Starting phenix.real_space_refine
on Sat Apr  4 23:29:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dqk_27655/04_2026/8dqk_27655.map"
  }
  resolution = 4.0
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    3844      2.51       5
     N    1002      2.21       5
     O    1024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5891
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5891
          Classifications: {'peptide': 733}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 691}
          Chain breaks: 3
  Time building chain proxies: 1.26, per 1000 atoms: 0.21
  Number of scatterers: 5891
  At special positions: 0
  Unit cell: (83.83, 84.66, 107.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O    1024      8.00
     N    1002      7.00
     C    3844      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: 0.48
  Conformation dependent library (CDL) restraints added in 320.6 milliseconds
  

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      60.7% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 129
      Proline residue:  A 107  - end of helix
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 169 through 176
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.548A  pdb=" N   THR A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 257
      removed outlier: 4.087A  pdb=" N   THR A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   LEU A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
      Proline residue:  A 251  - end of helix
    Processing helix  chain 'A' and resid 262 through 268
    Processing helix  chain 'A' and resid 279 through 302
    Processing helix  chain 'A' and resid 302 through 316
    Processing helix  chain 'A' and resid 405 through 422
      removed outlier: 3.720A  pdb=" N   LEU A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 4.485A  pdb=" N   PHE A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 579 through 585
      removed outlier: 3.590A  pdb=" N   ALA A 583 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 592
      removed outlier: 4.054A  pdb=" N   ALA A 590 " --> pdb=" O   SER A 587 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 592 " --> pdb=" O   TYR A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 610
    Processing helix  chain 'A' and resid 611 through 616
      removed outlier: 3.912A  pdb=" N   PHE A 614 " --> pdb=" O   ALA A 611 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A 616 " --> pdb=" O   ALA A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 643
      removed outlier: 4.219A  pdb=" N   VAL A 636 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 686
    Processing helix  chain 'A' and resid 689 through 693
    Processing helix  chain 'A' and resid 698 through 711
    Processing helix  chain 'A' and resid 713 through 732
      removed outlier: 4.366A  pdb=" N   PHE A 717 " --> pdb=" O   PHE A 713 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   PHE A 720 " --> pdb=" O   ILE A 716 " (cutoff:3.500A)
      Proline residue:  A 725  - end of helix
    Processing helix  chain 'A' and resid 740 through 765
    Processing helix  chain 'A' and resid 768 through 800
      removed outlier: 4.159A  pdb=" N   TYR A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LEU A 788 " --> pdb=" O   CYS A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.666A  pdb=" N   VAL A 827 " --> pdb=" O   ASP A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 833
      No H-bonds generated for 'chain 'A' and resid 831 through 833'
    Processing helix  chain 'A' and resid 834 through 857
      removed outlier: 4.041A  pdb=" N   ILE A 838 " --> pdb=" O   MET A 834 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE A 839 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE A 840 " --> pdb=" O   THR A 836 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN A 844 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 849 " --> pdb=" O   ILE A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 867
    Processing helix  chain 'A' and resid 868 through 889
      Proline residue:  A 882  - end of helix
      removed outlier: 4.404A  pdb=" N   LEU A 888 " --> pdb=" O   ALA A 884 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY A 889 " --> pdb=" O   LYS A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 893
    Processing helix  chain 'A' and resid 894 through 916
      removed outlier: 4.618A  pdb=" N   VAL A 898 " --> pdb=" O   THR A 894 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL A 900 " --> pdb=" O   VAL A 896 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 99
    Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 360
      removed outlier: 6.507A  pdb=" N   LEU A 391 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   VAL A 392 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   CYS A 224 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL A 394 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   ASP A 189 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LEU A 430 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   CYS A 503 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ALA A 458 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ARG A 649 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   VAL A 460 " --> pdb=" O   ARG A 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436
      removed outlier: 6.404A  pdb=" N   ARG A 465 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1858
        1.34 -     1.46: 1547
        1.46 -     1.58: 2631
        1.58 -     1.70: 0
        1.70 -     1.81: 33
  Bond restraints: 6069
  Sorted by residual:
  bond pdb=" CA  ARG A 348 "
       pdb=" CB  ARG A 348 "
    ideal  model  delta    sigma   weight residual
    1.529  1.560 -0.031 1.66e-02 3.63e+03 3.57e+00
  bond pdb=" CB  GLU A 668 "
       pdb=" CG  GLU A 668 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.61e+00
  bond pdb=" N   LYS A 406 "
       pdb=" CA  LYS A 406 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.019 1.29e-02 6.01e+03 2.19e+00
  bond pdb=" C   TYR A 881 "
       pdb=" N   PRO A 882 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  bond pdb=" CB  ASN A 161 "
       pdb=" CG  ASN A 161 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.88e-01
  ... (remaining 6064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 8016
        1.80 -     3.61: 208
        3.61 -     5.41: 42
        5.41 -     7.21: 11
        7.21 -     9.01: 2
  Bond angle restraints: 8279
  Sorted by residual:
  angle pdb=" N   VAL A 866 "
        pdb=" CA  VAL A 866 "
        pdb=" C   VAL A 866 "
      ideal   model   delta    sigma   weight residual
     112.83  106.74    6.09 9.90e-01 1.02e+00 3.78e+01
  angle pdb=" C   ILE A 664 "
        pdb=" N   ASN A 665 "
        pdb=" CA  ASN A 665 "
      ideal   model   delta    sigma   weight residual
     121.54  128.24   -6.70 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" N   GLN A 279 "
        pdb=" CA  GLN A 279 "
        pdb=" C   GLN A 279 "
      ideal   model   delta    sigma   weight residual
     112.12  108.00    4.12 1.34e+00 5.57e-01 9.47e+00
  angle pdb=" CA  ARG A 675 "
        pdb=" CB  ARG A 675 "
        pdb=" CG  ARG A 675 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.63e+00
  angle pdb=" C   VAL A 609 "
        pdb=" CA  VAL A 609 "
        pdb=" CB  VAL A 609 "
      ideal   model   delta    sigma   weight residual
     111.88  107.99    3.89 1.37e+00 5.33e-01 8.05e+00
  ... (remaining 8274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3222
       17.97 -    35.93: 253
       35.93 -    53.90: 25
       53.90 -    71.86: 7
       71.86 -    89.83: 3
  Dihedral angle restraints: 3510
    sinusoidal: 1379
      harmonic: 2131
  Sorted by residual:
  dihedral pdb=" CA  TRP A 863 "
           pdb=" C   TRP A 863 "
           pdb=" N   LEU A 864 "
           pdb=" CA  LEU A 864 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.85  -28.15     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  GLN A 405 "
           pdb=" C   GLN A 405 "
           pdb=" N   LYS A 406 "
           pdb=" CA  LYS A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ILE A 841 "
           pdb=" C   ILE A 841 "
           pdb=" N   PHE A 842 "
           pdb=" CA  PHE A 842 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.17  -16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 3507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 663
       0.044 -    0.088: 188
       0.088 -    0.132: 55
       0.132 -    0.176: 8
       0.176 -    0.220: 3
  Chirality restraints: 917
  Sorted by residual:
  chirality pdb=" CB  ILE A 427 "
            pdb=" CA  ILE A 427 "
            pdb=" CG1 ILE A 427 "
            pdb=" CG2 ILE A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASN A 665 "
            pdb=" N   ASN A 665 "
            pdb=" C   ASN A 665 "
            pdb=" CB  ASN A 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CB  ILE A 624 "
            pdb=" CA  ILE A 624 "
            pdb=" CG1 ILE A 624 "
            pdb=" CG2 ILE A 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 914 not shown)

  Planarity restraints: 1043
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 217 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO A 218 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 166 "    0.033 5.00e-02 4.00e+02   5.06e-02 4.10e+00
        pdb=" N   PRO A 167 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 167 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 167 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 779 "   -0.012 2.00e-02 2.50e+03   1.09e-02 2.97e+00
        pdb=" CG  TRP A 779 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 779 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 779 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 779 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 779 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 779 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1040 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 100
        2.69 -     3.24: 6008
        3.24 -     3.79: 9288
        3.79 -     4.35: 11698
        4.35 -     4.90: 18853
  Nonbonded interactions: 45947
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 361 "
            pdb=" N   HIS A 362 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" NE2 GLN A 777 "
            pdb=" O   PHE A 878 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" O   ALA A 606 "
            pdb=" OG1 THR A 610 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" N   ILE A 664 "
            pdb=" OE2 GLU A 668 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   ALA A 240 "
            pdb=" OG  SER A 243 "
     model   vdw
     2.318 3.040
  ... (remaining 45942 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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.960
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5812
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6069  Z= 0.144
  Angle     :  0.720   9.014   8279  Z= 0.398
  Chirality :  0.045   0.220    917
  Planarity :  0.005   0.052   1043
  Dihedral  : 12.564  89.826   2136
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.62 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.14 (0.32), residues: 725
  helix:  0.74 (0.27), residues: 392
  sheet: -0.64 (0.58), residues: 72
  loop : -0.53 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 399 
 TYR   0.029   0.002   TYR A 696 
 PHE   0.022   0.002   PHE A 773 
 TRP   0.030   0.002   TRP A 779 
 HIS   0.005   0.001   HIS A 879 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6069)
  covalent geometry    : angle       0.72047 ( 8279)
  hydrogen bonds       : bond        0.09896 (  312)
  hydrogen bonds       : angle       4.22912 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4370 (tpp) cc_final: 0.4125 (tpp)
REVERT: A  308 LYS cc_start: 0.8552 (pptt) cc_final: 0.8210 (pptt)
REVERT: A  493 MET cc_start: 0.4007 (ppp) cc_final: 0.2897 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0696
  time to fit residues: 7.5960
Evaluate side-chains
  49 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0050
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0370
   overall best weight:    1.3476

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN
A 352 HIS
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.095258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.086900 restraints weight = 38761.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.088248 restraints weight = 27608.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.089207 restraints weight = 21005.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.089981 restraints weight = 16660.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.090589 restraints weight = 13686.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6069  Z= 0.123
  Angle     :  0.597   6.351   8279  Z= 0.303
  Chirality :  0.043   0.208    917
  Planarity :  0.005   0.053   1043
  Dihedral  :  4.140  25.166    802
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.62 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  5.88 %
    Favored  : 92.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.32), residues: 725
  helix:  0.92 (0.27), residues: 391
  sheet: -0.01 (0.64), residues: 61
  loop : -0.48 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 774 
 TYR   0.013   0.002   TYR A 696 
 PHE   0.016   0.002   PHE A 658 
 TRP   0.019   0.001   TRP A 779 
 HIS   0.003   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6069)
  covalent geometry    : angle       0.59653 ( 8279)
  hydrogen bonds       : bond        0.03475 (  312)
  hydrogen bonds       : angle       4.06015 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 ILE cc_start: 0.9250 (pt) cc_final: 0.8835 (mt)
REVERT: A  493 MET cc_start: 0.4643 (ppp) cc_final: 0.4295 (ppp)
REVERT: A  670 LEU cc_start: 0.7941 (mt) cc_final: 0.7403 (pp)
REVERT: A  773 PHE cc_start: 0.7916 (t80) cc_final: 0.7470 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0750
  time to fit residues: 6.5534
Evaluate side-chains
  56 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  314 TYR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    0.4980
   chunk 57 optimal weight:    0.1980
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 879 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.084607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.076645 restraints weight = 38473.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.077859 restraints weight = 27620.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.078695 restraints weight = 21091.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.079283 restraints weight = 16926.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.079764 restraints weight = 14288.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6069  Z= 0.224
  Angle     :  0.718   8.742   8279  Z= 0.380
  Chirality :  0.045   0.149    917
  Planarity :  0.007   0.100   1043
  Dihedral  :  4.733  21.966    802
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.90 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.90 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.25 (0.31), residues: 725
  helix:  0.31 (0.26), residues: 389
  sheet:  0.09 (0.65), residues: 69
  loop : -0.79 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 175 
 TYR   0.035   0.003   TYR A 266 
 PHE   0.021   0.003   PHE A 267 
 TRP   0.029   0.003   TRP A 779 
 HIS   0.012   0.002   HIS A 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 6069)
  covalent geometry    : angle       0.71774 ( 8279)
  hydrogen bonds       : bond        0.04292 (  312)
  hydrogen bonds       : angle       4.66829 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4554 (tpp) cc_final: 0.4197 (tpp)
  outliers start: 14
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0803
  time to fit residues: 6.9115
Evaluate side-chains
  47 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 402 HIS
** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.084975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.077017 restraints weight = 39706.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.078175 restraints weight = 28781.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.079051 restraints weight = 21915.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.079693 restraints weight = 17658.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.080182 restraints weight = 14851.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6069  Z= 0.141
  Angle     :  0.606   7.065   8279  Z= 0.311
  Chirality :  0.042   0.167    917
  Planarity :  0.005   0.049   1043
  Dihedral  :  4.401  19.744    802
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.40 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.19 (0.32), residues: 725
  helix:  0.73 (0.26), residues: 383
  sheet:  0.31 (0.67), residues: 67
  loop : -0.66 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 366 
 TYR   0.020   0.002   TYR A 881 
 PHE   0.021   0.002   PHE A 717 
 TRP   0.019   0.002   TRP A 764 
 HIS   0.013   0.002   HIS A 642 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6069)
  covalent geometry    : angle       0.60602 ( 8279)
  hydrogen bonds       : bond        0.03632 (  312)
  hydrogen bonds       : angle       4.39269 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  135 MET cc_start: 0.4449 (tpp) cc_final: 0.4148 (tpp)
REVERT: A  442 LEU cc_start: 0.8528 (pt) cc_final: 0.8106 (tt)
REVERT: A  773 PHE cc_start: 0.7853 (t80) cc_final: 0.7182 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0746
  time to fit residues: 5.6754
Evaluate side-chains
  47 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  880 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 27 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 478 HIS
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.077799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.069792 restraints weight = 39482.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.071017 restraints weight = 27676.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.071852 restraints weight = 20982.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.072499 restraints weight = 16841.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.072988 restraints weight = 14021.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.6154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   6069  Z= 0.248
  Angle     :  0.766  10.811   8279  Z= 0.398
  Chirality :  0.047   0.170    917
  Planarity :  0.006   0.050   1043
  Dihedral  :  5.098  22.248    802
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.83 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.04 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.33 (0.31), residues: 725
  helix:  0.31 (0.26), residues: 390
  sheet:  0.73 (0.71), residues: 59
  loop : -1.11 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 175 
 TYR   0.023   0.003   TYR A 393 
 PHE   0.040   0.002   PHE A 614 
 TRP   0.037   0.003   TRP A 329 
 HIS   0.013   0.002   HIS A 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 6069)
  covalent geometry    : angle       0.76588 ( 8279)
  hydrogen bonds       : bond        0.04471 (  312)
  hydrogen bonds       : angle       5.05563 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4673 (tpp) cc_final: 0.4314 (tpp)
REVERT: A  193 THR cc_start: 0.9102 (m) cc_final: 0.8899 (p)
REVERT: A  264 GLU cc_start: 0.8251 (pt0) cc_final: 0.7984 (pt0)
REVERT: A  683 ILE cc_start: 0.9009 (pt) cc_final: 0.8763 (pt)
REVERT: A  773 PHE cc_start: 0.8115 (t80) cc_final: 0.7519 (t80)
REVERT: A  826 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6659 (m-80)
REVERT: A  834 MET cc_start: 0.8059 (ppp) cc_final: 0.7795 (ppp)
  outliers start: 22
  outliers final: 14
  residues processed: 73
  average time/residue: 0.0903
  time to fit residues: 8.5414
Evaluate side-chains
  58 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  900 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0670
   chunk 52 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9722

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 346 ASN
A 461 GLN
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.079506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.071737 restraints weight = 39326.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.072950 restraints weight = 27550.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.073749 restraints weight = 20796.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.074372 restraints weight = 16842.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.074826 restraints weight = 14060.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.6289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6069  Z= 0.152
  Angle     :  0.639   8.946   8279  Z= 0.327
  Chirality :  0.043   0.138    917
  Planarity :  0.005   0.046   1043
  Dihedral  :  4.646  18.514    802
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.14 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.58 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.02 (0.32), residues: 725
  helix:  0.68 (0.27), residues: 389
  sheet:  0.56 (0.73), residues: 55
  loop : -1.05 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 366 
 TYR   0.012   0.001   TYR A 881 
 PHE   0.032   0.002   PHE A 614 
 TRP   0.020   0.002   TRP A 764 
 HIS   0.008   0.001   HIS A 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6069)
  covalent geometry    : angle       0.63904 ( 8279)
  hydrogen bonds       : bond        0.03763 (  312)
  hydrogen bonds       : angle       4.67114 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  135 MET cc_start: 0.4699 (tpp) cc_final: 0.4454 (tpp)
REVERT: A  264 GLU cc_start: 0.8242 (pt0) cc_final: 0.8027 (pt0)
REVERT: A  773 PHE cc_start: 0.8013 (t80) cc_final: 0.7364 (t80)
REVERT: A  826 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6212 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0792
  time to fit residues: 7.0485
Evaluate side-chains
  60 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.079530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.071728 restraints weight = 39538.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.072973 restraints weight = 27425.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.073757 restraints weight = 20633.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.074400 restraints weight = 16643.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.074895 restraints weight = 13790.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.6471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6069  Z= 0.143
  Angle     :  0.644   8.683   8279  Z= 0.326
  Chirality :  0.042   0.146    917
  Planarity :  0.005   0.046   1043
  Dihedral  :  4.528  17.482    802
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.33 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.02 (0.32), residues: 725
  helix:  0.70 (0.27), residues: 389
  sheet:  0.47 (0.72), residues: 55
  loop : -0.98 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 288 
 TYR   0.012   0.002   TYR A 293 
 PHE   0.027   0.001   PHE A 614 
 TRP   0.020   0.002   TRP A 764 
 HIS   0.006   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6069)
  covalent geometry    : angle       0.64408 ( 8279)
  hydrogen bonds       : bond        0.03585 (  312)
  hydrogen bonds       : angle       4.60067 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.4664 (tpp) cc_final: 0.4394 (tpp)
REVERT: A  264 GLU cc_start: 0.8319 (pt0) cc_final: 0.8040 (pt0)
REVERT: A  641 MET cc_start: 0.8574 (tmm) cc_final: 0.7829 (tmm)
REVERT: A  773 PHE cc_start: 0.8003 (t80) cc_final: 0.7363 (t80)
REVERT: A  826 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6034 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 56
  average time/residue: 0.0705
  time to fit residues: 5.4653
Evaluate side-chains
  56 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0070
   overall best weight:    1.5604

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.079814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.071998 restraints weight = 38423.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.073249 restraints weight = 27373.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.074070 restraints weight = 20606.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.074693 restraints weight = 16396.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.075132 restraints weight = 13659.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.6702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6069  Z= 0.127
  Angle     :  0.622   8.764   8279  Z= 0.312
  Chirality :  0.042   0.140    917
  Planarity :  0.005   0.048   1043
  Dihedral  :  4.364  16.938    802
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.72 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.44 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.27 (0.32), residues: 725
  helix:  0.96 (0.27), residues: 382
  sheet:  0.36 (0.71), residues: 55
  loop : -0.88 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 640 
 TYR   0.014   0.001   TYR A 274 
 PHE   0.020   0.001   PHE A 614 
 TRP   0.022   0.002   TRP A 764 
 HIS   0.006   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6069)
  covalent geometry    : angle       0.62204 ( 8279)
  hydrogen bonds       : bond        0.03380 (  312)
  hydrogen bonds       : angle       4.44505 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 GLU cc_start: 0.8370 (pt0) cc_final: 0.7979 (pt0)
REVERT: A  390 MET cc_start: 0.6717 (mmp) cc_final: 0.6404 (mmp)
REVERT: A  442 LEU cc_start: 0.8548 (pt) cc_final: 0.8095 (tt)
REVERT: A  668 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7379 (pm20)
REVERT: A  773 PHE cc_start: 0.7978 (t80) cc_final: 0.7362 (t80)
REVERT: A  826 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5887 (m-80)
REVERT: A  834 MET cc_start: 0.7846 (ppp) cc_final: 0.7324 (ppp)
  outliers start: 16
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0775
  time to fit residues: 6.8711
Evaluate side-chains
  61 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  346 ASN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0050
   chunk 69 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.2198

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.079774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.071958 restraints weight = 39008.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.073191 restraints weight = 27305.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.074010 restraints weight = 20554.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.074647 restraints weight = 16497.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.075102 restraints weight = 13726.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.6783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6069  Z= 0.123
  Angle     :  0.627   8.876   8279  Z= 0.314
  Chirality :  0.042   0.154    917
  Planarity :  0.005   0.047   1043
  Dihedral  :  4.291  16.275    802
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.71 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.27 (0.32), residues: 725
  helix:  0.94 (0.27), residues: 382
  sheet:  0.21 (0.70), residues: 57
  loop : -0.79 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 640 
 TYR   0.010   0.001   TYR A 881 
 PHE   0.017   0.001   PHE A 614 
 TRP   0.020   0.002   TRP A 764 
 HIS   0.005   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6069)
  covalent geometry    : angle       0.62669 ( 8279)
  hydrogen bonds       : bond        0.03357 (  312)
  hydrogen bonds       : angle       4.46858 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 GLU cc_start: 0.8482 (pt0) cc_final: 0.8039 (pt0)
REVERT: A  390 MET cc_start: 0.6917 (mmp) cc_final: 0.6588 (mmp)
REVERT: A  442 LEU cc_start: 0.8597 (pt) cc_final: 0.8103 (tt)
REVERT: A  668 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7414 (pm20)
REVERT: A  773 PHE cc_start: 0.8011 (t80) cc_final: 0.7407 (t80)
REVERT: A  826 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.6034 (m-80)
REVERT: A  834 MET cc_start: 0.7817 (ppp) cc_final: 0.7356 (ppp)
REVERT: A  864 LEU cc_start: 0.1752 (OUTLIER) cc_final: 0.1195 (tt)
  outliers start: 12
  outliers final: 8
  residues processed: 58
  average time/residue: 0.0617
  time to fit residues: 5.0585
Evaluate side-chains
  59 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  826 TYR
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0010
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0970
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.080246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.072497 restraints weight = 39149.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.073697 restraints weight = 27388.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.074524 restraints weight = 20423.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.075119 restraints weight = 16312.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.075577 restraints weight = 13700.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.6901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6069  Z= 0.119
  Angle     :  0.628   9.172   8279  Z= 0.314
  Chirality :  0.042   0.154    917
  Planarity :  0.005   0.047   1043
  Dihedral  :  4.198  16.014    802
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.86 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 20.51 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.37 (0.32), residues: 725
  helix:  0.98 (0.27), residues: 382
  sheet:  0.15 (0.70), residues: 58
  loop : -0.67 (0.39), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 640 
 TYR   0.013   0.001   TYR A 274 
 PHE   0.014   0.001   PHE A 614 
 TRP   0.022   0.001   TRP A 764 
 HIS   0.005   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6069)
  covalent geometry    : angle       0.62755 ( 8279)
  hydrogen bonds       : bond        0.03264 (  312)
  hydrogen bonds       : angle       4.40413 (  903)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 GLU cc_start: 0.8426 (pt0) cc_final: 0.7977 (pt0)
REVERT: A  442 LEU cc_start: 0.8582 (pt) cc_final: 0.8083 (tt)
REVERT: A  668 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7412 (pm20)
REVERT: A  773 PHE cc_start: 0.7970 (t80) cc_final: 0.7373 (t80)
REVERT: A  834 MET cc_start: 0.7806 (ppp) cc_final: 0.7410 (ppp)
REVERT: A  864 LEU cc_start: 0.1862 (OUTLIER) cc_final: 0.1322 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0608
  time to fit residues: 4.8712
Evaluate side-chains
  57 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  668 GLU
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  864 LEU
Chi-restraints excluded: chain A residue  879 HIS
Chi-restraints excluded: chain A residue  914 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0870
   chunk 72 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.078449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.070780 restraints weight = 39504.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.071975 restraints weight = 27818.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.072778 restraints weight = 20838.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.073401 restraints weight = 16633.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.073856 restraints weight = 13909.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.7238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6069  Z= 0.144
  Angle     :  0.646   9.191   8279  Z= 0.325
  Chirality :  0.043   0.198    917
  Planarity :  0.005   0.051   1043
  Dihedral  :  4.298  15.863    802
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.19 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.33 (0.32), residues: 725
  helix:  0.95 (0.27), residues: 386
  sheet:  0.06 (0.70), residues: 58
  loop : -0.69 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 640 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.016   0.001   PHE A 614 
 TRP   0.018   0.002   TRP A 764 
 HIS   0.006   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6069)
  covalent geometry    : angle       0.64584 ( 8279)
  hydrogen bonds       : bond        0.03411 (  312)
  hydrogen bonds       : angle       4.52759 (  903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 945.07 seconds
wall clock time: 17 minutes 4.15 seconds (1024.15 seconds total)