Starting phenix.real_space_refine
on Sat Aug 23 08:20:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_28266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_28266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_28266.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_28266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8emv_28266/08_2025/8emv_28266.map"
  }
  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): 0.00s

  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: 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: 1.33, per 1000 atoms: 0.22
  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: 0.52
  Conformation dependent library (CDL) restraints added in 388.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.18
  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: 0.87

  Time building geometry restraints manager: 0.69 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:             1.290
  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:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.060
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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 aren 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
  covalent geometry    : bond        0.00705 ( 6075)
  covalent geometry    : angle       0.81279 ( 8227)
  hydrogen bonds       : bond        0.21576 (  201)
  hydrogen bonds       : angle       7.21270 (  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  : 0.249 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.8684 (tttt) cc_final: 0.8368 (tptp)
REVERT: A  291 MET cc_start: 0.8471 (ttm) cc_final: 0.8129 (ttm)
REVERT: A  413 GLU cc_start: 0.8411 (tt0) cc_final: 0.8192 (tt0)
REVERT: A  444 LYS cc_start: 0.8438 (tttm) cc_final: 0.8071 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1132
  time to fit residues: 11.1141
Evaluate side-chains
  57 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3215 r_free = 0.3215 target = 0.108767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.084453 restraints weight = 9207.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.086747 restraints weight = 6066.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.088341 restraints weight = 4665.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.089265 restraints weight = 3954.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.089795 restraints weight = 3579.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6075  Z= 0.125
  Angle     :  0.531   5.268   8227  Z= 0.280
  Chirality :  0.043   0.150    915
  Planarity :  0.005   0.045   1071
  Dihedral  :  4.745  26.296    816
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.24 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.66 (0.27), residues: 739
  helix: -0.96 (0.31), residues: 237
  sheet: -1.78 (0.41), residues: 130
  loop : -2.31 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   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   0.001   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6075)
  covalent geometry    : angle       0.53062 ( 8227)
  hydrogen bonds       : bond        0.04537 (  201)
  hydrogen bonds       : angle       4.98239 (  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
  81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  291 MET cc_start: 0.8528 (ttm) cc_final: 0.8253 (ttm)
REVERT: A  413 GLU cc_start: 0.8180 (tt0) cc_final: 0.7908 (tt0)
REVERT: A  444 LYS cc_start: 0.8456 (tttm) cc_final: 0.8068 (tptm)
REVERT: A  719 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: A  772 PHE cc_start: 0.7935 (t80) cc_final: 0.7718 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0960
  time to fit residues: 9.6717
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  : 0.263 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 15 optimal weight:    0.2980
   chunk 64 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3179 r_free = 0.3179 target = 0.106149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.081674 restraints weight = 9252.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.083735 restraints weight = 6194.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.085315 restraints weight = 4847.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.086225 restraints weight = 4137.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.086899 restraints weight = 3751.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6075  Z= 0.193
  Angle     :  0.565   6.099   8227  Z= 0.290
  Chirality :  0.044   0.162    915
  Planarity :  0.005   0.052   1071
  Dihedral  :  4.657  25.730    816
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.39 %
    Favored  : 85.93 %
  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: -1.97 (0.29), residues: 739
  helix: -0.09 (0.34), residues: 243
  sheet: -1.22 (0.44), residues: 130
  loop : -2.22 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  73 
 TYR   0.015   0.001   TYR A 299 
 PHE   0.025   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
  covalent geometry    : bond        0.00470 ( 6075)
  covalent geometry    : angle       0.56485 ( 8227)
  hydrogen bonds       : bond        0.04593 (  201)
  hydrogen bonds       : angle       4.75328 (  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
  76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8502 (ttm) cc_final: 0.8254 (ttm)
REVERT: A  413 GLU cc_start: 0.8116 (tt0) cc_final: 0.7866 (tt0)
REVERT: A  444 LYS cc_start: 0.8425 (tttm) cc_final: 0.7981 (tptm)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0915
  time to fit residues: 8.4143
Evaluate side-chains
  67 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  468 LYS
Chi-restraints excluded: chain A residue  614 CYS
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:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 166 GLN
A 379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.106464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.082060 restraints weight = 9273.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.084236 restraints weight = 6264.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.085679 restraints weight = 4890.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.086541 restraints weight = 4180.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.087187 restraints weight = 3793.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6075  Z= 0.237
  Angle     :  0.590   5.956   8227  Z= 0.302
  Chirality :  0.045   0.156    915
  Planarity :  0.005   0.054   1071
  Dihedral  :  4.745  25.507    816
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.76 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.30), residues: 739
  helix:  0.15 (0.34), residues: 244
  sheet: -1.19 (0.43), residues: 130
  loop : -2.08 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  73 
 TYR   0.014   0.002   TYR A 299 
 PHE   0.025   0.002   PHE A 197 
 TRP   0.007   0.001   TRP A  54 
 HIS   0.006   0.001   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 6075)
  covalent geometry    : angle       0.58977 ( 8227)
  hydrogen bonds       : bond        0.04749 (  201)
  hydrogen bonds       : angle       4.79613 (  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
  80 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8714 (tttt) cc_final: 0.8227 (tptp)
REVERT: A  291 MET cc_start: 0.8503 (ttm) cc_final: 0.8279 (ttm)
REVERT: A  413 GLU cc_start: 0.8078 (tt0) cc_final: 0.7876 (tt0)
  outliers start: 16
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0784
  time to fit residues: 7.6399
Evaluate side-chains
  69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  330 SER
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
Chi-restraints excluded: chain A residue  811 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0570
   chunk 68 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.107837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.083220 restraints weight = 9379.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.085291 restraints weight = 6204.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.086868 restraints weight = 4855.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.087749 restraints weight = 4134.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.088257 restraints weight = 3749.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1816

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= 0.101
  Angle     :  0.504   6.402   8227  Z= 0.257
  Chirality :  0.042   0.164    915
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.261  23.287    816
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.83 %
    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 aren not related in a simple way.
  whole: -1.17 (0.31), residues: 739
  helix:  0.64 (0.36), residues: 239
  sheet: -0.97 (0.43), residues: 129
  loop : -1.67 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A 299 
 PHE   0.030   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A 776 
 HIS   0.001   0.000   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6075)
  covalent geometry    : angle       0.50392 ( 8227)
  hydrogen bonds       : bond        0.03338 (  201)
  hydrogen bonds       : angle       4.35097 (  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
  85 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8474 (ttm) cc_final: 0.8238 (ttm)
REVERT: A  315 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7769 (tt)
REVERT: A  444 LYS cc_start: 0.8472 (tttm) cc_final: 0.8084 (tptm)
REVERT: A  655 ASP cc_start: 0.8072 (p0) cc_final: 0.7569 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0701
  time to fit residues: 7.5367
Evaluate side-chains
  70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  315 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  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:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0000
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.7590

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 254 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.106530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.082610 restraints weight = 9253.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.084464 restraints weight = 6517.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.085846 restraints weight = 5253.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.086646 restraints weight = 4549.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.086844 restraints weight = 4158.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6075  Z= 0.183
  Angle     :  0.552   6.378   8227  Z= 0.281
  Chirality :  0.044   0.157    915
  Planarity :  0.004   0.054   1071
  Dihedral  :  4.417  24.300    816
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.22 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.30), residues: 739
  helix:  0.62 (0.35), residues: 244
  sheet: -0.94 (0.43), residues: 129
  loop : -1.73 (0.31), residues: 366

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   0.029   0.002   PHE A 197 
 TRP   0.005   0.001   TRP A  54 
 HIS   0.003   0.001   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 6075)
  covalent geometry    : angle       0.55209 ( 8227)
  hydrogen bonds       : bond        0.04116 (  201)
  hydrogen bonds       : angle       4.50335 (  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
  77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8459 (ttm) cc_final: 0.8212 (ttm)
REVERT: A  413 GLU cc_start: 0.8035 (tt0) cc_final: 0.7820 (tt0)
REVERT: A  655 ASP cc_start: 0.8063 (p0) cc_final: 0.7580 (t0)
REVERT: A  808 HIS cc_start: 0.9501 (OUTLIER) cc_final: 0.8785 (p-80)
  outliers start: 19
  outliers final: 13
  residues processed: 70
  average time/residue: 0.0604
  time to fit residues: 5.7649
Evaluate side-chains
  72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   39 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  425 MET
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  808 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.086400 restraints weight = 9218.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.088473 restraints weight = 6379.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.089879 restraints weight = 5053.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.090573 restraints weight = 4354.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.091312 restraints weight = 3996.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2019

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= 0.095
  Angle     :  0.501   7.244   8227  Z= 0.253
  Chirality :  0.042   0.166    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  4.047  22.380    816
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.29 %
    Favored  : 82.42 %
  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: -0.73 (0.31), residues: 739
  helix:  0.98 (0.36), residues: 239
  sheet: -0.82 (0.44), residues: 131
  loop : -1.34 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   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 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6075)
  covalent geometry    : angle       0.50114 ( 8227)
  hydrogen bonds       : bond        0.03039 (  201)
  hydrogen bonds       : angle       4.17455 (  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
  82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8458 (ttm) cc_final: 0.8245 (ttm)
REVERT: A  413 GLU cc_start: 0.8083 (tt0) cc_final: 0.7840 (tt0)
REVERT: A  444 LYS cc_start: 0.8433 (tttm) cc_final: 0.8065 (tptm)
REVERT: A  655 ASP cc_start: 0.7954 (p0) cc_final: 0.7598 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 77
  average time/residue: 0.0790
  time to fit residues: 8.0147
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  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
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  362 GLU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  425 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0020
   chunk 70 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6990

-------------------------------------------------------------------------------
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 = 0.3203 r_free = 0.3203 target = 0.107668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.083208 restraints weight = 9132.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.085450 restraints weight = 6130.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.086920 restraints weight = 4761.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.087791 restraints weight = 4064.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.088265 restraints weight = 3681.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2098

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= 0.100
  Angle     :  0.499   7.436   8227  Z= 0.252
  Chirality :  0.042   0.158    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.960  21.956    816
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.44 %
    Favored  : 82.11 %
  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: -0.55 (0.31), residues: 739
  helix:  1.09 (0.36), residues: 239
  sheet: -0.82 (0.43), residues: 129
  loop : -1.16 (0.32), residues: 371

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   0.004   0.001   TRP A 776 
 HIS   0.001   0.000   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6075)
  covalent geometry    : angle       0.49877 ( 8227)
  hydrogen bonds       : bond        0.03070 (  201)
  hydrogen bonds       : angle       4.13006 (  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
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 GLU cc_start: 0.8031 (tt0) cc_final: 0.7778 (tt0)
REVERT: A  444 LYS cc_start: 0.8454 (tttm) cc_final: 0.8119 (tptm)
REVERT: A  655 ASP cc_start: 0.7999 (p0) cc_final: 0.7610 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0777
  time to fit residues: 7.4516
Evaluate side-chains
  74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
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  362 GLU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  425 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 67 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 49 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 46 optimal weight:    7.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3253 r_free = 0.3253 target = 0.111026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.084811 restraints weight = 9275.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.087749 restraints weight = 5377.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.089712 restraints weight = 3847.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.090908 restraints weight = 3130.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.091715 restraints weight = 2758.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2304

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= 0.083
  Angle     :  0.482   7.961   8227  Z= 0.243
  Chirality :  0.041   0.163    915
  Planarity :  0.004   0.050   1071
  Dihedral  :  3.730  21.011    816
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.06 %
    Favored  : 82.42 %
  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: -0.34 (0.32), residues: 739
  helix:  1.25 (0.36), residues: 239
  sheet: -0.78 (0.43), residues: 129
  loop : -0.98 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.007   0.001   TYR A  53 
 PHE   0.032   0.001   PHE A 197 
 TRP   0.004   0.000   TRP A 776 
 HIS   0.001   0.000   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00187 ( 6075)
  covalent geometry    : angle       0.48210 ( 8227)
  hydrogen bonds       : bond        0.02701 (  201)
  hydrogen bonds       : angle       3.97747 (  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
  79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8413 (ttm) cc_final: 0.7964 (tpp)
REVERT: A  413 GLU cc_start: 0.7995 (tt0) cc_final: 0.7708 (tt0)
REVERT: A  444 LYS cc_start: 0.8477 (tttm) cc_final: 0.8120 (tptm)
REVERT: A  655 ASP cc_start: 0.7996 (p0) cc_final: 0.7652 (t0)
REVERT: A  772 PHE cc_start: 0.7230 (t80) cc_final: 0.7018 (t80)
  outliers start: 10
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0810
  time to fit residues: 8.0206
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  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  362 GLU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  451 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0670
   chunk 22 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.9920

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.109726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.086062 restraints weight = 9204.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.088137 restraints weight = 6388.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.089404 restraints weight = 5053.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.090348 restraints weight = 4376.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.090984 restraints weight = 3970.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6075  Z= 0.119
  Angle     :  0.509   7.790   8227  Z= 0.259
  Chirality :  0.042   0.153    915
  Planarity :  0.004   0.049   1071
  Dihedral  :  3.878  21.556    816
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.44 %
    Favored  : 82.11 %
  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: -0.32 (0.31), residues: 739
  helix:  1.26 (0.36), residues: 239
  sheet: -0.75 (0.43), residues: 129
  loop : -0.98 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.011   0.001   TYR A 299 
 PHE   0.032   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A 776 
 HIS   0.002   0.001   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6075)
  covalent geometry    : angle       0.50868 ( 8227)
  hydrogen bonds       : bond        0.03214 (  201)
  hydrogen bonds       : angle       4.08965 (  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
  76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 GLU cc_start: 0.7972 (tt0) cc_final: 0.7719 (tt0)
REVERT: A  444 LYS cc_start: 0.8457 (tttm) cc_final: 0.8158 (tptm)
REVERT: A  655 ASP cc_start: 0.7982 (p0) cc_final: 0.7629 (t0)
REVERT: A  808 HIS cc_start: 0.9483 (OUTLIER) cc_final: 0.8892 (p-80)
  outliers start: 16
  outliers final: 13
  residues processed: 71
  average time/residue: 0.0954
  time to fit residues: 8.9145
Evaluate side-chains
  74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  362 GLU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  468 LYS
Chi-restraints excluded: chain A residue  617 MET
Chi-restraints excluded: chain A residue  652 THR
Chi-restraints excluded: chain A residue  808 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0770
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6540

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.111242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.087596 restraints weight = 9127.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.089572 restraints weight = 6305.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.091047 restraints weight = 5015.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.091779 restraints weight = 4314.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.092459 restraints weight = 3949.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2316

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= 0.095
  Angle     :  0.496   7.932   8227  Z= 0.251
  Chirality :  0.041   0.150    915
  Planarity :  0.004   0.049   1071
  Dihedral  :  3.787  20.773    816
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.51 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.32), residues: 739
  helix:  1.36 (0.35), residues: 239
  sheet: -0.72 (0.43), residues: 129
  loop : -0.91 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.008   0.001   TYR A  53 
 PHE   0.028   0.001   PHE A 197 
 TRP   0.004   0.000   TRP A 776 
 HIS   0.001   0.000   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6075)
  covalent geometry    : angle       0.49566 ( 8227)
  hydrogen bonds       : bond        0.02942 (  201)
  hydrogen bonds       : angle       4.02212 (  570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 965.54 seconds
wall clock time: 17 minutes 19.45 seconds (1039.45 seconds total)