Starting phenix.real_space_refine
on Fri Aug 22 22:23:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8et7_28587/08_2025/8et7_28587.map"
  }
  resolution = 3.77
  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=   0.003 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    2698      2.51       5
     N     670      2.21       5
     O     707      1.98       5
     H    4007      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8111
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 8064
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 25, 'TRANS': 506}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'2PM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.90, per 1000 atoms: 0.23
  Number of scatterers: 8111
  At special positions: 0
  Unit cell: (112.32, 56.16, 73.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     O     707      8.00
     N     670      7.00
     C    2698      6.00
     H    4007      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A  71 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 336.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  978

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 1 sheets defined
      77.4% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'A' and resid 15 through 32
      removed outlier: 3.501A  pdb=" N   ALA A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 4.003A  pdb=" N   GLY A  38 " --> pdb=" O   PRO A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.979A  pdb=" N   ALA A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLU A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN A  60 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   CYS A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.659A  pdb=" N   VAL A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 89
      removed outlier: 3.572A  pdb=" N   CYS A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 4.174A  pdb=" N   ALA A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 145 through 166
      removed outlier: 4.369A  pdb=" N   ASP A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 3.618A  pdb=" N   ALA A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 194
      removed outlier: 3.720A  pdb=" N   CYS A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 4.174A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 258
    Processing helix  chain 'A' and resid 260 through 278
      Proline residue:  A 271  - end of helix
      removed outlier: 3.784A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 281
      No H-bonds generated for 'chain 'A' and resid 279 through 281'
    Processing helix  chain 'A' and resid 285 through 292
    Processing helix  chain 'A' and resid 294 through 310
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.678A  pdb=" N   LEU A 317 " --> pdb=" O   PRO A 314 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 318 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.911A  pdb=" N   ARG A 339 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 367
    Processing helix  chain 'A' and resid 374 through 385
    Processing helix  chain 'A' and resid 385 through 401
      removed outlier: 4.186A  pdb=" N   ALA A 389 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   ARG A 399 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 423
    Processing helix  chain 'A' and resid 428 through 457
      removed outlier: 3.896A  pdb=" N   ILE A 432 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR A 433 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR A 457 " --> pdb=" O   ASN A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 491
      removed outlier: 4.014A  pdb=" N   LEU A 472 " --> pdb=" O   VAL A 468 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   CYS A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
      removed outlier: 3.857A  pdb=" N   GLU A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 510
      removed outlier: 3.637A  pdb=" N   ILE A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 524 through 530
      removed outlier: 3.682A  pdb=" N   ASN A 530 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49

    264 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.68

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3998
        1.03 -     1.23: 12
        1.23 -     1.42: 1766
        1.42 -     1.62: 2401
        1.62 -     1.81: 43
  Bond restraints: 8220
  Sorted by residual:
  bond pdb=" C15 2PM A 601 "
       pdb=" N1  2PM A 601 "
    ideal  model  delta    sigma   weight residual
    1.448  1.512 -0.064 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" C14 2PM A 601 "
       pdb=" C15 2PM A 601 "
    ideal  model  delta    sigma   weight residual
    1.513  1.572 -0.059 2.00e-02 2.50e+03 8.83e+00
  bond pdb=" C16 2PM A 601 "
       pdb=" N1  2PM A 601 "
    ideal  model  delta    sigma   weight residual
    1.446  1.504 -0.058 2.00e-02 2.50e+03 8.28e+00
  bond pdb=" C17 2PM A 601 "
       pdb=" N1  2PM A 601 "
    ideal  model  delta    sigma   weight residual
    1.446  1.492 -0.046 2.00e-02 2.50e+03 5.37e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.85e+00
  ... (remaining 8215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 13569
        0.98 -     1.96: 1183
        1.96 -     2.95: 44
        2.95 -     3.93: 18
        3.93 -     4.91: 10
  Bond angle restraints: 14824
  Sorted by residual:
  angle pdb=" N   VAL A 212 "
        pdb=" CA  VAL A 212 "
        pdb=" C   VAL A 212 "
      ideal   model   delta    sigma   weight residual
     109.34  113.83   -4.49 2.08e+00 2.31e-01 4.66e+00
  angle pdb=" C15 2PM A 601 "
        pdb=" N1  2PM A 601 "
        pdb=" C16 2PM A 601 "
      ideal   model   delta    sigma   weight residual
     112.87  108.18    4.69 3.00e+00 1.11e-01 2.44e+00
  angle pdb=" N   CYS A 281 "
        pdb=" CA  CYS A 281 "
        pdb=" C   CYS A 281 "
      ideal   model   delta    sigma   weight residual
     110.97  112.63   -1.66 1.09e+00 8.42e-01 2.31e+00
  angle pdb=" N   GLU A 386 "
        pdb=" CA  GLU A 386 "
        pdb=" C   GLU A 386 "
      ideal   model   delta    sigma   weight residual
     111.69  113.52   -1.83 1.23e+00 6.61e-01 2.20e+00
  angle pdb=" N   ILE A 461 "
        pdb=" CA  ILE A 461 "
        pdb=" C   ILE A 461 "
      ideal   model   delta    sigma   weight residual
     109.34  112.37   -3.03 2.08e+00 2.31e-01 2.13e+00
  ... (remaining 14819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 3622
       17.24 -    34.48: 211
       34.48 -    51.71: 74
       51.71 -    68.95: 33
       68.95 -    86.19: 2
  Dihedral angle restraints: 3942
    sinusoidal: 2086
      harmonic: 1856
  Sorted by residual:
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 142 "
           pdb=" CB  CYS A 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.20   32.80     1      1.00e+01 1.00e-02 1.53e+01
  dihedral pdb=" CB  CYS A  50 "
           pdb=" SG  CYS A  50 "
           pdb=" SG  CYS A 121 "
           pdb=" CB  CYS A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -113.35   27.35     1      1.00e+01 1.00e-02 1.07e+01
  dihedral pdb=" CA  LEU A  23 "
           pdb=" CB  LEU A  23 "
           pdb=" CG  LEU A  23 "
           pdb=" CD1 LEU A  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  129.98   50.02     3      1.50e+01 4.44e-03 8.85e+00
  ... (remaining 3939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 430
       0.025 -    0.051: 158
       0.051 -    0.076: 58
       0.076 -    0.102: 20
       0.102 -    0.127: 8
  Chirality restraints: 674
  Sorted by residual:
  chirality pdb=" CA  VAL A  74 "
            pdb=" N   VAL A  74 "
            pdb=" C   VAL A  74 "
            pdb=" CB  VAL A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  THR A 480 "
            pdb=" N   THR A 480 "
            pdb=" C   THR A 480 "
            pdb=" CB  THR A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A  71 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.52    0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 671 not shown)

  Planarity restraints: 1216
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 282 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO A 283 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 480 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO A 481 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "    0.018 5.00e-02 4.00e+02   2.79e-02 1.25e+00
        pdb=" N   PRO A 271 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1213 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 719
        2.24 -     2.83: 17899
        2.83 -     3.42: 20994
        3.42 -     4.01: 27283
        4.01 -     4.60: 42172
  Nonbonded interactions: 109067
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 305 "
            pdb="HD22 ASN A 309 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" OE1 GLN A 342 "
            pdb=" H   GLN A 342 "
     model   vdw
     1.683 2.450
  nonbonded pdb=" O   ARG A  90 "
            pdb=" H   GLY A 119 "
     model   vdw
     1.766 2.450
  nonbonded pdb=" H   ARG A 175 "
            pdb=" OE2 GLU A 284 "
     model   vdw
     1.771 2.450
  nonbonded pdb=" O   VAL A 249 "
            pdb=" HG  SER A 252 "
     model   vdw
     1.785 2.450
  ... (remaining 109062 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:             0.550
  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:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.160
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
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   0.064   4218  Z= 0.160
  Angle     :  0.505   5.614   5761  Z= 0.262
  Chirality :  0.034   0.127    674
  Planarity :  0.003   0.031    709
  Dihedral  : 11.060  86.190   1481
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  5.19 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.38), residues: 530
  helix:  2.32 (0.28), residues: 345
  sheet:  None (None), residues: 0
  loop : -0.86 (0.48), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 175 
 TYR   0.012   0.001   TYR A 240 
 PHE   0.014   0.001   PHE A 275 
 TRP   0.006   0.001   TRP A 288 
 HIS   0.002   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4213)
  covalent geometry    : angle       0.49269 ( 5749)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       1.12026 (    6)
  hydrogen bonds       : bond        0.14986 (  264)
  hydrogen bonds       : angle       5.57493 (  777)
  link_BETA1-4         : bond        0.00366 (    1)
  link_BETA1-4         : angle       1.90629 (    3)
  link_NAG-ASN         : bond        0.00786 (    1)
  link_NAG-ASN         : angle       4.20562 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9113 (m) cc_final: 0.8737 (p)
REVERT: A   70 LEU cc_start: 0.8765 (tp) cc_final: 0.8521 (tp)
REVERT: A  209 GLN cc_start: 0.8718 (tt0) cc_final: 0.8463 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1377
  time to fit residues: 32.0887
Evaluate side-chains
  126 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.178288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.153255 restraints weight = 18543.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.159743 restraints weight = 7276.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.163639 restraints weight = 3787.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.165960 restraints weight = 2396.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.167541 restraints weight = 1754.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4218  Z= 0.140
  Angle     :  0.573   4.720   5761  Z= 0.302
  Chirality :  0.035   0.122    674
  Planarity :  0.004   0.036    709
  Dihedral  :  5.126  38.876    620
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.92 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.37), residues: 530
  helix:  2.13 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.82 (0.50), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  51 
 TYR   0.012   0.001   TYR A 240 
 PHE   0.019   0.001   PHE A 275 
 TRP   0.006   0.001   TRP A 491 
 HIS   0.005   0.002   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4213)
  covalent geometry    : angle       0.56951 ( 5749)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       0.88607 (    6)
  hydrogen bonds       : bond        0.05446 (  264)
  hydrogen bonds       : angle       4.64546 (  777)
  link_BETA1-4         : bond        0.00404 (    1)
  link_BETA1-4         : angle       1.47158 (    3)
  link_NAG-ASN         : bond        0.00138 (    1)
  link_NAG-ASN         : angle       2.10648 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9252 (m) cc_final: 0.8849 (p)
REVERT: A  347 THR cc_start: 0.8101 (m) cc_final: 0.7722 (m)
REVERT: A  364 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8380 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1093
  time to fit residues: 19.8298
Evaluate side-chains
  122 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  364 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0030
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 297 GLN
A 346 HIS
A 367 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.179429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.154840 restraints weight = 18667.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.161197 restraints weight = 7255.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.164975 restraints weight = 3770.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.167317 restraints weight = 2413.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.168525 restraints weight = 1756.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4218  Z= 0.122
  Angle     :  0.531   4.585   5761  Z= 0.275
  Chirality :  0.034   0.123    674
  Planarity :  0.005   0.051    709
  Dihedral  :  4.996  37.904    620
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.44 %
    Favored  : 83.73 %
  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 aren not related in a simple way.
  whole:  1.95 (0.38), residues: 530
  helix:  2.28 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.83 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 233 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.016   0.001   PHE A 275 
 TRP   0.005   0.001   TRP A 429 
 HIS   0.009   0.002   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4213)
  covalent geometry    : angle       0.52725 ( 5749)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       0.93678 (    6)
  hydrogen bonds       : bond        0.04997 (  264)
  hydrogen bonds       : angle       4.43611 (  777)
  link_BETA1-4         : bond        0.00490 (    1)
  link_BETA1-4         : angle       1.49190 (    3)
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       2.24109 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9285 (m) cc_final: 0.8865 (p)
REVERT: A  193 MET cc_start: 0.8629 (ttp) cc_final: 0.8370 (ttt)
REVERT: A  364 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: A  455 GLU cc_start: 0.8847 (tp30) cc_final: 0.8400 (tp30)
  outliers start: 12
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1065
  time to fit residues: 18.3724
Evaluate side-chains
  125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  411 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.177069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.152497 restraints weight = 18898.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.158774 restraints weight = 7360.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.162486 restraints weight = 3826.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.164723 restraints weight = 2423.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.166169 restraints weight = 1781.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4218  Z= 0.116
  Angle     :  0.519   4.622   5761  Z= 0.268
  Chirality :  0.034   0.121    674
  Planarity :  0.004   0.033    709
  Dihedral  :  4.883  37.294    620
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.57 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.38), residues: 530
  helix:  2.45 (0.28), residues: 355
  sheet:  None (None), residues: 0
  loop : -0.77 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 439 
 TYR   0.017   0.001   TYR A 240 
 PHE   0.014   0.001   PHE A 275 
 TRP   0.005   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4213)
  covalent geometry    : angle       0.51535 ( 5749)
  SS BOND              : bond        0.00087 (    3)
  SS BOND              : angle       0.86225 (    6)
  hydrogen bonds       : bond        0.04632 (  264)
  hydrogen bonds       : angle       4.33258 (  777)
  link_BETA1-4         : bond        0.00402 (    1)
  link_BETA1-4         : angle       1.54335 (    3)
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       2.27274 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  135 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 GLU cc_start: 0.8265 (mp0) cc_final: 0.7821 (mp0)
REVERT: A   45 THR cc_start: 0.9281 (m) cc_final: 0.8871 (p)
REVERT: A  193 MET cc_start: 0.8603 (ttp) cc_final: 0.8337 (ttt)
REVERT: A  233 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7436 (mtm180)
REVERT: A  364 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8392 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1071
  time to fit residues: 18.4214
Evaluate side-chains
  131 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   24 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  233 ARG
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.169475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.145296 restraints weight = 18881.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.151419 restraints weight = 7339.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.155072 restraints weight = 3805.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.157292 restraints weight = 2429.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158395 restraints weight = 1777.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4218  Z= 0.181
  Angle     :  0.569   4.631   5761  Z= 0.308
  Chirality :  0.036   0.127    674
  Planarity :  0.004   0.038    709
  Dihedral  :  5.067  38.168    620
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.80 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.38), residues: 530
  helix:  2.16 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.06 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.015   0.002   TYR A 240 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4213)
  covalent geometry    : angle       0.56495 ( 5749)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       0.88642 (    6)
  hydrogen bonds       : bond        0.05329 (  264)
  hydrogen bonds       : angle       4.69792 (  777)
  link_BETA1-4         : bond        0.00260 (    1)
  link_BETA1-4         : angle       1.71080 (    3)
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       2.52727 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  136 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9271 (m) cc_final: 0.8929 (p)
REVERT: A  146 TRP cc_start: 0.8325 (p-90) cc_final: 0.7971 (p90)
REVERT: A  193 MET cc_start: 0.8679 (ttp) cc_final: 0.8426 (ttt)
REVERT: A  364 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 129
  average time/residue: 0.1067
  time to fit residues: 18.9635
Evaluate side-chains
  124 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  411 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0870
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.3764

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.170065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146088 restraints weight = 18737.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152144 restraints weight = 7213.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.155741 restraints weight = 3743.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.157983 restraints weight = 2395.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.159320 restraints weight = 1744.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4218  Z= 0.151
  Angle     :  0.544   4.655   5761  Z= 0.287
  Chirality :  0.035   0.129    674
  Planarity :  0.004   0.046    709
  Dihedral  :  4.924  36.945    620
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.69 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.38), residues: 530
  helix:  2.18 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.15 (0.49), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.016   0.001   TYR A 240 
 PHE   0.013   0.001   PHE A 275 
 TRP   0.008   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4213)
  covalent geometry    : angle       0.54054 ( 5749)
  SS BOND              : bond        0.00103 (    3)
  SS BOND              : angle       0.77427 (    6)
  hydrogen bonds       : bond        0.05102 (  264)
  hydrogen bonds       : angle       4.51400 (  777)
  link_BETA1-4         : bond        0.00217 (    1)
  link_BETA1-4         : angle       1.50384 (    3)
  link_NAG-ASN         : bond        0.00078 (    1)
  link_NAG-ASN         : angle       2.26895 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9272 (m) cc_final: 0.8933 (p)
REVERT: A  193 MET cc_start: 0.8682 (ttp) cc_final: 0.8445 (ttt)
REVERT: A  364 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8392 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 120
  average time/residue: 0.1007
  time to fit residues: 16.9830
Evaluate side-chains
  123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  446 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.168301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144514 restraints weight = 18994.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.150395 restraints weight = 7254.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.153919 restraints weight = 3761.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.156101 restraints weight = 2406.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.157194 restraints weight = 1776.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4218  Z= 0.169
  Angle     :  0.556   4.704   5761  Z= 0.297
  Chirality :  0.035   0.131    674
  Planarity :  0.004   0.035    709
  Dihedral  :  4.954  36.822    620
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.92 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.38), residues: 530
  helix:  2.10 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.23 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.015   0.002   TYR A  72 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4213)
  covalent geometry    : angle       0.55201 ( 5749)
  SS BOND              : bond        0.00383 (    3)
  SS BOND              : angle       0.99126 (    6)
  hydrogen bonds       : bond        0.05162 (  264)
  hydrogen bonds       : angle       4.58337 (  777)
  link_BETA1-4         : bond        0.00216 (    1)
  link_BETA1-4         : angle       1.53301 (    3)
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       2.30599 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9285 (m) cc_final: 0.8975 (p)
REVERT: A  193 MET cc_start: 0.8685 (ttp) cc_final: 0.8456 (ttt)
REVERT: A  364 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8359 (tt)
  outliers start: 16
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1019
  time to fit residues: 16.4605
Evaluate side-chains
  119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   24 THR
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  362 GLN
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  446 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0670
   overall best weight:    0.9922

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.170090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146342 restraints weight = 18964.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152268 restraints weight = 7178.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.155751 restraints weight = 3693.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.157983 restraints weight = 2357.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.159299 restraints weight = 1724.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4218  Z= 0.130
  Angle     :  0.525   4.570   5761  Z= 0.274
  Chirality :  0.034   0.129    674
  Planarity :  0.004   0.036    709
  Dihedral  :  4.797  36.378    620
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.16 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.38), residues: 530
  helix:  2.28 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.11 (0.50), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.013   0.001   PHE A 275 
 TRP   0.007   0.001   TRP A 429 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4213)
  covalent geometry    : angle       0.52220 ( 5749)
  SS BOND              : bond        0.00078 (    3)
  SS BOND              : angle       0.50260 (    6)
  hydrogen bonds       : bond        0.04828 (  264)
  hydrogen bonds       : angle       4.32862 (  777)
  link_BETA1-4         : bond        0.00282 (    1)
  link_BETA1-4         : angle       1.43318 (    3)
  link_NAG-ASN         : bond        0.00068 (    1)
  link_NAG-ASN         : angle       2.12663 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9329 (m) cc_final: 0.9004 (p)
REVERT: A  193 MET cc_start: 0.8652 (ttp) cc_final: 0.8418 (ttt)
REVERT: A  364 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8341 (tt)
  outliers start: 12
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1013
  time to fit residues: 16.1113
Evaluate side-chains
  116 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  446 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.168028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144577 restraints weight = 18985.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.150376 restraints weight = 7145.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.153862 restraints weight = 3684.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.155874 restraints weight = 2343.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.157097 restraints weight = 1744.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.5372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4218  Z= 0.149
  Angle     :  0.539   4.730   5761  Z= 0.286
  Chirality :  0.034   0.129    674
  Planarity :  0.004   0.036    709
  Dihedral  :  4.827  37.038    620
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.10 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.38), residues: 530
  helix:  2.16 (0.27), residues: 365
  sheet:  None (None), residues: 0
  loop : -1.02 (0.51), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 233 
 TYR   0.014   0.001   TYR A  72 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.002   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4213)
  covalent geometry    : angle       0.53648 ( 5749)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.57753 (    6)
  hydrogen bonds       : bond        0.04901 (  264)
  hydrogen bonds       : angle       4.38938 (  777)
  link_BETA1-4         : bond        0.00193 (    1)
  link_BETA1-4         : angle       1.40065 (    3)
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       2.15430 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 THR cc_start: 0.9281 (m) cc_final: 0.8978 (p)
REVERT: A  193 MET cc_start: 0.8644 (ttp) cc_final: 0.8433 (ttt)
REVERT: A  364 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8309 (tt)
  outliers start: 12
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1202
  time to fit residues: 17.9025
Evaluate side-chains
  119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   24 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  446 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.170468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.147061 restraints weight = 18806.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.152932 restraints weight = 7083.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.156483 restraints weight = 3629.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158583 restraints weight = 2295.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.159852 restraints weight = 1690.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.5489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4218  Z= 0.113
  Angle     :  0.516   4.580   5761  Z= 0.267
  Chirality :  0.034   0.128    674
  Planarity :  0.004   0.045    709
  Dihedral  :  4.692  36.507    620
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.87 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.39), residues: 530
  helix:  2.36 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.93 (0.52), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 233 
 TYR   0.013   0.001   TYR A  72 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.006   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4213)
  covalent geometry    : angle       0.51347 ( 5749)
  SS BOND              : bond        0.00078 (    3)
  SS BOND              : angle       0.50026 (    6)
  hydrogen bonds       : bond        0.04590 (  264)
  hydrogen bonds       : angle       4.14285 (  777)
  link_BETA1-4         : bond        0.00328 (    1)
  link_BETA1-4         : angle       1.35798 (    3)
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       2.03256 (    3)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   98 is missing expected H atoms. Skipping.
Residue LEU  100 is missing expected H atoms. Skipping.
Residue SER  101 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue MET  319 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue THR  327 is missing expected H atoms. Skipping.
Residue LYS  329 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue ILE  421 is missing expected H atoms. Skipping.
Residue LEU  427 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 PHE cc_start: 0.8844 (m-80) cc_final: 0.8556 (m-80)
REVERT: A   45 THR cc_start: 0.9272 (m) cc_final: 0.8975 (p)
REVERT: A  193 MET cc_start: 0.8604 (ttp) cc_final: 0.8393 (ttt)
REVERT: A  364 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8286 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 115
  average time/residue: 0.1005
  time to fit residues: 15.9164
Evaluate side-chains
  117 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  241 GLN
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  446 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 43 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0570
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5016

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS
A 447 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.171714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.148502 restraints weight = 18671.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.154342 restraints weight = 6988.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.157860 restraints weight = 3567.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.159924 restraints weight = 2237.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.161358 restraints weight = 1645.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4218  Z= 0.108
  Angle     :  0.516   4.638   5761  Z= 0.267
  Chirality :  0.034   0.163    674
  Planarity :  0.004   0.041    709
  Dihedral  :  4.674  36.352    620
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.34 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.39), residues: 530
  helix:  2.42 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.80 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 233 
 TYR   0.027   0.002   TYR A  72 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.006   0.001   TRP A 354 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 4213)
  covalent geometry    : angle       0.51367 ( 5749)
  SS BOND              : bond        0.00051 (    3)
  SS BOND              : angle       0.40494 (    6)
  hydrogen bonds       : bond        0.04385 (  264)
  hydrogen bonds       : angle       4.02475 (  777)
  link_BETA1-4         : bond        0.00297 (    1)
  link_BETA1-4         : angle       1.26060 (    3)
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.82103 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1692.37 seconds
wall clock time: 29 minutes 29.16 seconds (1769.16 seconds total)