Starting phenix.real_space_refine
on Thu Jul  2 23:10:31 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8emv_28266/07_2026/8emv_28266.cif"
  }
  resolution = 3.6
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5939 atoms to isotropic.
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
     Ca      1      9.91       5
     S      31      5.16       5
     C    3795      2.51       5
     N    1013      2.21       5
     O    1109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5949
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 5948
          Classifications: {'peptide': 747}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 47, 'TRANS': 699}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.25, per 1000 atoms: 0.21
  Number of scatterers: 5949
  At special positions: 0
  Unit cell: (62.64, 98.28, 103.68, 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)
     Ca      1     19.99
     S      31     16.00
     O    1109      8.00
     N    1013      7.00
     C    3795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 379.9 milliseconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      33.3% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 25
      removed outlier: 3.743A  pdb=" N   ARG A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 127 through 140
    Processing helix  chain 'A' and resid 148 through 163
      removed outlier: 3.503A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 4.287A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 194
      removed outlier: 3.641A  pdb=" N   GLU A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 208
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 223 through 233
      removed outlier: 3.662A  pdb=" N   ASP A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 268 through 280
      removed outlier: 4.887A  pdb=" N   LEU A 274 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 3.736A  pdb=" N   GLU A 287 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.639A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.927A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 399
    Processing helix  chain 'A' and resid 418 through 434
      removed outlier: 3.672A  pdb=" N   PHE A 433 " --> pdb=" O   CYS A 429 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 434 " --> pdb=" O   ARG A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 611
    Processing helix  chain 'A' and resid 622 through 632
    Processing helix  chain 'A' and resid 632 through 641
    Processing helix  chain 'A' and resid 661 through 666
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.674A  pdb=" N   ARG A 706 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 816
      No H-bonds generated for 'chain 'A' and resid 814 through 816'
    Processing helix  chain 'A' and resid 868 through 881
      removed outlier: 4.689A  pdb=" N   ALA A 878 " --> pdb=" O   ARG A 874 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU A 879 " --> pdb=" O   GLN A 875 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65
      removed outlier: 4.116A  pdb=" N   THR A  55 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   THR A  42 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A  26 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388
      removed outlier: 6.706A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 363 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 598 through 599
      removed outlier: 5.978A  pdb=" N   GLU A 598 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   SER A 619 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A 644 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 618 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 671 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 786
      removed outlier: 4.518A  pdb=" N   LYS A 785 " --> pdb=" O   ASN A 726 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 726 " --> pdb=" O   LYS A 785 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A 839 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLY A 735 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA A 837 " --> pdb=" O   GLY A 735 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 763
      removed outlier: 5.058A  pdb=" N   LYS A 761 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   VAL A 749 " --> pdb=" O   LYS A 761 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   ARG A 763 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL A 747 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   GLU A 800 " --> pdb=" O   PHE A 805 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   PHE A 805 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)

    201 hydrogen bonds defined for protein.
    570 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.99

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1898
        1.34 -     1.45: 878
        1.45 -     1.57: 3246
        1.57 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 6075
  Sorted by residual:
  bond pdb=" C   PRO A 370 "
       pdb=" N   PRO A 371 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.054 1.20e-02 6.94e+03 2.04e+01
  bond pdb=" C   PRO A 454 "
       pdb=" N   SER A 455 "
    ideal  model  delta    sigma   weight residual
    1.329  1.233  0.095 3.03e-02 1.09e+03 9.92e+00
  bond pdb=" C   LEU A 835 "
       pdb=" N   PRO A 836 "
    ideal  model  delta    sigma   weight residual
    1.333  1.349 -0.016 1.17e-02 7.31e+03 1.99e+00
  bond pdb=" CB  CYS A 669 "
       pdb=" SG  CYS A 669 "
    ideal  model  delta    sigma   weight residual
    1.808  1.763  0.045 3.30e-02 9.18e+02 1.85e+00
  bond pdb=" C   LEU A 453 "
       pdb=" N   PRO A 454 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.25e-02 6.40e+03 1.72e+00
  ... (remaining 6070 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 7808
        1.66 -     3.31: 353
        3.31 -     4.97: 54
        4.97 -     6.63: 6
        6.63 -     8.28: 6
  Bond angle restraints: 8227
  Sorted by residual:
  angle pdb=" C   SER A 200 "
        pdb=" N   GLU A 201 "
        pdb=" CA  GLU A 201 "
      ideal   model   delta    sigma   weight residual
     121.54  129.14   -7.60 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   GLY A 380 "
        pdb=" N   PHE A 381 "
        pdb=" CA  PHE A 381 "
      ideal   model   delta    sigma   weight residual
     122.82  128.33   -5.51 1.42e+00 4.96e-01 1.50e+01
  angle pdb=" N   LEU A 835 "
        pdb=" CA  LEU A 835 "
        pdb=" C   LEU A 835 "
      ideal   model   delta    sigma   weight residual
     109.81  117.69   -7.88 2.21e+00 2.05e-01 1.27e+01
  angle pdb=" N   PRO A 370 "
        pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
      ideal   model   delta    sigma   weight residual
     110.70  114.57   -3.87 1.22e+00 6.72e-01 1.00e+01
  angle pdb=" CA  PRO A 370 "
        pdb=" C   PRO A 370 "
        pdb=" N   PRO A 371 "
      ideal   model   delta    sigma   weight residual
     117.93  121.50   -3.57 1.20e+00 6.94e-01 8.86e+00
  ... (remaining 8222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3225
       16.47 -    32.94: 405
       32.94 -    49.41: 65
       49.41 -    65.88: 23
       65.88 -    82.35: 7
  Dihedral angle restraints: 3725
    sinusoidal: 1539
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" CA  LYS A 238 "
           pdb=" C   LYS A 238 "
           pdb=" N   PRO A 239 "
           pdb=" CA  PRO A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.53  -29.47     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 236 "
           pdb=" C   LYS A 236 "
           pdb=" N   GLY A 237 "
           pdb=" CA  GLY A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.95   24.05     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  PRO A 239 "
           pdb=" C   PRO A 239 "
           pdb=" N   TYR A 240 "
           pdb=" CA  TYR A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 3722 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 548
       0.039 -    0.078: 254
       0.078 -    0.117: 77
       0.117 -    0.156: 26
       0.156 -    0.195: 10
  Chirality restraints: 915
  Sorted by residual:
  chirality pdb=" CB  VAL A 116 "
            pdb=" CA  VAL A 116 "
            pdb=" CG1 VAL A 116 "
            pdb=" CG2 VAL A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CB  VAL A 621 "
            pdb=" CA  VAL A 621 "
            pdb=" CG1 VAL A 621 "
            pdb=" CG2 VAL A 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CA  LEU A 835 "
            pdb=" N   LEU A 835 "
            pdb=" C   LEU A 835 "
            pdb=" CB  LEU A 835 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.71e-01
  ... (remaining 912 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 369 "    0.046 5.00e-02 4.00e+02   6.97e-02 7.77e+00
        pdb=" N   PRO A 370 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 111 "   -0.041 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO A 112 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO A 322 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2031
        2.85 -     3.36: 5011
        3.36 -     3.88: 9084
        3.88 -     4.39: 10476
        4.39 -     4.90: 18462
  Nonbonded interactions: 45064
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 225 "
            pdb=" OD1 ASP A 225 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" O   SER A 591 "
            pdb=" OG  SER A 591 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OE1 GLU A 577 "
            pdb=" OG  SER A 581 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" N   ASP A 125 "
            pdb=" OD1 ASP A 125 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   SER A 404 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.382 3.040
  ... (remaining 45059 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.690
  Find NCS groups from input model:        0.020
  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:1.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.095   6075  Z= 0.300
  Angle     :  0.813   8.282   8227  Z= 0.461
  Chirality :  0.052   0.195    915
  Planarity :  0.007   0.070   1071
  Dihedral  : 15.162  82.355   2307
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.26 (0.24), residues: 739
  helix: -3.01 (0.23), residues: 235
  sheet: -2.29 (0.41), residues: 124
  loop : -2.89 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  73 
 TYR   0.019   0.002   TYR A 648 
 PHE   0.018   0.002   PHE A 799 
 TRP   0.009   0.002   TRP A  54 
 HIS   0.005   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00705 /  0.30 ( 6075)
  covalent geometry    : angle       0.81279 /  0.46 ( 8227)
  hydrogen bonds       : bond        0.21576 / 13.44 (  201)
  hydrogen bonds       : angle       7.21270 /  4.94 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.8684 (tttt) cc_final: 0.8369 (tptp)
REVERT: A  291 MET cc_start: 0.8471 (ttm) cc_final: 0.8129 (ttm)
REVERT: A  444 LYS cc_start: 0.8439 (tttm) cc_final: 0.8071 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0967
  time to fit residues: 9.4550
Evaluate side-chains
  56 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 ASN
A 166 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.105184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.080065 restraints weight = 9235.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.082515 restraints weight = 5898.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.084038 restraints weight = 4465.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.085189 restraints weight = 3773.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.085577 restraints weight = 3366.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6075  Z= 0.124
  Angle     :  0.531   5.225   8227  Z= 0.281
  Chirality :  0.043   0.152    915
  Planarity :  0.005   0.045   1071
  Dihedral  :  4.728  26.153    816
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.55 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.27), residues: 739
  helix: -0.96 (0.31), residues: 237
  sheet: -1.79 (0.41), residues: 130
  loop : -2.30 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  73 
 TYR   0.013   0.001   TYR A 820 
 PHE   0.030   0.001   PHE A 197 
 TRP   0.005   0.001   TRP A 131 
 HIS   0.002   0.000   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 ( 6075)
  covalent geometry    : angle       0.53135 /  0.28 ( 8227)
  hydrogen bonds       : bond        0.04466 /  2.94 (  201)
  hydrogen bonds       : angle       4.95369 /  3.40 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  291 MET cc_start: 0.8542 (ttm) cc_final: 0.8312 (ttm)
REVERT: A  444 LYS cc_start: 0.8485 (tttm) cc_final: 0.8080 (tptm)
REVERT: A  719 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8706 (mm)
REVERT: A  772 PHE cc_start: 0.8003 (t80) cc_final: 0.7779 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 0.0781
  time to fit residues: 7.6816
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  652 THR
Chi-restraints excluded: chain A residue  719 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0060
   chunk 20 optimal weight:    0.0270
   chunk 73 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    0.9658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.086570 restraints weight = 9129.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.088695 restraints weight = 6259.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.090132 restraints weight = 4918.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.090980 restraints weight = 4232.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.091498 restraints weight = 3852.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6075  Z= 0.118
  Angle     :  0.511   6.471   8227  Z= 0.262
  Chirality :  0.042   0.165    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  4.329  24.549    816
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.62 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.29), residues: 739
  helix:  0.12 (0.34), residues: 238
  sheet: -1.16 (0.45), residues: 130
  loop : -2.03 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  73 
 TYR   0.011   0.001   TYR A 299 
 PHE   0.028   0.001   PHE A 197 
 TRP   0.003   0.001   TRP A  54 
 HIS   0.003   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6075)
  covalent geometry    : angle       0.51064 /  0.26 ( 8227)
  hydrogen bonds       : bond        0.03788 /  2.50 (  201)
  hydrogen bonds       : angle       4.48946 /  3.09 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8452 (ttm) cc_final: 0.8230 (ttm)
REVERT: A  444 LYS cc_start: 0.8433 (tttm) cc_final: 0.7965 (tptm)
REVERT: A  655 ASP cc_start: 0.8037 (p0) cc_final: 0.7558 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0694
  time to fit residues: 7.0608
Evaluate side-chains
  71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0370
   chunk 8 optimal weight:    0.0370
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.4142

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.104920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.079813 restraints weight = 9251.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.081986 restraints weight = 6123.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.083618 restraints weight = 4748.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.084295 restraints weight = 4027.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.085123 restraints weight = 3683.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6075  Z= 0.152
  Angle     :  0.523   5.787   8227  Z= 0.268
  Chirality :  0.043   0.157    915
  Planarity :  0.004   0.051   1071
  Dihedral  :  4.338  24.594    816
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.08 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.30), residues: 739
  helix:  0.40 (0.35), residues: 243
  sheet: -0.99 (0.44), residues: 129
  loop : -1.93 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  73 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.026   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A  54 
 HIS   0.004   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.15 ( 6075)
  covalent geometry    : angle       0.52281 /  0.27 ( 8227)
  hydrogen bonds       : bond        0.03972 /  2.63 (  201)
  hydrogen bonds       : angle       4.44277 /  3.07 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8479 (tttm) cc_final: 0.8085 (tptm)
REVERT: A  655 ASP cc_start: 0.8159 (p0) cc_final: 0.7648 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0667
  time to fit residues: 7.0272
Evaluate side-chains
  71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0050
   overall best weight:    0.6996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.083459 restraints weight = 9355.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.085729 restraints weight = 6243.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.087283 restraints weight = 4819.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.088047 restraints weight = 4086.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.088687 restraints weight = 3722.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6075  Z= 0.097
  Angle     :  0.486   6.336   8227  Z= 0.249
  Chirality :  0.042   0.164    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  4.054  23.206    816
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.61 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.31), residues: 739
  helix:  0.82 (0.36), residues: 238
  sheet: -1.10 (0.43), residues: 129
  loop : -1.51 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 746 
 PHE   0.030   0.001   PHE A 197 
 TRP   0.003   0.000   TRP A 131 
 HIS   0.002   0.000   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 6075)
  covalent geometry    : angle       0.48585 /  0.25 ( 8227)
  hydrogen bonds       : bond        0.03215 /  2.17 (  201)
  hydrogen bonds       : angle       4.20884 /  2.89 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8461 (tttm) cc_final: 0.8012 (tptm)
REVERT: A  655 ASP cc_start: 0.7990 (p0) cc_final: 0.7653 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0641
  time to fit residues: 6.4290
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.107525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.082806 restraints weight = 9234.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.084986 restraints weight = 6254.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.086422 restraints weight = 4897.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.087281 restraints weight = 4197.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.087858 restraints weight = 3817.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6075  Z= 0.148
  Angle     :  0.513   6.602   8227  Z= 0.262
  Chirality :  0.043   0.161    915
  Planarity :  0.004   0.051   1071
  Dihedral  :  4.153  23.658    816
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.91 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.31), residues: 739
  helix:  0.92 (0.36), residues: 239
  sheet: -0.97 (0.42), residues: 127
  loop : -1.55 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  73 
 TYR   0.011   0.001   TYR A 299 
 PHE   0.030   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A  54 
 HIS   0.003   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 6075)
  covalent geometry    : angle       0.51290 /  0.26 ( 8227)
  hydrogen bonds       : bond        0.03639 /  2.42 (  201)
  hydrogen bonds       : angle       4.30283 /  2.97 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8446 (tttm) cc_final: 0.8080 (tptm)
REVERT: A  655 ASP cc_start: 0.8073 (p0) cc_final: 0.7673 (t0)
REVERT: A  778 GLU cc_start: 0.7043 (pm20) cc_final: 0.6762 (pm20)
  outliers start: 16
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0711
  time to fit residues: 6.6576
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.109779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.085292 restraints weight = 9182.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.087555 restraints weight = 6127.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.089042 restraints weight = 4752.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.089958 restraints weight = 4048.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.090694 restraints weight = 3662.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.095
  Angle     :  0.484   7.134   8227  Z= 0.247
  Chirality :  0.042   0.166    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.939  22.088    816
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.68 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.31), residues: 739
  helix:  1.20 (0.36), residues: 233
  sheet: -0.94 (0.43), residues: 129
  loop : -1.23 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 746 
 PHE   0.032   0.001   PHE A 197 
 TRP   0.003   0.001   TRP A 776 
 HIS   0.001   0.000   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.10 ( 6075)
  covalent geometry    : angle       0.48382 /  0.25 ( 8227)
  hydrogen bonds       : bond        0.03036 /  2.02 (  201)
  hydrogen bonds       : angle       4.12831 /  2.84 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8458 (tttm) cc_final: 0.8082 (tptm)
REVERT: A  655 ASP cc_start: 0.7975 (p0) cc_final: 0.7668 (t0)
REVERT: A  778 GLU cc_start: 0.7095 (pm20) cc_final: 0.6884 (pm20)
  outliers start: 12
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0900
  time to fit residues: 8.1275
Evaluate side-chains
  66 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0870
   overall best weight:    0.7160

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.111035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.087034 restraints weight = 9100.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.089143 restraints weight = 6296.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.090419 restraints weight = 4986.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.091478 restraints weight = 4315.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.091699 restraints weight = 3909.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.098
  Angle     :  0.491   7.386   8227  Z= 0.248
  Chirality :  0.041   0.161    915
  Planarity :  0.004   0.051   1071
  Dihedral  :  3.861  21.764    816
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.44 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.31), residues: 739
  helix:  1.31 (0.36), residues: 233
  sheet: -0.71 (0.43), residues: 129
  loop : -1.13 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 299 
 PHE   0.032   0.001   PHE A 197 
 TRP   0.003   0.000   TRP A 776 
 HIS   0.002   0.000   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 ( 6075)
  covalent geometry    : angle       0.49050 /  0.25 ( 8227)
  hydrogen bonds       : bond        0.03041 /  2.03 (  201)
  hydrogen bonds       : angle       4.05875 /  2.78 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8438 (tttm) cc_final: 0.8086 (tptm)
REVERT: A  655 ASP cc_start: 0.7880 (p0) cc_final: 0.7603 (t0)
  outliers start: 12
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0876
  time to fit residues: 7.6710
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.1586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.106097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.082171 restraints weight = 9292.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.084020 restraints weight = 6546.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.085434 restraints weight = 5252.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.086192 restraints weight = 4545.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.086643 restraints weight = 4170.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6075  Z= 0.219
  Angle     :  0.582   7.860   8227  Z= 0.294
  Chirality :  0.045   0.148    915
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.363  23.160    816
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.60 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.31), residues: 739
  helix:  1.00 (0.35), residues: 238
  sheet: -0.78 (0.43), residues: 127
  loop : -1.37 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  73 
 TYR   0.014   0.002   TYR A 299 
 PHE   0.032   0.002   PHE A 197 
 TRP   0.006   0.001   TRP A  54 
 HIS   0.004   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00539 /  0.22 ( 6075)
  covalent geometry    : angle       0.58156 /  0.29 ( 8227)
  hydrogen bonds       : bond        0.04261 /  2.81 (  201)
  hydrogen bonds       : angle       4.47886 /  3.10 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8436 (tttm) cc_final: 0.8077 (tptm)
REVERT: A  655 ASP cc_start: 0.8048 (p0) cc_final: 0.7651 (t0)
  outliers start: 12
  outliers final: 12
  residues processed: 64
  average time/residue: 0.0821
  time to fit residues: 6.9686
Evaluate side-chains
  69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.107645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.083782 restraints weight = 9250.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.085813 restraints weight = 6466.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.087144 restraints weight = 5141.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.087925 restraints weight = 4453.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.088556 restraints weight = 4072.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6075  Z= 0.144
  Angle     :  0.532   7.816   8227  Z= 0.271
  Chirality :  0.043   0.147    915
  Planarity :  0.004   0.054   1071
  Dihedral  :  4.216  21.974    816
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.44 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.31), residues: 739
  helix:  1.14 (0.35), residues: 239
  sheet: -0.76 (0.43), residues: 127
  loop : -1.31 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  73 
 TYR   0.011   0.001   TYR A 299 
 PHE   0.033   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A  54 
 HIS   0.002   0.001   HIS A 808 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.14 ( 6075)
  covalent geometry    : angle       0.53188 /  0.27 ( 8227)
  hydrogen bonds       : bond        0.03589 /  2.39 (  201)
  hydrogen bonds       : angle       4.30541 /  2.96 (  570)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 LYS cc_start: 0.8435 (tttm) cc_final: 0.8121 (tptm)
REVERT: A  655 ASP cc_start: 0.7974 (p0) cc_final: 0.7626 (t0)
  outliers start: 13
  outliers final: 13
  residues processed: 66
  average time/residue: 0.0944
  time to fit residues: 8.1804
Evaluate side-chains
  68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
Chi-restraints excluded: chain A residue  652 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0670
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 467 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.110735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.086966 restraints weight = 9154.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.089053 restraints weight = 6338.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090458 restraints weight = 5015.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.091187 restraints weight = 4324.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.091833 restraints weight = 3960.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6075  Z= 0.091
  Angle     :  0.497   7.979   8227  Z= 0.252
  Chirality :  0.041   0.158    915
  Planarity :  0.004   0.052   1071
  Dihedral  :  3.868  20.766    816
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.90 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.31), residues: 739
  helix:  1.47 (0.36), residues: 233
  sheet: -0.80 (0.43), residues: 129
  loop : -1.01 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 470 
 TYR   0.008   0.001   TYR A 746 
 PHE   0.032   0.001   PHE A 197 
 TRP   0.003   0.000   TRP A 776 
 HIS   0.001   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00211 /  0.09 ( 6075)
  covalent geometry    : angle       0.49724 /  0.25 ( 8227)
  hydrogen bonds       : bond        0.02879 /  1.93 (  201)
  hydrogen bonds       : angle       4.05397 /  2.76 (  570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 977.90 seconds
wall clock time: 17 minutes 29.51 seconds (1049.51 seconds total)