 (0.56), residues: 62
  loop : -1.75 (0.45), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 464 
 TYR   0.018   0.001   TYR T  51 
 PHE   0.012   0.001   PHE B 245 
 TRP   0.011   0.001   TRP C  48 
 HIS   0.003   0.001   HIS H 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6549)
  covalent geometry    : angle       0.57006 ( 8899)
  hydrogen bonds       : bond        0.03333 (  422)
  hydrogen bonds       : angle       4.27196 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.366 
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: H   25 TYR cc_start: 0.9077 (t80) cc_final: 0.8727 (t80)
REVERT: B   74 THR cc_start: 0.8036 (p) cc_final: 0.7790 (p)
REVERT: C   91 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8045 (mm-30)
REVERT: C  112 LYS cc_start: 0.7564 (mttt) cc_final: 0.7153 (ttmt)
  outliers start: 13
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1945
  time to fit residues: 27.4751
Evaluate side-chains
  103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain H residue  348 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
C  28 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.133660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.114866 restraints weight = 32310.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.119962 restraints weight = 14718.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.123105 restraints weight = 8651.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.125150 restraints weight = 5915.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126539 restraints weight = 4425.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6549  Z= 0.175
  Angle     :  0.604  10.980   8899  Z= 0.305
  Chirality :  0.078   1.723   1050
  Planarity :  0.004   0.042   1150
  Dihedral  :  4.323  47.902    887
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.99 %
    Favored  : 82.12 %
  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 aren not related in a simple way.
  whole:  1.26 (0.31), residues: 821
  helix:  2.32 (0.22), residues: 536
  sheet: -3.12 (0.56), residues: 62
  loop : -1.74 (0.45), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.009   0.001   TYR B  99 
 PHE   0.017   0.001   PHE B 245 
 TRP   0.011   0.002   TRP C  48 
 HIS   0.003   0.001   HIS H 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6549)
  covalent geometry    : angle       0.60402 ( 8899)
  hydrogen bonds       : bond        0.03513 (  422)
  hydrogen bonds       : angle       4.41517 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.376 
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: B   74 THR cc_start: 0.8415 (p) cc_final: 0.8209 (p)
REVERT: C   91 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: C  112 LYS cc_start: 0.7663 (mttt) cc_final: 0.7262 (ttmt)
  outliers start: 13
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2042
  time to fit residues: 28.2630
Evaluate side-chains
  105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain H residue  348 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B  23 GLN
C  28 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.135117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.116352 restraints weight = 32316.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.121467 restraints weight = 14703.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.124672 restraints weight = 8636.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.126700 restraints weight = 5870.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.128100 restraints weight = 4386.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.5160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6549  Z= 0.128
  Angle     :  0.575  11.030   8899  Z= 0.287
  Chirality :  0.078   1.705   1050
  Planarity :  0.004   0.042   1150
  Dihedral  :  4.295  48.658    887
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.84 %
    Favored  : 82.41 %
  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 aren not related in a simple way.
  whole:  1.40 (0.31), residues: 821
  helix:  2.40 (0.22), residues: 536
  sheet: -3.05 (0.56), residues: 62
  loop : -1.64 (0.45), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  41 
 TYR   0.015   0.001   TYR T  51 
 PHE   0.012   0.001   PHE B 245 
 TRP   0.011   0.001   TRP C  48 
 HIS   0.003   0.001   HIS H 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6549)
  covalent geometry    : angle       0.57501 ( 8899)
  hydrogen bonds       : bond        0.03357 (  422)
  hydrogen bonds       : angle       4.28625 ( 1260)

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.376 
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: B   74 THR cc_start: 0.8336 (p) cc_final: 0.8095 (p)
REVERT: C   91 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8074 (mm-30)
REVERT: C  112 LYS cc_start: 0.7631 (mttt) cc_final: 0.7236 (ttmt)
  outliers start: 12
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1904
  time to fit residues: 26.7699
Evaluate side-chains
  106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain H residue   39 ASP
Chi-restraints excluded: chain H residue  302 VAL
Chi-restraints excluded: chain H residue  348 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  152 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
C  28 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.134734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.115968 restraints weight = 31868.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.121051 restraints weight = 14737.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124239 restraints weight = 8673.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.126246 restraints weight = 5898.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.127471 restraints weight = 4432.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6549  Z= 0.134
  Angle     :  0.579  11.006   8899  Z= 0.289
  Chirality :  0.078   1.713   1050
  Planarity :  0.004   0.042   1150
  Dihedral  :  4.248  49.093    887
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.42 %
    Favored  : 81.69 %
  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 aren not related in a simple way.
  whole:  1.47 (0.32), residues: 821
  helix:  2.43 (0.23), residues: 537
  sheet: -3.00 (0.57), residues: 62
  loop : -1.57 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 312 
 TYR   0.008   0.001   TYR B  99 
 PHE   0.014   0.001   PHE B 245 
 TRP   0.013   0.001   TRP C  48 
 HIS   0.002   0.001   HIS H 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6549)
  covalent geometry    : angle       0.57918 ( 8899)
  hydrogen bonds       : bond        0.03342 (  422)
  hydrogen bonds       : angle       4.27495 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2317.68 seconds
wall clock time: 40 minutes 13.32 seconds (2413.32 seconds total)