Starting phenix.real_space_refine
on Tue Feb  3 16:15:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kzd_62660/02_2026/9kzd_62660.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2969      2.51       5
     N     791      2.21       5
     O     899      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4678
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1517
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 8, 'TRANS': 193}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1608
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1553
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
  Time building chain proxies: 1.24, per 1000 atoms: 0.27
  Number of scatterers: 4678
  At special positions: 0
  Unit cell: (91.336, 99.724, 91.336, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     899      8.00
     N     791      7.00
     C    2969      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 154 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 276.9 milliseconds
  

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 13 sheets defined
      9.7% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'H' and resid 29 through 37
      removed outlier: 3.640A  pdb=" N   THR H  36 " --> pdb=" O   THR H  29 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   TYR H  37 " --> pdb=" O   PHE H  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 29 through 37'
    Processing helix  chain 'H' and resid 82 through 84
      No H-bonds generated for 'chain 'H' and resid 82 through 84'
    Processing helix  chain 'H' and resid 95 through 98
    Processing helix  chain 'H' and resid 216 through 219
    Processing helix  chain 'L' and resid 141 through 146
    Processing helix  chain 'L' and resid 204 through 209
      removed outlier: 4.591A  pdb=" N   HIS L 209 " --> pdb=" O   ASP L 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.557A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 4.076A  pdb=" N   GLY A 482 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.984A  pdb=" N   THR H 125 " --> pdb=" O   GLY H  11 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR H 122 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP H  38 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET H  39 " --> pdb=" O   ILE H  56 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   ARG H  43 " --> pdb=" O   TRP H  52 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   TRP H  52 " --> pdb=" O   ARG H  43 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL H  45 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU H  50 " --> pdb=" O   VAL H  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.984A  pdb=" N   THR H 125 " --> pdb=" O   GLY H  11 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR H 122 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   CYS H 104 " --> pdb=" O   TRP H 118 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   TRP H 118 " --> pdb=" O   CYS H 104 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG H 106 " --> pdb=" O   ASP H 116 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 24
      removed outlier: 3.772A  pdb=" N   ALA H  86 " --> pdb=" O   GLU H  81 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU H  81 " --> pdb=" O   ALA H  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 151 through 154
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
      removed outlier: 4.403A  pdb=" N   LYS H 158 " --> pdb=" O   LEU H 193 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LEU H 193 " --> pdb=" O   LYS H 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 210 through 215
      removed outlier: 3.719A  pdb=" N   VAL H 222 " --> pdb=" O   VAL H 213 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.231A  pdb=" N   LEU L  11 " --> pdb=" O   ARG L 123 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLU L 125 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24
      removed outlier: 3.786A  pdb=" N   ILE L  21 " --> pdb=" O   LEU L  89 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE L  87 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP L  86 " --> pdb=" O   SER L  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 54 through 55
    Processing sheet with id=AB1, first strand: chain 'L' and resid 134 through 136
      removed outlier: 3.610A  pdb=" N   ASN L 157 " --> pdb=" O   SER L 134 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   CYS L 154 " --> pdb=" O   SER L 197 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 165 through 167
    Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.903A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 453
      removed outlier: 3.658A  pdb=" N   TYR A 453 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLN A 493 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    118 hydrogen bonds defined for protein.
    276 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: 0.60

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1492
        1.35 -     1.47: 1249
        1.47 -     1.58: 2033
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 4796
  Sorted by residual:
  bond pdb=" C   SER L 223 "
       pdb=" N   PRO L 224 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.53e+00
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.19e-02 7.06e+03 1.49e+00
  bond pdb=" N   ILE A 410 "
       pdb=" CA  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.24e+00
  bond pdb=" C   SER L 223 "
       pdb=" O   SER L 223 "
    ideal  model  delta    sigma   weight residual
    1.233  1.238 -0.005 4.80e-03 4.34e+04 1.23e+00
  bond pdb=" N   MET L 113 "
       pdb=" CA  MET L 113 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.008 6.90e-03 2.10e+04 1.21e+00
  ... (remaining 4791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 6373
        1.86 -     3.72: 132
        3.72 -     5.58: 13
        5.58 -     7.44: 0
        7.44 -     9.30: 3
  Bond angle restraints: 6521
  Sorted by residual:
  angle pdb=" C   TYR A 489 "
        pdb=" N   SER A 490 "
        pdb=" CA  SER A 490 "
      ideal   model   delta    sigma   weight residual
     120.06  124.39   -4.33 1.19e+00 7.06e-01 1.32e+01
  angle pdb=" N   ILE L  29 "
        pdb=" CA  ILE L  29 "
        pdb=" C   ILE L  29 "
      ideal   model   delta    sigma   weight residual
     112.43  109.18    3.25 9.20e-01 1.18e+00 1.25e+01
  angle pdb=" C   GLY A 447 "
        pdb=" N   ASN A 448 "
        pdb=" CA  ASN A 448 "
      ideal   model   delta    sigma   weight residual
     122.08  126.87   -4.79 1.47e+00 4.63e-01 1.06e+01
  angle pdb=" C   HIS H 215 "
        pdb=" N   LYS H 216 "
        pdb=" CA  LYS H 216 "
      ideal   model   delta    sigma   weight residual
     120.58  124.65   -4.07 1.32e+00 5.74e-01 9.51e+00
  angle pdb=" N   ILE A 468 "
        pdb=" CA  ILE A 468 "
        pdb=" C   ILE A 468 "
      ideal   model   delta    sigma   weight residual
     112.80  109.33    3.47 1.15e+00 7.56e-01 9.13e+00
  ... (remaining 6516 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.36: 2557
       10.36 -    20.72: 185
       20.72 -    31.08: 66
       31.08 -    41.45: 19
       41.45 -    51.81: 11
  Dihedral angle restraints: 2838
    sinusoidal: 1092
      harmonic: 1746
  Sorted by residual:
  dihedral pdb=" CA  TYR A 380 "
           pdb=" C   TYR A 380 "
           pdb=" N   GLY A 381 "
           pdb=" CA  GLY A 381 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.16  -20.84     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  GLY A 381 "
           pdb=" C   GLY A 381 "
           pdb=" N   VAL A 382 "
           pdb=" CA  VAL A 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.42   16.58     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" SG  CYS A 391 "
           pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" CA  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   27.19   51.81     1      2.00e+01 2.50e-03 9.16e+00
  ... (remaining 2835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 490
       0.032 -    0.064: 135
       0.064 -    0.097: 55
       0.097 -    0.129: 34
       0.129 -    0.161: 2
  Chirality restraints: 716
  Sorted by residual:
  chirality pdb=" CG  LEU A 492 "
            pdb=" CB  LEU A 492 "
            pdb=" CD1 LEU A 492 "
            pdb=" CD2 LEU A 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CA  ASN A 448 "
            pdb=" N   ASN A 448 "
            pdb=" C   ASN A 448 "
            pdb=" CB  ASN A 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE L  91 "
            pdb=" N   ILE L  91 "
            pdb=" C   ILE L  91 "
            pdb=" CB  ILE L  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  ... (remaining 713 not shown)

  Planarity restraints: 840
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 490 "   -0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO A 491 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 337 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 163 "    0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO H 164 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO H 164 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO H 164 "    0.019 5.00e-02 4.00e+02
  ... (remaining 837 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1253
        2.80 -     3.32: 4131
        3.32 -     3.85: 7476
        3.85 -     4.37: 8472
        4.37 -     4.90: 14881
  Nonbonded interactions: 36213
  Sorted by model distance:
  nonbonded pdb=" O   SER H 109 "
            pdb=" OH  TYR H 114 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   GLN H 111 "
            pdb=" OG  SER A 383 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   GLN A 409 "
            pdb=" NE2 GLN A 409 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" OG  SER A 469 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG  SER L  26 "
            pdb=" OE1 GLN L  27 "
     model   vdw
     2.320 3.040
  ... (remaining 36208 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:             20.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.360
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6423
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      :  0.003   0.037   4804  Z= 0.150
  Angle     :  0.654   9.295   6537  Z= 0.395
  Chirality :  0.041   0.161    716
  Planarity :  0.004   0.036    840
  Dihedral  :  9.145  50.586   1702
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.57 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  :  7.92 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.04 (0.28), residues: 595
  helix: -4.71 (0.37), residues: 36
  sheet: -1.85 (0.37), residues: 167
  loop : -3.05 (0.26), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 231 
 TYR   0.009   0.001   TYR A 380 
 PHE   0.007   0.001   PHE H  76 
 TRP   0.006   0.001   TRP H  41 
 HIS   0.003   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4796)
  covalent geometry    : angle       0.65313 ( 6521)
  SS BOND              : bond        0.00276 (    8)
  SS BOND              : angle       0.91306 (   16)
  hydrogen bonds       : bond        0.24312 (  113)
  hydrogen bonds       : angle      11.45129 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    2 VAL cc_start: 0.7999 (t) cc_final: 0.7699 (p)
REVERT: H   13 VAL cc_start: 0.7143 (p) cc_final: 0.6764 (t)
REVERT: H   54 SER cc_start: 0.8221 (p) cc_final: 0.7866 (m)
REVERT: H   94 LEU cc_start: 0.7156 (mt) cc_final: 0.6906 (mt)
REVERT: H  112 PHE cc_start: 0.7244 (p90) cc_final: 0.6850 (p90)
REVERT: H  117 LEU cc_start: 0.7811 (tp) cc_final: 0.7475 (tp)
REVERT: H  163 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6702 (pp20)
REVERT: H  181 PHE cc_start: 0.7505 (m-80) cc_final: 0.6993 (m-80)
REVERT: H  219 ASN cc_start: 0.7608 (t0) cc_final: 0.7332 (t0)
REVERT: L    3 GLN cc_start: 0.7358 (mm-40) cc_final: 0.7079 (mm-40)
REVERT: L   39 LEU cc_start: 0.7654 (tt) cc_final: 0.7318 (tt)
REVERT: L   45 LYS cc_start: 0.7510 (ttmm) cc_final: 0.7182 (mttm)
REVERT: L   51 LYS cc_start: 0.7423 (ttpt) cc_final: 0.7220 (ttpt)
REVERT: L   52 LEU cc_start: 0.8516 (pt) cc_final: 0.7957 (pt)
REVERT: L   55 TYR cc_start: 0.6486 (p90) cc_final: 0.6268 (p90)
REVERT: L   88 THR cc_start: 0.7864 (p) cc_final: 0.7622 (t)
REVERT: L   94 LEU cc_start: 0.6124 (mt) cc_final: 0.5676 (mp)
REVERT: L  105 GLN cc_start: 0.7320 (tt0) cc_final: 0.6805 (tt0)
REVERT: L  113 MET cc_start: 0.6604 (mmt) cc_final: 0.6202 (mmt)
REVERT: L  116 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7617 (t)
REVERT: L  169 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7261 (tptt)
REVERT: A  378 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7280 (mtmt)
REVERT: A  390 LEU cc_start: 0.7945 (tm) cc_final: 0.7664 (tt)
REVERT: A  395 VAL cc_start: 0.7815 (t) cc_final: 0.7363 (m)
REVERT: A  401 VAL cc_start: 0.7566 (t) cc_final: 0.7313 (p)
REVERT: A  517 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6310 (pt)
  outliers start: 18
  outliers final: 7
  residues processed: 160
  average time/residue: 0.0610
  time to fit residues: 12.5354
Evaluate side-chains
  141 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
L  40 ASN
L  44 GLN
L 105 GLN
L 186 GLN
** L 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 ASN
A 437 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.161821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.139670 restraints weight = 8490.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.143843 restraints weight = 4505.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.146410 restraints weight = 2847.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.148130 restraints weight = 2040.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.149242 restraints weight = 1593.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   4804  Z= 0.300
  Angle     :  0.789   8.604   6537  Z= 0.414
  Chirality :  0.050   0.195    716
  Planarity :  0.006   0.044    840
  Dihedral  :  7.309  49.807    677
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.94 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 15.83 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.40 (0.31), residues: 595
  helix: -4.13 (0.49), residues: 24
  sheet: -1.59 (0.38), residues: 172
  loop : -2.60 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  75 
 TYR   0.022   0.002   TYR L  55 
 PHE   0.027   0.003   PHE H  30 
 TRP   0.027   0.003   TRP A 353 
 HIS   0.007   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 4796)
  covalent geometry    : angle       0.78703 ( 6521)
  SS BOND              : bond        0.00480 (    8)
  SS BOND              : angle       1.41083 (   16)
  hydrogen bonds       : bond        0.04698 (  113)
  hydrogen bonds       : angle       8.65104 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   94 LEU cc_start: 0.7374 (mt) cc_final: 0.7155 (mt)
REVERT: H  112 PHE cc_start: 0.7336 (p90) cc_final: 0.6984 (p90)
REVERT: H  118 TRP cc_start: 0.8300 (m100) cc_final: 0.7921 (m100)
REVERT: H  125 THR cc_start: 0.7776 (m) cc_final: 0.7460 (p)
REVERT: H  158 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7844 (mttm)
REVERT: H  163 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6665 (pp20)
REVERT: H  181 PHE cc_start: 0.7704 (m-80) cc_final: 0.7167 (m-80)
REVERT: H  219 ASN cc_start: 0.7650 (t0) cc_final: 0.7446 (t0)
REVERT: L   45 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7530 (mttt)
REVERT: L   51 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7306 (ttpt)
REVERT: L   52 LEU cc_start: 0.8355 (pt) cc_final: 0.7881 (pt)
REVERT: L   65 SER cc_start: 0.7353 (p) cc_final: 0.6970 (m)
REVERT: L  116 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7706 (t)
REVERT: L  169 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7484 (tptt)
REVERT: L  201 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7190 (pp)
REVERT: A  357 ARG cc_start: 0.6068 (ttt180) cc_final: 0.4862 (ttp-170)
REVERT: A  378 LYS cc_start: 0.7536 (mtmt) cc_final: 0.7311 (mtmt)
REVERT: A  390 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: A  395 VAL cc_start: 0.7861 (t) cc_final: 0.7450 (m)
REVERT: A  423 TYR cc_start: 0.7082 (t80) cc_final: 0.6828 (t80)
REVERT: A  462 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7465 (mmtp)
  outliers start: 26
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0646
  time to fit residues: 11.8001
Evaluate side-chains
  149 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  158 LYS
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0870
   chunk 51 optimal weight:    0.0010
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0970
   chunk 58 optimal weight:    0.0050
   chunk 10 optimal weight:    0.1980
   chunk 52 optimal weight:    0.3980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.0494

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

Flipped N/Q/H residues before XYZ refinement:
L  40 ASN
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.168811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.147551 restraints weight = 8524.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.151770 restraints weight = 4422.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.154327 restraints weight = 2721.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.156045 restraints weight = 1915.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.157045 restraints weight = 1473.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4804  Z= 0.120
  Angle     :  0.650   8.842   6537  Z= 0.332
  Chirality :  0.046   0.169    716
  Planarity :  0.005   0.042    840
  Dihedral  :  6.519  50.870    674
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.22 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.31), residues: 595
  helix: -3.09 (0.75), residues: 30
  sheet: -1.64 (0.35), residues: 184
  loop : -2.33 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 457 
 TYR   0.022   0.002   TYR L  55 
 PHE   0.032   0.002   PHE H  30 
 TRP   0.011   0.001   TRP H  41 
 HIS   0.004   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4796)
  covalent geometry    : angle       0.64772 ( 6521)
  SS BOND              : bond        0.00340 (    8)
  SS BOND              : angle       1.21381 (   16)
  hydrogen bonds       : bond        0.03544 (  113)
  hydrogen bonds       : angle       7.96464 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7197 (p90) cc_final: 0.6899 (p90)
REVERT: H  125 THR cc_start: 0.7802 (m) cc_final: 0.7483 (p)
REVERT: H  158 LYS cc_start: 0.7990 (tttm) cc_final: 0.7709 (mttm)
REVERT: H  219 ASN cc_start: 0.7602 (t0) cc_final: 0.7380 (t0)
REVERT: L   45 LYS cc_start: 0.7521 (ttmm) cc_final: 0.7252 (mttm)
REVERT: L   51 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7162 (ttpt)
REVERT: L  113 MET cc_start: 0.6686 (mmt) cc_final: 0.6225 (mmt)
REVERT: L  116 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7696 (t)
REVERT: L  169 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7623 (tptt)
REVERT: L  201 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7174 (pp)
REVERT: A  390 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7598 (tt)
REVERT: A  395 VAL cc_start: 0.7695 (t) cc_final: 0.7380 (m)
REVERT: A  462 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7426 (mmtp)
  outliers start: 21
  outliers final: 10
  residues processed: 139
  average time/residue: 0.0620
  time to fit residues: 10.8768
Evaluate side-chains
  137 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   chunk 25 optimal weight:    0.0020
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0870
   chunk 10 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.2366

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

Flipped N/Q/H residues before XYZ refinement:
H  40 HIS
A 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.167533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.146112 restraints weight = 8618.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.150380 restraints weight = 4517.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.152988 restraints weight = 2809.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.154700 restraints weight = 1977.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.155903 restraints weight = 1517.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   4804  Z= 0.182
  Angle     :  0.737  12.992   6537  Z= 0.376
  Chirality :  0.049   0.257    716
  Planarity :  0.005   0.037    840
  Dihedral  :  6.084  51.622    664
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 17.37 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.32), residues: 595
  helix: -2.93 (0.77), residues: 30
  sheet: -1.28 (0.38), residues: 171
  loop : -2.34 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 457 
 TYR   0.022   0.002   TYR L  55 
 PHE   0.036   0.002   PHE H  30 
 TRP   0.012   0.002   TRP H  41 
 HIS   0.005   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4796)
  covalent geometry    : angle       0.72459 ( 6521)
  SS BOND              : bond        0.01249 (    8)
  SS BOND              : angle       2.80067 (   16)
  hydrogen bonds       : bond        0.03764 (  113)
  hydrogen bonds       : angle       7.79910 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7181 (p90) cc_final: 0.6824 (p90)
REVERT: H  125 THR cc_start: 0.7821 (m) cc_final: 0.7556 (p)
REVERT: H  158 LYS cc_start: 0.8036 (tttm) cc_final: 0.7831 (mttm)
REVERT: H  163 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6072 (pp20)
REVERT: L   51 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7166 (ttpt)
REVERT: L  116 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7719 (t)
REVERT: L  169 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7676 (tptt)
REVERT: L  201 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7226 (pp)
REVERT: L  229 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.4038 (t80)
REVERT: A  378 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7205 (ttmm)
REVERT: A  390 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7539 (tt)
REVERT: A  395 VAL cc_start: 0.7802 (t) cc_final: 0.7460 (m)
REVERT: A  450 ASN cc_start: 0.6713 (OUTLIER) cc_final: 0.6411 (t0)
REVERT: A  517 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6401 (pt)
  outliers start: 34
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0580
  time to fit residues: 9.8948
Evaluate side-chains
  147 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  450 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0170
   overall best weight:    0.1996

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

Flipped N/Q/H residues before XYZ refinement:
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.146744 restraints weight = 8568.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.150817 restraints weight = 4467.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.153531 restraints weight = 2805.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.155072 restraints weight = 1965.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.156188 restraints weight = 1534.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   4804  Z= 0.165
  Angle     :  0.729  13.099   6537  Z= 0.371
  Chirality :  0.049   0.265    716
  Planarity :  0.005   0.038    840
  Dihedral  :  6.099  52.099    664
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.43 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 18.53 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.32), residues: 595
  helix: -2.65 (0.83), residues: 30
  sheet: -1.14 (0.39), residues: 171
  loop : -2.30 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  75 
 TYR   0.020   0.002   TYR L  55 
 PHE   0.038   0.002   PHE H  30 
 TRP   0.012   0.001   TRP H  41 
 HIS   0.006   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4796)
  covalent geometry    : angle       0.72229 ( 6521)
  SS BOND              : bond        0.00873 (    8)
  SS BOND              : angle       2.10849 (   16)
  hydrogen bonds       : bond        0.03492 (  113)
  hydrogen bonds       : angle       7.59548 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7211 (p90) cc_final: 0.6900 (p90)
REVERT: H  125 THR cc_start: 0.7894 (m) cc_final: 0.7617 (p)
REVERT: H  158 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7754 (mttm)
REVERT: H  163 GLU cc_start: 0.6340 (pp20) cc_final: 0.6009 (pp20)
REVERT: L  116 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7745 (t)
REVERT: L  169 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7680 (tptt)
REVERT: L  201 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7196 (pp)
REVERT: L  229 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4129 (t80)
REVERT: A  378 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7098 (ttmm)
REVERT: A  390 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7640 (tt)
REVERT: A  395 VAL cc_start: 0.7746 (t) cc_final: 0.7394 (m)
REVERT: A  396 TYR cc_start: 0.7481 (m-80) cc_final: 0.7232 (m-80)
REVERT: A  462 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7382 (mmtp)
REVERT: A  517 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6509 (pt)
  outliers start: 32
  outliers final: 19
  residues processed: 139
  average time/residue: 0.0508
  time to fit residues: 9.1126
Evaluate side-chains
  145 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  158 LYS
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0270
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0770
   chunk 19 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.2396

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

Flipped N/Q/H residues before XYZ refinement:
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 144 GLN
A 360 ASN
A 437 ASN
A 450 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.145769 restraints weight = 8699.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.150043 restraints weight = 4499.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.152759 restraints weight = 2787.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.154335 restraints weight = 1948.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.155483 restraints weight = 1513.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   4804  Z= 0.177
  Angle     :  0.740  13.046   6537  Z= 0.376
  Chirality :  0.050   0.268    716
  Planarity :  0.005   0.039    840
  Dihedral  :  6.279  52.929    664
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.61 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  6.95 %
    Allowed  : 17.95 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.33), residues: 595
  helix: -2.80 (0.90), residues: 24
  sheet: -1.17 (0.39), residues: 171
  loop : -2.20 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  75 
 TYR   0.025   0.002   TYR A 495 
 PHE   0.040   0.002   PHE H  30 
 TRP   0.013   0.002   TRP H  41 
 HIS   0.006   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4796)
  covalent geometry    : angle       0.73313 ( 6521)
  SS BOND              : bond        0.00838 (    8)
  SS BOND              : angle       2.10587 (   16)
  hydrogen bonds       : bond        0.03605 (  113)
  hydrogen bonds       : angle       7.50195 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7249 (p90) cc_final: 0.6931 (p90)
REVERT: H  118 TRP cc_start: 0.8301 (m100) cc_final: 0.7958 (m100)
REVERT: H  125 THR cc_start: 0.7889 (m) cc_final: 0.7619 (p)
REVERT: H  158 LYS cc_start: 0.8068 (tttm) cc_final: 0.7756 (mttm)
REVERT: H  163 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6103 (pp20)
REVERT: L  116 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7756 (t)
REVERT: L  169 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7685 (tptt)
REVERT: L  201 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7193 (pp)
REVERT: L  229 PHE cc_start: 0.4723 (OUTLIER) cc_final: 0.4164 (t80)
REVERT: A  362 VAL cc_start: 0.5609 (OUTLIER) cc_final: 0.5386 (t)
REVERT: A  378 LYS cc_start: 0.7548 (mtmt) cc_final: 0.7108 (ttmm)
REVERT: A  390 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7661 (tt)
REVERT: A  395 VAL cc_start: 0.7758 (t) cc_final: 0.7424 (m)
REVERT: A  396 TYR cc_start: 0.7476 (m-80) cc_final: 0.7227 (m-80)
REVERT: A  462 LYS cc_start: 0.7722 (mmtp) cc_final: 0.7426 (mmtp)
REVERT: A  517 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6488 (pt)
  outliers start: 36
  outliers final: 25
  residues processed: 143
  average time/residue: 0.0501
  time to fit residues: 9.2075
Evaluate side-chains
  155 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue   99 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  138 PHE
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 39 optimal weight:    0.1980
   chunk 2 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 58 optimal weight:    0.0870
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0970
   chunk 21 optimal weight:    0.4980
   chunk 12 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.1114

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

Flipped N/Q/H residues before XYZ refinement:
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 437 ASN
A 450 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.168769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.147319 restraints weight = 8591.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.151566 restraints weight = 4461.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.154219 restraints weight = 2766.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.155980 restraints weight = 1938.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.156898 restraints weight = 1482.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4804  Z= 0.130
  Angle     :  0.704  12.460   6537  Z= 0.357
  Chirality :  0.048   0.237    716
  Planarity :  0.005   0.040    840
  Dihedral  :  6.087  53.048    664
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 18.15 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.33), residues: 595
  helix: -2.29 (0.92), residues: 30
  sheet: -1.12 (0.38), residues: 171
  loop : -2.21 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 457 
 TYR   0.018   0.001   TYR L  55 
 PHE   0.038   0.002   PHE H  30 
 TRP   0.012   0.001   TRP H  41 
 HIS   0.004   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4796)
  covalent geometry    : angle       0.69846 ( 6521)
  SS BOND              : bond        0.00784 (    8)
  SS BOND              : angle       1.96903 (   16)
  hydrogen bonds       : bond        0.03200 (  113)
  hydrogen bonds       : angle       7.35341 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7211 (p90) cc_final: 0.6906 (p90)
REVERT: H  125 THR cc_start: 0.7841 (m) cc_final: 0.7622 (p)
REVERT: H  158 LYS cc_start: 0.8022 (tttm) cc_final: 0.7737 (mttm)
REVERT: H  163 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5727 (pp20)
REVERT: L   88 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7813 (p)
REVERT: L  116 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7728 (t)
REVERT: L  169 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7665 (tptt)
REVERT: L  201 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7135 (pp)
REVERT: L  229 PHE cc_start: 0.4519 (OUTLIER) cc_final: 0.4058 (t80)
REVERT: A  362 VAL cc_start: 0.5625 (OUTLIER) cc_final: 0.5412 (t)
REVERT: A  378 LYS cc_start: 0.7504 (mtmt) cc_final: 0.7060 (ttmm)
REVERT: A  390 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7636 (tt)
REVERT: A  395 VAL cc_start: 0.7738 (t) cc_final: 0.7406 (m)
REVERT: A  396 TYR cc_start: 0.7441 (m-80) cc_final: 0.7114 (m-80)
REVERT: A  462 LYS cc_start: 0.7721 (mmtp) cc_final: 0.7397 (mmtp)
REVERT: A  517 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6477 (pt)
  outliers start: 31
  outliers final: 16
  residues processed: 138
  average time/residue: 0.0602
  time to fit residues: 10.5177
Evaluate side-chains
  145 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 45 optimal weight:    0.3980
   chunk 31 optimal weight:    0.2980
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
L  40 ASN
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 105 GLN
A 360 ASN
A 437 ASN
A 450 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.165443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144097 restraints weight = 8676.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.148330 restraints weight = 4537.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.150960 restraints weight = 2827.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.152644 restraints weight = 1984.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.153655 restraints weight = 1535.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   4804  Z= 0.247
  Angle     :  0.783  12.260   6537  Z= 0.404
  Chirality :  0.051   0.287    716
  Planarity :  0.006   0.042    840
  Dihedral  :  6.511  53.010    664
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.77 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 18.15 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.33), residues: 595
  helix: -2.61 (0.97), residues: 24
  sheet: -1.13 (0.39), residues: 173
  loop : -2.21 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  75 
 TYR   0.021   0.002   TYR A 423 
 PHE   0.041   0.002   PHE H  30 
 TRP   0.014   0.002   TRP H 118 
 HIS   0.007   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 4796)
  covalent geometry    : angle       0.77633 ( 6521)
  SS BOND              : bond        0.00870 (    8)
  SS BOND              : angle       2.23773 (   16)
  hydrogen bonds       : bond        0.03821 (  113)
  hydrogen bonds       : angle       7.57626 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7292 (p90) cc_final: 0.6991 (p90)
REVERT: H  118 TRP cc_start: 0.8371 (m100) cc_final: 0.7810 (m100)
REVERT: H  125 THR cc_start: 0.7845 (m) cc_final: 0.7622 (p)
REVERT: H  158 LYS cc_start: 0.8083 (tttm) cc_final: 0.7772 (mttm)
REVERT: H  163 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6154 (pp20)
REVERT: L  113 MET cc_start: 0.6545 (mmt) cc_final: 0.6064 (mmt)
REVERT: L  116 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7741 (t)
REVERT: L  169 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7688 (tptt)
REVERT: L  201 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7188 (pp)
REVERT: L  229 PHE cc_start: 0.4653 (OUTLIER) cc_final: 0.4133 (t80)
REVERT: A  362 VAL cc_start: 0.5796 (OUTLIER) cc_final: 0.5592 (t)
REVERT: A  378 LYS cc_start: 0.7510 (mtmt) cc_final: 0.7250 (mtmt)
REVERT: A  390 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7724 (tp)
REVERT: A  396 TYR cc_start: 0.7498 (m-80) cc_final: 0.7220 (m-80)
REVERT: A  462 LYS cc_start: 0.7733 (mmtp) cc_final: 0.7406 (mmtp)
REVERT: A  517 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6501 (pt)
  outliers start: 37
  outliers final: 27
  residues processed: 143
  average time/residue: 0.0578
  time to fit residues: 10.4677
Evaluate side-chains
  158 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   40 ASN
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  105 GLN
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 56 optimal weight:    0.2980
   chunk 51 optimal weight:    0.0370
   chunk 31 optimal weight:    0.0370
   chunk 44 optimal weight:    0.0870
   chunk 58 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    0.1980
   chunk 5 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.0892

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

Flipped N/Q/H residues before XYZ refinement:
L  40 ASN
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 105 GLN
A 360 ASN
A 450 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.168553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.147287 restraints weight = 8420.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.151542 restraints weight = 4395.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.154219 restraints weight = 2728.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.155894 restraints weight = 1909.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.157069 restraints weight = 1468.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   4804  Z= 0.134
  Angle     :  0.728  12.427   6537  Z= 0.371
  Chirality :  0.048   0.242    716
  Planarity :  0.005   0.048    840
  Dihedral  :  6.227  53.229    664
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 19.11 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.34), residues: 595
  helix: -2.69 (0.92), residues: 24
  sheet: -1.13 (0.38), residues: 171
  loop : -2.06 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  75 
 TYR   0.016   0.002   TYR L  55 
 PHE   0.040   0.002   PHE H  30 
 TRP   0.014   0.001   TRP H  41 
 HIS   0.005   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4796)
  covalent geometry    : angle       0.72090 ( 6521)
  SS BOND              : bond        0.00764 (    8)
  SS BOND              : angle       2.18190 (   16)
  hydrogen bonds       : bond        0.03245 (  113)
  hydrogen bonds       : angle       7.30857 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7197 (p90) cc_final: 0.6920 (p90)
REVERT: H  158 LYS cc_start: 0.8020 (tttm) cc_final: 0.7738 (mttm)
REVERT: H  163 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5805 (pp20)
REVERT: L   88 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7763 (p)
REVERT: L  116 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7773 (t)
REVERT: L  169 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7705 (tptt)
REVERT: L  201 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7155 (pp)
REVERT: L  229 PHE cc_start: 0.4454 (OUTLIER) cc_final: 0.4159 (t80)
REVERT: A  362 VAL cc_start: 0.5673 (OUTLIER) cc_final: 0.5453 (t)
REVERT: A  378 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7050 (ttmm)
REVERT: A  390 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7547 (tt)
REVERT: A  395 VAL cc_start: 0.7720 (t) cc_final: 0.7474 (m)
REVERT: A  396 TYR cc_start: 0.7412 (m-80) cc_final: 0.7052 (m-80)
REVERT: A  462 LYS cc_start: 0.7617 (mmtp) cc_final: 0.7337 (mmtp)
REVERT: A  517 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6404 (pt)
  outliers start: 29
  outliers final: 17
  residues processed: 135
  average time/residue: 0.0535
  time to fit residues: 9.1972
Evaluate side-chains
  144 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   40 ASN
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0470
   chunk 12 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 28 optimal weight:    0.1980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.2276

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

Flipped N/Q/H residues before XYZ refinement:
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.167431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.146194 restraints weight = 8568.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.150395 restraints weight = 4445.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.153056 restraints weight = 2781.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.154820 restraints weight = 1944.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.155764 restraints weight = 1477.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   4804  Z= 0.180
  Angle     :  0.794  14.073   6537  Z= 0.397
  Chirality :  0.050   0.259    716
  Planarity :  0.005   0.046    840
  Dihedral  :  6.378  53.217    664
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 19.88 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.34), residues: 595
  helix: -2.59 (0.96), residues: 24
  sheet: -1.18 (0.38), residues: 171
  loop : -2.10 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  75 
 TYR   0.020   0.002   TYR A 423 
 PHE   0.040   0.002   PHE H  30 
 TRP   0.015   0.002   TRP H 118 
 HIS   0.006   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4796)
  covalent geometry    : angle       0.78776 ( 6521)
  SS BOND              : bond        0.00833 (    8)
  SS BOND              : angle       2.17998 (   16)
  hydrogen bonds       : bond        0.03663 (  113)
  hydrogen bonds       : angle       7.39231 (  276)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: H  112 PHE cc_start: 0.7268 (p90) cc_final: 0.6943 (p90)
REVERT: H  118 TRP cc_start: 0.8455 (m100) cc_final: 0.7892 (m100)
REVERT: H  158 LYS cc_start: 0.8013 (tttm) cc_final: 0.7725 (mttm)
REVERT: H  163 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6000 (pp20)
REVERT: L   88 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7721 (p)
REVERT: L  116 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7690 (t)
REVERT: L  169 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7701 (tptt)
REVERT: L  201 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7162 (pp)
REVERT: L  229 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.4091 (t80)
REVERT: A  362 VAL cc_start: 0.5871 (OUTLIER) cc_final: 0.5670 (t)
REVERT: A  378 LYS cc_start: 0.7519 (mtmt) cc_final: 0.7075 (ttmm)
REVERT: A  390 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7720 (tp)
REVERT: A  395 VAL cc_start: 0.7725 (t) cc_final: 0.7439 (m)
REVERT: A  396 TYR cc_start: 0.7443 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  462 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7371 (mmtp)
REVERT: A  497 PHE cc_start: 0.4982 (m-10) cc_final: 0.4306 (m-10)
REVERT: A  517 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6501 (pt)
  outliers start: 29
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0601
  time to fit residues: 10.0957
Evaluate side-chains
  146 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   95 ARG
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  136 VAL
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain H residue  159 ASP
Chi-restraints excluded: chain H residue  163 GLU
Chi-restraints excluded: chain H residue  191 TYR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   88 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  152 VAL
Chi-restraints excluded: chain L residue  201 LEU
Chi-restraints excluded: chain L residue  217 THR
Chi-restraints excluded: chain L residue  226 THR
Chi-restraints excluded: chain L residue  229 PHE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  517 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0270
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 23 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0870
   chunk 42 optimal weight:    0.0470
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.1314

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

Flipped N/Q/H residues before XYZ refinement:
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 437 ASN
A 450 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.168610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.147574 restraints weight = 8608.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.151827 restraints weight = 4434.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.154449 restraints weight = 2753.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.156167 restraints weight = 1924.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.157116 restraints weight = 1464.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   4804  Z= 0.142
  Angle     :  0.757  13.816   6537  Z= 0.378
  Chirality :  0.048   0.236    716
  Planarity :  0.005   0.047    840
  Dihedral  :  6.249  53.250    664
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 19.50 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.33), residues: 595
  helix: -2.24 (0.93), residues: 30
  sheet: -1.21 (0.38), residues: 171
  loop : -2.12 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  75 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.040   0.002   PHE H  30 
 TRP   0.013   0.001   TRP H  41 
 HIS   0.005   0.001   HIS H  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4796)
  covalent geometry    : angle       0.75133 ( 6521)
  SS BOND              : bond        0.00784 (    8)
  SS BOND              : angle       2.04267 (   16)
  hydrogen bonds       : bond        0.03378 (  113)
  hydrogen bonds       : angle       7.28886 (  276)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1245.89 seconds
wall clock time: 22 minutes 17.24 seconds (1337.24 seconds total)