Starting phenix.real_space_refine
on Sat Aug 23 08:02:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zpb_60331/08_2025/8zpb_60331.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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: 8
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      24      5.16       5
     Cl      1      4.86       5
     Na      2      4.78       5
     C    3560      2.51       5
     N     845      2.21       5
     O     986      1.98       5
     H    5257      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 10676
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 8801
          Classifications: {'peptide': 551}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 1779
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 93
          Unusual residues: {' CL': 1, ' NA': 2, 'LNR': 1, 'PTY': 1}
          Classifications: {'undetermined': 5, 'water': 51}
          Link IDs: {None: 55}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 23
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.12, per 1000 atoms: 0.20
  Number of scatterers: 10676
  At special positions: 0
  Unit cell: (98.44, 74.52, 79.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Cl      1     17.00
     S      24     16.00
     P       1     15.00
     Na      2     11.00
     O     986      8.00
     N     845      7.00
     C    3560      6.00
     H    5257      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " 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
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 276.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1224

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      69.7% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.631A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 91 through 121
      removed outlier: 3.972A  pdb=" N   LEU A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 4.825A  pdb=" N   MET A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 166
      removed outlier: 3.771A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 4.207A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TRP A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
      removed outlier: 3.804A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
      removed outlier: 3.631A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 4.205A  pdb=" N   TRP A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 372
    Processing helix  chain 'A' and resid 375 through 379
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 389 through 397
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.820A  pdb=" N   ASP A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 441 through 458
    Processing helix  chain 'A' and resid 459 through 462
      removed outlier: 3.688A  pdb=" N   THR A 462 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 462'
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.580A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 494
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.555A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 594 through 597
    Processing helix  chain 'A' and resid 598 through 604
      removed outlier: 4.399A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLN A 603 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.037A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57
      removed outlier: 3.912A  pdb=" N   ARG A  56 " --> pdb=" O   GLN B 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 544 through 545
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.692A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13

    340 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.77

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5250
        1.03 -     1.23: 20
        1.23 -     1.42: 2447
        1.42 -     1.62: 3026
        1.62 -     1.81: 39
  Bond restraints: 10782
  Sorted by residual:
  bond pdb=" CAE LNR A 701 "
       pdb=" CAI LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.384  1.524 -0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" CAG LNR A 701 "
       pdb=" CAJ LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.384  1.524 -0.140 2.00e-02 2.50e+03 4.91e+01
  bond pdb=" CAF LNR A 701 "
       pdb=" CAK LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.386  1.524 -0.138 2.00e-02 2.50e+03 4.76e+01
  bond pdb=" CAI LNR A 701 "
       pdb=" CAJ LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.402  1.317  0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" CAG LNR A 701 "
       pdb=" CAK LNR A 701 "
    ideal  model  delta    sigma   weight residual
    1.395  1.316  0.079 2.00e-02 2.50e+03 1.55e+01
  ... (remaining 10777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 18221
        1.14 -     2.28: 1067
        2.28 -     3.42: 70
        3.42 -     4.57: 19
        4.57 -     5.71: 3
  Bond angle restraints: 19380
  Sorted by residual:
  angle pdb=" N   MET A 107 "
        pdb=" CA  MET A 107 "
        pdb=" C   MET A 107 "
      ideal   model   delta    sigma   weight residual
     112.75  108.87    3.88 1.36e+00 5.41e-01 8.15e+00
  angle pdb=" CA  SER A 182 "
        pdb=" C   SER A 182 "
        pdb=" O   SER A 182 "
      ideal   model   delta    sigma   weight residual
     121.01  117.76    3.25 1.18e+00 7.18e-01 7.61e+00
  angle pdb=" N   PRO A 183 "
        pdb=" CA  PRO A 183 "
        pdb=" C   PRO A 183 "
      ideal   model   delta    sigma   weight residual
     114.35  110.97    3.38 1.25e+00 6.40e-01 7.31e+00
  angle pdb=" CA  TRP A  80 "
        pdb=" C   TRP A  80 "
        pdb=" O   TRP A  80 "
      ideal   model   delta    sigma   weight residual
     119.41  116.41    3.00 1.13e+00 7.83e-01 7.07e+00
  angle pdb=" CA  SER A 182 "
        pdb=" C   SER A 182 "
        pdb=" N   PRO A 183 "
      ideal   model   delta    sigma   weight residual
     117.60  120.69   -3.09 1.18e+00 7.18e-01 6.85e+00
  ... (remaining 19375 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.82: 4766
       23.82 -    47.64: 267
       47.64 -    71.46: 85
       71.46 -    95.28: 2
       95.28 -   119.11: 1
  Dihedral angle restraints: 5121
    sinusoidal: 2620
      harmonic: 2501
  Sorted by residual:
  dihedral pdb=" N1  PTY A 705 "
           pdb=" C2  PTY A 705 "
           pdb=" C3  PTY A 705 "
           pdb=" O11 PTY A 705 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33 -175.56 -119.11     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" CA  ILE B  51 "
           pdb=" C   ILE B  51 "
           pdb=" N   GLN B  52 "
           pdb=" CA  GLN B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.11  -17.89     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  TRP A 128 "
           pdb=" C   TRP A 128 "
           pdb=" N   LYS A 129 "
           pdb=" CA  LYS A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.13   15.87     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 5118 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 665
       0.046 -    0.091: 129
       0.091 -    0.137: 30
       0.137 -    0.182: 1
       0.182 -    0.228: 1
  Chirality restraints: 826
  Sorted by residual:
  chirality pdb=" CAL LNR A 701 "
            pdb=" CAH LNR A 701 "
            pdb=" CAK LNR A 701 "
            pdb=" OAD LNR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.51    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  VAL A  79 "
            pdb=" N   VAL A  79 "
            pdb=" C   VAL A  79 "
            pdb=" CB  VAL A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  VAL B   2 "
            pdb=" N   VAL B   2 "
            pdb=" C   VAL B   2 "
            pdb=" CB  VAL B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 823 not shown)

  Planarity restraints: 1563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 102 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   LEU A 102 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU A 102 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE A 103 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 213 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.33e+00
        pdb=" C   PHE A 213 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE A 213 "    0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 214 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 391 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.98e+00
        pdb=" N   PRO A 392 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1560 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 629
        2.19 -     2.79: 21815
        2.79 -     3.39: 32592
        3.39 -     4.00: 43958
        4.00 -     4.60: 68263
  Nonbonded interactions: 167257
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  52 "
            pdb="HH22 ARG B  71 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OE2 GLU B   6 "
            pdb=" H   CYS B  95 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" O   PHE A 495 "
            pdb="HE21 GLN A 608 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" OE1 GLU B   6 "
            pdb=" H   GLY B 113 "
     model   vdw
     1.655 2.450
  nonbonded pdb="HH22 ARG A  81 "
            pdb=" O   HOH A 810 "
     model   vdw
     1.663 2.450
  ... (remaining 167252 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 individual isotropic
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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     13.140
  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:8.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
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      :  0.005   0.140   5527  Z= 0.261
  Angle     :  0.563   5.707   7530  Z= 0.328
  Chirality :  0.039   0.228    826
  Planarity :  0.004   0.051    922
  Dihedral  : 15.800 119.105   1882
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.52 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.33), residues: 659
  helix:  1.10 (0.27), residues: 389
  sheet: -1.46 (0.86), residues: 33
  loop :  0.24 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 301 
 TYR   0.015   0.002   TYR A 572 
 PHE   0.014   0.001   PHE A 409 
 TRP   0.015   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 5525)
  covalent geometry    : angle       0.56311 ( 7526)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.68477 (    4)
  hydrogen bonds       : bond        0.12741 (  334)
  hydrogen bonds       : angle       6.00121 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7750 (t60)
REVERT: A  121 ARG cc_start: 0.8502 (mtm180) cc_final: 0.7511 (mtp180)
  outliers start: 6
  outliers final: 4
  residues processed: 90
  average time/residue: 1.0220
  time to fit residues: 97.1722
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  610 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.111408 restraints weight = 15308.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.09
r_work: 0.3554 rms_B_bonded: 1.33 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.0806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5527  Z= 0.213
  Angle     :  0.547   5.591   7530  Z= 0.297
  Chirality :  0.040   0.134    826
  Planarity :  0.005   0.062    922
  Dihedral  :  8.390  78.020    757
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.44 %
    Favored  : 84.77 %
  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:  1.00 (0.33), residues: 659
  helix:  1.03 (0.26), residues: 389
  sheet: -1.78 (0.71), residues: 33
  loop :  0.67 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 301 
 TYR   0.015   0.002   TYR A  87 
 PHE   0.017   0.002   PHE A 409 
 TRP   0.009   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 5525)
  covalent geometry    : angle       0.54607 ( 7526)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       1.28962 (    4)
  hydrogen bonds       : bond        0.04840 (  334)
  hydrogen bonds       : angle       5.35798 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.7678 (t60)
REVERT: A  121 ARG cc_start: 0.8413 (mtm180) cc_final: 0.7608 (mtp180)
REVERT: A  206 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6815 (tttt)
REVERT: A  341 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7243 (ptm-80)
REVERT: A  509 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7928 (mtt)
REVERT: A  612 GLN cc_start: 0.7755 (mp-120) cc_final: 0.7528 (pm20)
  outliers start: 10
  outliers final: 5
  residues processed: 90
  average time/residue: 1.0713
  time to fit residues: 101.8122
Evaluate side-chains
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  610 GLN
Chi-restraints excluded: chain B residue   25 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 63 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.117604 restraints weight = 15203.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.08
r_work: 0.3581 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5527  Z= 0.148
  Angle     :  0.493   5.424   7530  Z= 0.267
  Chirality :  0.037   0.129    826
  Planarity :  0.004   0.045    922
  Dihedral  :  7.522  68.866    756
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.72 %
    Favored  : 85.13 %
  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:  1.26 (0.33), residues: 659
  helix:  1.27 (0.27), residues: 385
  sheet: -1.75 (0.68), residues: 33
  loop :  0.74 (0.44), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 301 
 TYR   0.014   0.001   TYR A  87 
 PHE   0.014   0.001   PHE A 316 
 TRP   0.008   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5525)
  covalent geometry    : angle       0.49313 ( 7526)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       0.88955 (    4)
  hydrogen bonds       : bond        0.04234 (  334)
  hydrogen bonds       : angle       5.07915 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.7723 (t60)
REVERT: A  121 ARG cc_start: 0.8387 (mtm180) cc_final: 0.7571 (mtp180)
REVERT: A  206 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6788 (tttt)
REVERT: A  341 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7241 (ptm-80)
REVERT: A  509 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7715 (mtm)
REVERT: B   82 MET cc_start: 0.9046 (mtp) cc_final: 0.8822 (mtp)
REVERT: B  115 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7523 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 92
  average time/residue: 1.0418
  time to fit residues: 101.4676
Evaluate side-chains
  91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  610 GLN
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.128281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.110240 restraints weight = 14828.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.12
r_work: 0.3061 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5527  Z= 0.157
  Angle     :  0.495   5.382   7530  Z= 0.268
  Chirality :  0.037   0.128    826
  Planarity :  0.004   0.045    922
  Dihedral  :  7.142  66.747    755
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.72 %
    Favored  : 84.95 %
  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:  1.31 (0.33), residues: 659
  helix:  1.30 (0.27), residues: 385
  sheet: -1.61 (0.68), residues: 33
  loop :  0.78 (0.44), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 301 
 TYR   0.014   0.002   TYR A  87 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.009   0.001   TRP A  59 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5525)
  covalent geometry    : angle       0.49461 ( 7526)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.95930 (    4)
  hydrogen bonds       : bond        0.04224 (  334)
  hydrogen bonds       : angle       5.04891 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7699 (t60)
REVERT: A  121 ARG cc_start: 0.8345 (mtm180) cc_final: 0.7274 (mtp180)
REVERT: A  206 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6660 (tttt)
REVERT: A  304 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7679 (mm-30)
REVERT: A  359 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7889 (m-80)
REVERT: B   56 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8163 (ttp80)
REVERT: B  115 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7132 (tm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 87
  average time/residue: 1.0945
  time to fit residues: 100.3297
Evaluate side-chains
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.137965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.123108 restraints weight = 13906.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 0.94
r_work: 0.3086 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5527  Z= 0.165
  Angle     :  0.497   5.319   7530  Z= 0.269
  Chirality :  0.038   0.127    826
  Planarity :  0.004   0.046    922
  Dihedral  :  6.474  65.484    752
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.08 %
    Favored  : 84.59 %
  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:  1.31 (0.33), residues: 659
  helix:  1.30 (0.27), residues: 385
  sheet: -1.58 (0.67), residues: 33
  loop :  0.77 (0.44), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 301 
 TYR   0.014   0.002   TYR A  87 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.009   0.001   TRP A  59 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5525)
  covalent geometry    : angle       0.49694 ( 7526)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       1.01152 (    4)
  hydrogen bonds       : bond        0.04248 (  334)
  hydrogen bonds       : angle       5.05483 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8416 (OUTLIER) cc_final: 0.7685 (t60)
REVERT: A  121 ARG cc_start: 0.8314 (mtm180) cc_final: 0.7278 (mtp180)
REVERT: A  206 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6738 (tttt)
REVERT: A  304 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7647 (mm-30)
REVERT: A  341 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7168 (ptm-80)
REVERT: A  359 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (m-80)
REVERT: B   56 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8159 (ttp80)
REVERT: B  115 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7160 (tm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 87
  average time/residue: 1.1131
  time to fit residues: 102.0928
Evaluate side-chains
  94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 12 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 15 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.142566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.128464 restraints weight = 13977.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 0.89
r_work: 0.3161 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 1.92 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5527  Z= 0.122
  Angle     :  0.464   5.219   7530  Z= 0.251
  Chirality :  0.036   0.125    826
  Planarity :  0.004   0.043    922
  Dihedral  :  6.122  63.214    752
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.44 %
    Favored  : 84.59 %
  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:  1.53 (0.34), residues: 659
  helix:  1.49 (0.27), residues: 385
  sheet: -1.60 (0.70), residues: 39
  loop :  0.94 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 301 
 TYR   0.014   0.001   TYR B  30 
 PHE   0.012   0.001   PHE A 316 
 TRP   0.008   0.001   TRP A 556 
 HIS   0.001   0.000   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5525)
  covalent geometry    : angle       0.46370 ( 7526)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.68190 (    4)
  hydrogen bonds       : bond        0.03838 (  334)
  hydrogen bonds       : angle       4.84357 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.7686 (t60)
REVERT: A  121 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7306 (mtp180)
REVERT: A  341 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7147 (ptm-80)
REVERT: B   56 ARG cc_start: 0.8490 (tmm-80) cc_final: 0.8122 (ttp80)
REVERT: B  115 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7303 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 88
  average time/residue: 1.0861
  time to fit residues: 100.8365
Evaluate side-chains
  86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.141513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.127333 restraints weight = 13829.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 0.89
r_work: 0.3193 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5527  Z= 0.146
  Angle     :  0.480   5.237   7530  Z= 0.260
  Chirality :  0.037   0.125    826
  Planarity :  0.004   0.043    922
  Dihedral  :  6.200  64.854    752
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.80 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.34), residues: 659
  helix:  1.46 (0.27), residues: 385
  sheet: -1.62 (0.69), residues: 39
  loop :  0.97 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  87 
 PHE   0.014   0.001   PHE A 409 
 TRP   0.008   0.001   TRP A  59 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5525)
  covalent geometry    : angle       0.48011 ( 7526)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       0.89228 (    4)
  hydrogen bonds       : bond        0.04052 (  334)
  hydrogen bonds       : angle       4.91526 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7722 (t60)
REVERT: A  121 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7401 (mtp180)
REVERT: A  268 THR cc_start: 0.8476 (m) cc_final: 0.8151 (p)
REVERT: A  304 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7610 (mm-30)
REVERT: A  359 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7961 (m-80)
REVERT: B   56 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8166 (ttp80)
REVERT: B  115 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7377 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 87
  average time/residue: 1.1288
  time to fit residues: 103.5940
Evaluate side-chains
  91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   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 184 ASN
B  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.126201 restraints weight = 14068.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 0.86
r_work: 0.3101 rms_B_bonded: 1.04 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5527  Z= 0.143
  Angle     :  0.477   5.205   7530  Z= 0.258
  Chirality :  0.037   0.126    826
  Planarity :  0.004   0.043    922
  Dihedral  :  6.160  65.130    752
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.26 %
    Favored  : 84.77 %
  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:  1.55 (0.34), residues: 659
  helix:  1.48 (0.27), residues: 385
  sheet: -1.57 (0.70), residues: 39
  loop :  0.97 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 301 
 TYR   0.013   0.001   TYR A  87 
 PHE   0.013   0.001   PHE A 316 
 TRP   0.009   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5525)
  covalent geometry    : angle       0.47702 ( 7526)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.83307 (    4)
  hydrogen bonds       : bond        0.04011 (  334)
  hydrogen bonds       : angle       4.88507 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7693 (t60)
REVERT: A  121 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7285 (mtp180)
REVERT: A  304 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7548 (mm-30)
REVERT: A  359 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (m-80)
REVERT: B   56 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8120 (ttp80)
REVERT: B  115 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7270 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 85
  average time/residue: 1.1162
  time to fit residues: 100.1360
Evaluate side-chains
  90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.140658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.126465 restraints weight = 13834.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 0.89
r_work: 0.3153 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5527  Z= 0.160
  Angle     :  0.492   5.208   7530  Z= 0.266
  Chirality :  0.037   0.124    826
  Planarity :  0.004   0.044    922
  Dihedral  :  6.258  66.242    752
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.62 %
    Favored  : 84.59 %
  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:  1.48 (0.34), residues: 659
  helix:  1.43 (0.27), residues: 385
  sheet: -1.64 (0.69), residues: 39
  loop :  0.96 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 301 
 TYR   0.014   0.002   TYR A  87 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.010   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5525)
  covalent geometry    : angle       0.49113 ( 7526)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       0.96586 (    4)
  hydrogen bonds       : bond        0.04164 (  334)
  hydrogen bonds       : angle       4.95380 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.7694 (t60)
REVERT: A  121 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7319 (mtp180)
REVERT: A  268 THR cc_start: 0.8445 (m) cc_final: 0.8117 (p)
REVERT: A  304 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7581 (mm-30)
REVERT: A  359 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7899 (m-80)
REVERT: A  509 MET cc_start: 0.8120 (mtm) cc_final: 0.7507 (mtt)
REVERT: B   56 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8161 (ttp80)
REVERT: B  115 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7231 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 86
  average time/residue: 1.1256
  time to fit residues: 102.1398
Evaluate side-chains
  91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  382 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
B  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.140000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.125384 restraints weight = 13993.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 0.93
r_work: 0.3100 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5527  Z= 0.134
  Angle     :  0.473   5.174   7530  Z= 0.256
  Chirality :  0.037   0.125    826
  Planarity :  0.004   0.042    922
  Dihedral  :  6.111  65.480    752
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.44 %
    Favored  : 84.77 %
  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:  1.57 (0.34), residues: 659
  helix:  1.51 (0.27), residues: 385
  sheet: -1.53 (0.72), residues: 39
  loop :  0.95 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 301 
 TYR   0.015   0.001   TYR B  30 
 PHE   0.013   0.001   PHE A 316 
 TRP   0.011   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5525)
  covalent geometry    : angle       0.47309 ( 7526)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       0.75551 (    4)
  hydrogen bonds       : bond        0.03940 (  334)
  hydrogen bonds       : angle       4.84760 (  951)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  204 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8411 (OUTLIER) cc_final: 0.7671 (t60)
REVERT: A  121 ARG cc_start: 0.8271 (mtm180) cc_final: 0.7254 (mtp180)
REVERT: A  268 THR cc_start: 0.8405 (m) cc_final: 0.8076 (p)
REVERT: A  304 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7538 (mm-30)
REVERT: A  509 MET cc_start: 0.8102 (mtm) cc_final: 0.7495 (mtt)
REVERT: B   56 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8132 (ttp80)
REVERT: B  115 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7234 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 84
  average time/residue: 1.1463
  time to fit residues: 101.3778
Evaluate side-chains
  88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 TRP
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  115 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.127516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.108904 restraints weight = 14867.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.18
r_work: 0.3024 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5527  Z= 0.156
  Angle     :  0.489   5.194   7530  Z= 0.265
  Chirality :  0.037   0.126    826
  Planarity :  0.004   0.044    922
  Dihedral  :  6.197  66.223    752
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.62 %
    Favored  : 84.95 %
  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:  1.50 (0.34), residues: 659
  helix:  1.44 (0.27), residues: 385
  sheet: -1.64 (0.71), residues: 39
  loop :  0.96 (0.45), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 301 
 TYR   0.014   0.001   TYR A  87 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.012   0.001   TRP A 556 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5525)
  covalent geometry    : angle       0.48895 ( 7526)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.96238 (    4)
  hydrogen bonds       : bond        0.04129 (  334)
  hydrogen bonds       : angle       4.94002 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4088.63 seconds
wall clock time: 70 minutes 12.77 seconds (4212.77 seconds total)