Starting phenix.real_space_refine
on Tue Mar  3 16:25:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/03_2026/7swf_25472.cif"
  }
  resolution = 3.79
  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=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P      34      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    4227      2.51       5
     N    1214      2.21       5
     O    1361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6873
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 778, 6167
          Classifications: {'peptide': 778}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 43, 'TRANS': 734}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 370
          Classifications: {'RNA': 17}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 14}
    Chain: "D"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 335
          Classifications: {'DNA': 1, 'RNA': 16}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 15}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.57, per 1000 atoms: 0.23
  Number of scatterers: 6873
  At special positions: 0
  Unit cell: (80.99, 101.92, 114.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P      34     15.00
     Mg      1     11.99
     O    1361      8.00
     N    1214      7.00
     C    4227      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: 0.74
  Conformation dependent library (CDL) restraints added in 261.7 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 11 sheets defined
      31.9% alpha, 10.3% beta
      15 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 185
    Processing helix  chain 'A' and resid 263 through 283
      removed outlier: 3.521A  pdb=" N   ALA A 267 " --> pdb=" O   CYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 348
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 460 through 472
      removed outlier: 3.806A  pdb=" N   ALA A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   CYS A 472 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 488
      removed outlier: 3.917A  pdb=" N   VAL A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 565 through 584
    Processing helix  chain 'A' and resid 602 through 617
    Processing helix  chain 'A' and resid 618 through 620
      No H-bonds generated for 'chain 'A' and resid 618 through 620'
    Processing helix  chain 'A' and resid 636 through 648
      removed outlier: 4.212A  pdb=" N   GLU A 646 " --> pdb=" O   LYS A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 663
    Processing helix  chain 'A' and resid 665 through 679
      removed outlier: 3.826A  pdb=" N   LYS A 675 " --> pdb=" O   ASN A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 771 through 784
    Processing helix  chain 'A' and resid 798 through 800
      No H-bonds generated for 'chain 'A' and resid 798 through 800'
    Processing helix  chain 'A' and resid 801 through 819
    Processing helix  chain 'A' and resid 903 through 915
    Processing helix  chain 'A' and resid 928 through 941
      removed outlier: 4.038A  pdb=" N   ALA A 934 " --> pdb=" O   PRO A 930 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   HIS A 935 " --> pdb=" O   ALA A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 945
      removed outlier: 3.791A  pdb=" N   LEU A 945 " --> pdb=" O   ARG A 942 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 942 through 945'
    Processing helix  chain 'A' and resid 978 through 982
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 144
    Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 316
      removed outlier: 3.590A  pdb=" N   SER A 314 " --> pdb=" O   ASN A 325 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197
    Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 300
      removed outlier: 3.727A  pdb=" N   GLN A 299 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374
    Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390
      removed outlier: 4.042A  pdb=" N   SER A 440 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532
      removed outlier: 3.563A  pdb=" N   LEU A 521 " --> pdb=" O   CYS A 532 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL A 686 " --> pdb=" O   LYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597
      removed outlier: 7.008A  pdb=" N   ALA A 556 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE A 629 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 703 through 705
      removed outlier: 5.994A  pdb=" N   ILE A 704 " --> pdb=" O   ILE A 791 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   VAL A 828 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   ASP A 898 " --> pdb=" O   VAL A 828 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   PHE A 830 " --> pdb=" O   LEU A 896 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 707 through 711
      removed outlier: 3.623A  pdb=" N   ILE A 723 " --> pdb=" O   THR A 711 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER A 722 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 761
      removed outlier: 3.707A  pdb=" N   TRP A 759 " --> pdb=" O   VAL A 767 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL A 767 " --> pdb=" O   TRP A 759 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    591 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1751
        1.33 -     1.45: 1422
        1.45 -     1.57: 3794
        1.57 -     1.69: 66
        1.69 -     1.81: 50
  Bond restraints: 7083
  Sorted by residual:
  bond pdb=" N   VAL A 173 "
       pdb=" CA  VAL A 173 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.17e-02 7.31e+03 6.80e+00
  bond pdb=" N   VAL A 286 "
       pdb=" CA  VAL A 286 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 6.80e+00
  bond pdb=" N   ARG A 288 "
       pdb=" CA  ARG A 288 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.50e+00
  bond pdb=" N   ILE A 178 "
       pdb=" CA  ILE A 178 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.35e+00
  bond pdb=" N   VAL A 182 "
       pdb=" CA  VAL A 182 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.17e-02 7.31e+03 6.26e+00
  ... (remaining 7078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 9438
        1.89 -     3.77: 267
        3.77 -     5.66: 26
        5.66 -     7.54: 12
        7.54 -     9.43: 1
  Bond angle restraints: 9744
  Sorted by residual:
  angle pdb=" C3'   C D   7 "
        pdb=" O3'   C D   7 "
        pdb=" P     A D   8 "
      ideal   model   delta    sigma   weight residual
     120.20  110.77    9.43 1.50e+00 4.44e-01 3.95e+01
  angle pdb=" C3'   U D   9 "
        pdb=" O3'   U D   9 "
        pdb=" P     U D  10 "
      ideal   model   delta    sigma   weight residual
     120.20  113.70    6.50 1.50e+00 4.44e-01 1.88e+01
  angle pdb=" CA  ARG A 836 "
        pdb=" C   ARG A 836 "
        pdb=" O   ARG A 836 "
      ideal   model   delta    sigma   weight residual
     122.64  118.36    4.28 1.25e+00 6.40e-01 1.17e+01
  angle pdb=" C   THR A 711 "
        pdb=" CA  THR A 711 "
        pdb=" CB  THR A 711 "
      ideal   model   delta    sigma   weight residual
     111.23  115.95   -4.72 1.42e+00 4.96e-01 1.11e+01
  angle pdb=" CA  HIS A 837 "
        pdb=" C   HIS A 837 "
        pdb=" O   HIS A 837 "
      ideal   model   delta    sigma   weight residual
     121.16  117.41    3.75 1.13e+00 7.83e-01 1.10e+01
  ... (remaining 9739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 4189
       35.68 -    71.36: 150
       71.36 -   107.03: 14
      107.03 -   142.71: 0
      142.71 -   178.39: 2
  Dihedral angle restraints: 4355
    sinusoidal: 2084
      harmonic: 2271
  Sorted by residual:
  dihedral pdb=" C4'   C D  20 "
           pdb=" C3'   C D  20 "
           pdb=" O3'   C D  20 "
           pdb=" P     A D  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.39 -178.39     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  SER A 855 "
           pdb=" C   SER A 855 "
           pdb=" N   GLY A 856 "
           pdb=" CA  GLY A 856 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  MET A 320 "
           pdb=" C   MET A 320 "
           pdb=" N   GLY A 321 "
           pdb=" CA  GLY A 321 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 4352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1019
       0.086 -    0.171: 92
       0.171 -    0.257: 3
       0.257 -    0.343: 0
       0.343 -    0.429: 2
  Chirality restraints: 1116
  Sorted by residual:
  chirality pdb=" P     A D   8 "
            pdb=" OP1   A D   8 "
            pdb=" OP2   A D   8 "
            pdb=" O5'   A D   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.84   -0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" P     U D   9 "
            pdb=" OP1   U D   9 "
            pdb=" OP2   U D   9 "
            pdb=" O5'   U D   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.79   -0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" CA  ILE A 177 "
            pdb=" N   ILE A 177 "
            pdb=" C   ILE A 177 "
            pdb=" CB  ILE A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1113 not shown)

  Planarity restraints: 1132
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 169 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.09e+00
        pdb=" C   SER A 169 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   SER A 169 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 170 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   6 "    0.020 2.00e-02 2.50e+03   1.07e-02 2.57e+00
        pdb=" N1    U B   6 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2    U B   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2    U B   6 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U B   6 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    U B   6 "    0.002 2.00e-02 2.50e+03
        pdb=" O4    U B   6 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B   6 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 929 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 930 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 930 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 930 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1129 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 94
        2.61 -     3.18: 6083
        3.18 -     3.76: 10865
        3.76 -     4.33: 14065
        4.33 -     4.90: 23025
  Nonbonded interactions: 54132
  Sorted by model distance:
  nonbonded pdb=" OP1   U D  12 "
            pdb="MG    MG A1001 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" OD2 ASP A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     2.044 2.170
  nonbonded pdb=" OD1 ASP A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     2.096 2.170
  nonbonded pdb=" O   VAL A 470 "
            pdb=" NE2 GLN A 473 "
     model   vdw
     2.176 3.120
  nonbonded pdb=" OG1 THR A 852 "
            pdb=" O   ARG A 854 "
     model   vdw
     2.187 3.040
  ... (remaining 54127 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7083  Z= 0.265
  Angle     :  0.726   9.427   9744  Z= 0.415
  Chirality :  0.049   0.429   1116
  Planarity :  0.004   0.038   1132
  Dihedral  : 17.156 178.388   2887
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  0.88 %
    Favored  : 97.79 %
  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 are not related in a simple way.
  whole: -1.82 (0.31), residues: 768
  helix:  1.31 (0.36), residues: 230
  sheet: -2.83 (0.42), residues: 131
  loop : -2.21 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 484 
 TYR   0.017   0.002   TYR A 312 
 PHE   0.018   0.002   PHE A 802 
 TRP   0.017   0.002   TRP A 308 
 HIS   0.004   0.001   HIS A 837 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 7083)
  covalent geometry    : angle       0.72605 ( 9744)
  hydrogen bonds       : bond        0.16661 (  247)
  hydrogen bonds       : angle       7.14361 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.6494 (mp10) cc_final: 0.6281 (mp10)
REVERT: A  335 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7765 (mt-10)
REVERT: A  504 ILE cc_start: 0.9138 (mt) cc_final: 0.8937 (pt)
REVERT: A  987 TYR cc_start: 0.8390 (p90) cc_final: 0.8111 (p90)
  outliers start: 9
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1124
  time to fit residues: 13.3379
Evaluate side-chains
  69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  837 HIS
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 489 ASN
A 671 ASN
A 677 ASN
A 760 GLN
** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 912 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.120742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082056 restraints weight = 15798.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.084680 restraints weight = 7281.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.086201 restraints weight = 4578.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.086994 restraints weight = 3489.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.087654 restraints weight = 3045.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7083  Z= 0.114
  Angle     :  0.601   7.773   9744  Z= 0.296
  Chirality :  0.041   0.187   1116
  Planarity :  0.004   0.037   1132
  Dihedral  : 15.560 162.377   1367
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.34 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.31), residues: 768
  helix:  1.76 (0.36), residues: 231
  sheet: -2.59 (0.40), residues: 147
  loop : -2.05 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 683 
 TYR   0.024   0.001   TYR A 185 
 PHE   0.015   0.001   PHE A 902 
 TRP   0.019   0.001   TRP A 732 
 HIS   0.002   0.001   HIS A 837 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7083)
  covalent geometry    : angle       0.60137 ( 9744)
  hydrogen bonds       : bond        0.03386 (  247)
  hydrogen bonds       : angle       4.91493 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  184 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: A  265 GLN cc_start: 0.6547 (mp10) cc_final: 0.6265 (mp10)
REVERT: A  492 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8379 (p0)
REVERT: A  493 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8657 (mm-40)
REVERT: A  498 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9077 (mmtt)
REVERT: A  732 TRP cc_start: 0.8073 (t60) cc_final: 0.7653 (t60)
REVERT: A  836 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7752 (mmt180)
REVERT: A  845 ASN cc_start: 0.7086 (t0) cc_final: 0.6793 (t0)
  outliers start: 9
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0852
  time to fit residues: 9.7288
Evaluate side-chains
  69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 22 optimal weight:    0.0870
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0470
   chunk 18 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 885 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 = 0.3755 r_free = 0.3755 target = 0.121944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.083453 restraints weight = 15574.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.085938 restraints weight = 7248.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.087508 restraints weight = 4531.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088503 restraints weight = 3455.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.088924 restraints weight = 2961.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7083  Z= 0.098
  Angle     :  0.588  11.844   9744  Z= 0.282
  Chirality :  0.040   0.160   1116
  Planarity :  0.004   0.037   1132
  Dihedral  : 15.457 161.671   1362
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.20 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.31), residues: 768
  helix:  1.76 (0.36), residues: 237
  sheet: -2.34 (0.41), residues: 143
  loop : -2.09 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 794 
 TYR   0.015   0.001   TYR A 987 
 PHE   0.011   0.001   PHE A 902 
 TRP   0.007   0.001   TRP A 308 
 HIS   0.002   0.000   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7083)
  covalent geometry    : angle       0.58785 ( 9744)
  hydrogen bonds       : bond        0.03022 (  247)
  hydrogen bonds       : angle       4.45762 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  265 GLN cc_start: 0.6349 (mp10) cc_final: 0.6086 (mp10)
REVERT: A  296 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7946 (ptpt)
REVERT: A  492 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8570 (p0)
REVERT: A  493 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8683 (mm-40)
REVERT: A  845 ASN cc_start: 0.7032 (t0) cc_final: 0.6764 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 82
  average time/residue: 0.0787
  time to fit residues: 8.8549
Evaluate side-chains
  72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0570
   chunk 26 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 885 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 = 0.3743 r_free = 0.3743 target = 0.121098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082111 restraints weight = 16030.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084693 restraints weight = 7426.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.086266 restraints weight = 4660.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087111 restraints weight = 3540.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.087667 restraints weight = 3071.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7083  Z= 0.105
  Angle     :  0.563   9.108   9744  Z= 0.272
  Chirality :  0.040   0.153   1116
  Planarity :  0.003   0.038   1132
  Dihedral  : 15.389 161.447   1362
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.91 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.31), residues: 768
  helix:  1.88 (0.36), residues: 237
  sheet: -2.24 (0.41), residues: 143
  loop : -2.05 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 794 
 TYR   0.013   0.001   TYR A 185 
 PHE   0.007   0.001   PHE A 874 
 TRP   0.011   0.001   TRP A 308 
 HIS   0.002   0.001   HIS A 837 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7083)
  covalent geometry    : angle       0.56273 ( 9744)
  hydrogen bonds       : bond        0.02941 (  247)
  hydrogen bonds       : angle       4.26242 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8432 (mp)
REVERT: A  265 GLN cc_start: 0.6477 (mp10) cc_final: 0.6189 (mp10)
REVERT: A  296 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7870 (ptpt)
REVERT: A  335 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7384 (mt-10)
REVERT: A  502 MET cc_start: 0.8462 (ppp) cc_final: 0.8159 (ppp)
REVERT: A  675 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.9005 (mttt)
REVERT: A  714 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6657 (tm-30)
REVERT: A  836 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7737 (mmt180)
REVERT: A  897 TRP cc_start: 0.9006 (t-100) cc_final: 0.8785 (t-100)
  outliers start: 21
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0781
  time to fit residues: 9.9651
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  675 LYS
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  884 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    0.0170
   chunk 58 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    2.5024

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

Flipped N/Q/H residues before XYZ refinement:
A 489 ASN
A 671 ASN
** A 885 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 = 0.3675 r_free = 0.3675 target = 0.117121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.079113 restraints weight = 16281.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.081603 restraints weight = 7568.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.083070 restraints weight = 4728.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.083911 restraints weight = 3598.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084529 restraints weight = 3122.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7083  Z= 0.181
  Angle     :  0.618   8.356   9744  Z= 0.306
  Chirality :  0.042   0.163   1116
  Planarity :  0.004   0.037   1132
  Dihedral  : 15.416 163.880   1362
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 17.08 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.31), residues: 768
  helix:  2.00 (0.36), residues: 229
  sheet: -2.07 (0.42), residues: 148
  loop : -2.03 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 183 
 TYR   0.014   0.001   TYR A 987 
 PHE   0.010   0.001   PHE A 874 
 TRP   0.008   0.001   TRP A 308 
 HIS   0.004   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7083)
  covalent geometry    : angle       0.61832 ( 9744)
  hydrogen bonds       : bond        0.03380 (  247)
  hydrogen bonds       : angle       4.32108 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.6507 (mp10) cc_final: 0.6231 (mp10)
REVERT: A  296 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7813 (ptpt)
REVERT: A  444 MET cc_start: 0.4096 (ppp) cc_final: 0.3827 (tmm)
REVERT: A  498 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9034 (mmtt)
REVERT: A  714 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6629 (tm-30)
REVERT: A  836 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7593 (mmt180)
  outliers start: 26
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0837
  time to fit residues: 10.0714
Evaluate side-chains
  77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  927 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 36 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 27 optimal weight:    0.4980
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.9022

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.120241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.082029 restraints weight = 15908.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.084655 restraints weight = 7303.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.086224 restraints weight = 4542.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.087113 restraints weight = 3437.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.087718 restraints weight = 2973.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7083  Z= 0.105
  Angle     :  0.582   9.597   9744  Z= 0.283
  Chirality :  0.040   0.146   1116
  Planarity :  0.004   0.038   1132
  Dihedral  : 15.334 160.803   1362
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.85 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.31), residues: 768
  helix:  1.96 (0.36), residues: 234
  sheet: -2.03 (0.44), residues: 141
  loop : -2.00 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 794 
 TYR   0.013   0.001   TYR A 987 
 PHE   0.007   0.001   PHE A 902 
 TRP   0.030   0.002   TRP A 732 
 HIS   0.002   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7083)
  covalent geometry    : angle       0.58216 ( 9744)
  hydrogen bonds       : bond        0.02929 (  247)
  hydrogen bonds       : angle       4.15780 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.6485 (mp10) cc_final: 0.6220 (mp10)
REVERT: A  296 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7894 (ptpt)
REVERT: A  498 LYS cc_start: 0.9355 (mmtm) cc_final: 0.9007 (mmtt)
REVERT: A  502 MET cc_start: 0.8393 (ppp) cc_final: 0.8173 (ppp)
REVERT: A  714 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6676 (tm-30)
REVERT: A  732 TRP cc_start: 0.8179 (t60) cc_final: 0.7918 (t60)
REVERT: A  836 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7689 (mmt-90)
REVERT: A  897 TRP cc_start: 0.8984 (t-100) cc_final: 0.8774 (t-100)
  outliers start: 14
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0893
  time to fit residues: 10.0114
Evaluate side-chains
  80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  884 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
** A 885 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 = 0.3623 r_free = 0.3623 target = 0.113515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.075420 restraints weight = 16515.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.077760 restraints weight = 7802.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.079198 restraints weight = 4933.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.079946 restraints weight = 3786.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.080511 restraints weight = 3304.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   7083  Z= 0.327
  Angle     :  0.758  12.217   9744  Z= 0.378
  Chirality :  0.046   0.209   1116
  Planarity :  0.004   0.037   1132
  Dihedral  : 15.537 165.549   1362
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.03 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.31), residues: 768
  helix:  1.53 (0.36), residues: 231
  sheet: -2.16 (0.42), residues: 157
  loop : -1.94 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 794 
 TYR   0.016   0.002   TYR A 185 
 PHE   0.014   0.002   PHE A 874 
 TRP   0.022   0.002   TRP A 732 
 HIS   0.008   0.002   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 ( 7083)
  covalent geometry    : angle       0.75844 ( 9744)
  hydrogen bonds       : bond        0.04096 (  247)
  hydrogen bonds       : angle       4.62234 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  265 GLN cc_start: 0.6302 (mp10) cc_final: 0.6102 (mp10)
REVERT: A  279 SER cc_start: 0.8211 (t) cc_final: 0.7872 (t)
REVERT: A  296 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7920 (ttmt)
REVERT: A  444 MET cc_start: 0.4154 (ppp) cc_final: 0.3846 (tmm)
REVERT: A  492 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8676 (p0)
REVERT: A  714 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6731 (tm-30)
REVERT: A  920 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8732 (ptm-80)
REVERT: A  987 TYR cc_start: 0.8764 (p90) cc_final: 0.8505 (p90)
  outliers start: 15
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0892
  time to fit residues: 9.4038
Evaluate side-chains
  75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  492 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  927 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
A 823 ASN
** A 885 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 = 0.3694 r_free = 0.3694 target = 0.118003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.079799 restraints weight = 16209.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082295 restraints weight = 7522.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.083845 restraints weight = 4697.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.084693 restraints weight = 3551.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085309 restraints weight = 3073.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7083  Z= 0.130
  Angle     :  0.637  12.801   9744  Z= 0.306
  Chirality :  0.041   0.164   1116
  Planarity :  0.004   0.038   1132
  Dihedral  : 15.482 163.154   1362
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.47 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.31), residues: 768
  helix:  1.87 (0.36), residues: 228
  sheet: -2.11 (0.44), residues: 142
  loop : -2.03 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 794 
 TYR   0.017   0.001   TYR A 987 
 PHE   0.008   0.001   PHE A 874 
 TRP   0.008   0.001   TRP A 759 
 HIS   0.003   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7083)
  covalent geometry    : angle       0.63735 ( 9744)
  hydrogen bonds       : bond        0.03088 (  247)
  hydrogen bonds       : angle       4.36397 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7188 (pttm)
REVERT: A  279 SER cc_start: 0.8126 (t) cc_final: 0.7912 (t)
REVERT: A  335 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7342 (mt-10)
REVERT: A  444 MET cc_start: 0.3994 (ppp) cc_final: 0.3717 (tmm)
REVERT: A  498 LYS cc_start: 0.9280 (mmtm) cc_final: 0.8994 (mmtt)
REVERT: A  714 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6638 (tm-30)
REVERT: A  821 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7698 (mt-10)
REVERT: A  897 TRP cc_start: 0.9061 (t-100) cc_final: 0.8761 (t-100)
REVERT: A  920 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8544 (ptm-80)
  outliers start: 15
  outliers final: 9
  residues processed: 88
  average time/residue: 0.0867
  time to fit residues: 10.2229
Evaluate side-chains
  77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  920 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 21 optimal weight:   30.0000
   chunk 78 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.116308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.078311 restraints weight = 16356.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.080733 restraints weight = 7612.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.082083 restraints weight = 4765.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.083057 restraints weight = 3683.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083516 restraints weight = 3141.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7083  Z= 0.194
  Angle     :  0.686  12.390   9744  Z= 0.333
  Chirality :  0.043   0.241   1116
  Planarity :  0.004   0.038   1132
  Dihedral  : 15.444 163.679   1362
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.91 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.31), residues: 768
  helix:  1.73 (0.36), residues: 230
  sheet: -2.27 (0.43), residues: 146
  loop : -2.00 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 794 
 TYR   0.013   0.001   TYR A 185 
 PHE   0.010   0.001   PHE A 874 
 TRP   0.024   0.002   TRP A 732 
 HIS   0.004   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 7083)
  covalent geometry    : angle       0.68574 ( 9744)
  hydrogen bonds       : bond        0.03376 (  247)
  hydrogen bonds       : angle       4.40104 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7184 (pttm)
REVERT: A  279 SER cc_start: 0.8057 (t) cc_final: 0.7788 (t)
REVERT: A  296 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7600 (ptpt)
REVERT: A  714 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: A  732 TRP cc_start: 0.8417 (t60) cc_final: 0.8179 (t60)
  outliers start: 13
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0897
  time to fit residues: 8.8833
Evaluate side-chains
  70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  308 TRP
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
** A 885 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 = 0.3678 r_free = 0.3678 target = 0.116831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.078919 restraints weight = 16094.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.081299 restraints weight = 7524.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.082760 restraints weight = 4710.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.083697 restraints weight = 3605.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.084101 restraints weight = 3098.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7083  Z= 0.179
  Angle     :  0.687  12.889   9744  Z= 0.332
  Chirality :  0.042   0.211   1116
  Planarity :  0.004   0.039   1132
  Dihedral  : 15.463 163.730   1362
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.77 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.30), residues: 768
  helix:  1.81 (0.36), residues: 229
  sheet: -2.28 (0.46), residues: 121
  loop : -2.19 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 794 
 TYR   0.013   0.001   TYR A 185 
 PHE   0.010   0.001   PHE A 874 
 TRP   0.022   0.002   TRP A 732 
 HIS   0.003   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7083)
  covalent geometry    : angle       0.68724 ( 9744)
  hydrogen bonds       : bond        0.03258 (  247)
  hydrogen bonds       : angle       4.36011 (  667)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7228 (pttm)
REVERT: A  296 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7635 (ptpt)
REVERT: A  714 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: A  732 TRP cc_start: 0.8418 (t60) cc_final: 0.8117 (t60)
REVERT: A  745 GLN cc_start: 0.8555 (pt0) cc_final: 0.8354 (pt0)
REVERT: A  897 TRP cc_start: 0.9073 (t-100) cc_final: 0.8810 (t-100)
  outliers start: 15
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0805
  time to fit residues: 8.1439
Evaluate side-chains
  70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  308 TRP
Chi-restraints excluded: chain A residue  488 HIS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  719 SER
Chi-restraints excluded: chain A residue  838 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0060
   chunk 50 optimal weight:    0.0070
   chunk 34 optimal weight:    0.4980
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.5018

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
** A 885 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 = 0.3708 r_free = 0.3708 target = 0.118600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.080599 restraints weight = 15848.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.083002 restraints weight = 7413.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084476 restraints weight = 4675.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.085293 restraints weight = 3564.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.085879 restraints weight = 3096.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7083  Z= 0.136
  Angle     :  0.669  13.082   9744  Z= 0.320
  Chirality :  0.041   0.195   1116
  Planarity :  0.004   0.039   1132
  Dihedral  : 15.396 163.171   1362
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.80 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.30), residues: 768
  helix:  1.95 (0.36), residues: 228
  sheet: -2.09 (0.47), residues: 117
  loop : -2.19 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 694 
 TYR   0.013   0.001   TYR A 185 
 PHE   0.009   0.001   PHE A 902 
 TRP   0.019   0.001   TRP A 732 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7083)
  covalent geometry    : angle       0.66943 ( 9744)
  hydrogen bonds       : bond        0.02977 (  247)
  hydrogen bonds       : angle       4.23865 (  667)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1309.39 seconds
wall clock time: 23 minutes 14.67 seconds (1394.67 seconds total)