Starting phenix.real_space_refine
on Tue Mar  3 17:27:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2026/6w62_21551.map"
  }
  resolution = 3.9
  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: 5
    Type Number    sf(0)   Gaussians
     P      24      5.49       5
     S      30      5.16       5
     C    4602      2.51       5
     N    1293      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  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: 7387
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 910, 6877
          Classifications: {'peptide': 910}
          Incomplete info: {'truncation_to_alanine': 143}
          Link IDs: {'PTRANS': 29, 'TRANS': 880}
          Chain breaks: 4
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 536
          Unresolved non-hydrogen angles: 671
          Unresolved non-hydrogen dihedrals: 447
          Unresolved non-hydrogen chiralities: 31
          Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 16, 'GLU:plan': 16, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 6, 'PHE:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 321
    Chain: "B"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 510
          Classifications: {'RNA': 24}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 8, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 7, 'rna3p': 16}
  Time building chain proxies: 1.80, per 1000 atoms: 0.24
  Number of scatterers: 7387
  At special positions: 0
  Unit cell: (79.8, 122.85, 107.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P      24     15.00
     O    1438      8.00
     N    1293      7.00
     C    4602      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: 0.67
  Conformation dependent library (CDL) restraints added in 184.9 milliseconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      52.7% alpha, 6.7% beta
      5 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 54
      Proline residue:  A  42  - end of helix
    Processing helix  chain 'A' and resid 70 through 80
    Processing helix  chain 'A' and resid 96 through 104
      removed outlier: 3.503A  pdb=" N   TYR A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 118
      removed outlier: 4.085A  pdb=" N   TYR A 116 " --> pdb=" O   GLN A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 142
    Processing helix  chain 'A' and resid 145 through 159
    Processing helix  chain 'A' and resid 168 through 176
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 308 through 331
      removed outlier: 4.363A  pdb=" N   ILE A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   THR A 316 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   THR A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN A 331 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 346
    Processing helix  chain 'A' and resid 364 through 368
    Processing helix  chain 'A' and resid 372 through 393
      removed outlier: 3.913A  pdb=" N   GLU A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 390 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 423
    Processing helix  chain 'A' and resid 429 through 439
    Processing helix  chain 'A' and resid 446 through 462
      removed outlier: 3.864A  pdb=" N   ASP A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 500
    Processing helix  chain 'A' and resid 533 through 540
    Processing helix  chain 'A' and resid 585 through 602
      removed outlier: 3.651A  pdb=" N   ARG A 599 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLN A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 721
      removed outlier: 4.168A  pdb=" N   LYS A 721 " --> pdb=" O   SER A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 746
    Processing helix  chain 'A' and resid 752 through 771
    Processing helix  chain 'A' and resid 772 through 778
      removed outlier: 4.523A  pdb=" N   LYS A 776 " --> pdb=" O   SER A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 787
    Processing helix  chain 'A' and resid 802 through 822
      removed outlier: 3.765A  pdb=" N   LEU A 822 " --> pdb=" O   PHE A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 846
    Processing helix  chain 'A' and resid 846 through 886
    Processing helix  chain 'A' and resid 905 through 914
    Processing helix  chain 'A' and resid 916 through 929
      removed outlier: 3.515A  pdb=" N   VAL A 920 " --> pdb=" O   LEU A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 971
      removed outlier: 3.534A  pdb=" N   GLU A 970 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU A 971 " --> pdb=" O   PRO A 968 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 967 through 971'
    Processing helix  chain 'A' and resid 972 through 983
      removed outlier: 3.699A  pdb=" N   ARG A 976 " --> pdb=" O   THR A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 1008
      removed outlier: 3.630A  pdb=" N   ALA A 994 " --> pdb=" O   ARG A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1015
    Processing helix  chain 'A' and resid 1018 through 1033
      removed outlier: 3.686A  pdb=" N   PHE A1022 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1072 through 1082
    Processing helix  chain 'A' and resid 1085 through 1090
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
      removed outlier: 3.517A  pdb=" N   ALA A 629 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84
      removed outlier: 3.819A  pdb=" N   LYS A  81 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479
      removed outlier: 3.786A  pdb=" N   GLY A 479 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY A 486 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LEU A 485 " --> pdb=" O   LYS A 515 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A 515 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 683
      removed outlier: 6.179A  pdb=" N   GLU A 660 " --> pdb=" O   PRO A 678 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A 642 " --> pdb=" O   LEU A 890 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689
      removed outlier: 3.633A  pdb=" N   TYR A 695 " --> pdb=" O   SER A 688 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 963 through 966
      removed outlier: 3.949A  pdb=" N   PHE A1040 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050
      removed outlier: 3.962A  pdb=" N   THR A1059 " --> pdb=" O   VAL A1070 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      13 hydrogen bonds
      26 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2260
        1.34 -     1.45: 1159
        1.45 -     1.57: 4056
        1.57 -     1.69: 47
        1.69 -     1.81: 51
  Bond restraints: 7573
  Sorted by residual:
  bond pdb=" N   ILE A 489 "
       pdb=" CA  ILE A 489 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.19e-02 7.06e+03 1.04e+01
  bond pdb=" N   SER A 490 "
       pdb=" CA  SER A 490 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.41e-02 5.03e+03 8.79e+00
  bond pdb=" N   VAL A 684 "
       pdb=" CA  VAL A 684 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.61e+00
  bond pdb=" N   VAL A 686 "
       pdb=" CA  VAL A 686 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.32e-02 5.74e+03 7.91e+00
  bond pdb=" N   SER A 803 "
       pdb=" CA  SER A 803 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.20e-02 6.94e+03 7.51e+00
  ... (remaining 7568 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 10169
        2.11 -     4.22: 159
        4.22 -     6.33: 13
        6.33 -     8.45: 4
        8.45 -    10.56: 1
  Bond angle restraints: 10346
  Sorted by residual:
  angle pdb=" N   PRO A 491 "
        pdb=" CA  PRO A 491 "
        pdb=" C   PRO A 491 "
      ideal   model   delta    sigma   weight residual
     113.53  124.09  -10.56 1.39e+00 5.18e-01 5.77e+01
  angle pdb=" N   PRO A 987 "
        pdb=" CA  PRO A 987 "
        pdb=" CB  PRO A 987 "
      ideal   model   delta    sigma   weight residual
     103.25  110.62   -7.37 1.05e+00 9.07e-01 4.93e+01
  angle pdb=" N   PRO A 955 "
        pdb=" CA  PRO A 955 "
        pdb=" CB  PRO A 955 "
      ideal   model   delta    sigma   weight residual
     103.25  110.12   -6.87 1.05e+00 9.07e-01 4.29e+01
  angle pdb=" N   PRO A 339 "
        pdb=" CA  PRO A 339 "
        pdb=" CB  PRO A 339 "
      ideal   model   delta    sigma   weight residual
     103.23  110.01   -6.78 1.07e+00 8.73e-01 4.02e+01
  angle pdb=" C   ILE A 488 "
        pdb=" N   ILE A 489 "
        pdb=" CA  ILE A 489 "
      ideal   model   delta    sigma   weight residual
     120.46  126.77   -6.31 1.37e+00 5.33e-01 2.12e+01
  ... (remaining 10341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.75: 4499
       35.75 -    71.50: 124
       71.50 -   107.25: 15
      107.25 -   142.99: 0
      142.99 -   178.74: 2
  Dihedral angle restraints: 4640
    sinusoidal: 1966
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" O4'   U B  -6 "
           pdb=" C1'   U B  -6 "
           pdb=" N1    U B  -6 "
           pdb=" C2    U B  -6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.26  178.74     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C B -11 "
           pdb=" C1'   C B -11 "
           pdb=" N1    C B -11 "
           pdb=" C2    C B -11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   55.42  176.58     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  LYS A 487 "
           pdb=" C   LYS A 487 "
           pdb=" N   ILE A 488 "
           pdb=" CA  ILE A 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.84   26.16     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 4637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1076
       0.069 -    0.137: 96
       0.137 -    0.206: 6
       0.206 -    0.275: 3
       0.275 -    0.343: 2
  Chirality restraints: 1183
  Sorted by residual:
  chirality pdb=" CA  SER A 490 "
            pdb=" N   SER A 490 "
            pdb=" C   SER A 490 "
            pdb=" CB  SER A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CA  PRO A 491 "
            pdb=" N   PRO A 491 "
            pdb=" C   PRO A 491 "
            pdb=" CB  PRO A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CA  LEU A 799 "
            pdb=" N   LEU A 799 "
            pdb=" C   LEU A 799 "
            pdb=" CB  LEU A 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1180 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 798 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   SER A 798 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   SER A 798 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU A 799 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 674 "    0.049 5.00e-02 4.00e+02   7.40e-02 8.77e+00
        pdb=" N   PRO A 675 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 675 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 675 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 845 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.95e+00
        pdb=" C   ALA A 845 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ALA A 845 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 846 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 78
        2.49 -     3.09: 5914
        3.09 -     3.69: 11592
        3.69 -     4.30: 16348
        4.30 -     4.90: 25760
  Nonbonded interactions: 59692
  Sorted by model distance:
  nonbonded pdb=" O2'   U B  -5 "
            pdb=" OP1   G B  -4 "
     model   vdw
     1.883 3.040
  nonbonded pdb=" O2'   G B   1 "
            pdb=" O5'   C B   2 "
     model   vdw
     2.064 3.040
  nonbonded pdb=" N   VAL A 686 "
            pdb=" OD1 ASP A 696 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   SER A 798 "
            pdb=" N   SER A 800 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OH  TYR A 473 "
            pdb=" O   LYS A 619 "
     model   vdw
     2.204 3.040
  ... (remaining 59687 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:             0.420
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.200
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
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   0.042   7573  Z= 0.209
  Angle     :  0.642  10.557  10346  Z= 0.410
  Chirality :  0.043   0.343   1183
  Planarity :  0.004   0.074   1236
  Dihedral  : 16.092 178.742   2906
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.22 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.27), residues: 900
  helix:  0.41 (0.25), residues: 439
  sheet: -2.39 (0.50), residues: 101
  loop : -3.38 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 715 
 TYR   0.012   0.001   TYR A 995 
 PHE   0.015   0.001   PHE A  51 
 TRP   0.035   0.002   TRP A  79 
 HIS   0.004   0.001   HIS A 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7573)
  covalent geometry    : angle       0.64182 (10346)
  hydrogen bonds       : bond        0.16345 (  371)
  hydrogen bonds       : angle       6.22960 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  821 LEU cc_start: 0.5408 (tp) cc_final: 0.5177 (tp)
REVERT: A  880 LEU cc_start: 0.8183 (mm) cc_final: 0.7961 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0787
  time to fit residues: 15.0828
Evaluate side-chains
  111 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
A 459 HIS
A 477 ASN
A 592 GLN
A 771 HIS
A 946 HIS
A 993 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.158541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.138336 restraints weight = 15091.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.141851 restraints weight = 8888.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.144212 restraints weight = 6110.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.145778 restraints weight = 4716.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.146765 restraints weight = 3928.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7573  Z= 0.157
  Angle     :  0.687   9.372  10346  Z= 0.354
  Chirality :  0.043   0.165   1183
  Planarity :  0.004   0.057   1236
  Dihedral  : 16.835 177.405   1356
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.56 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.25 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.28), residues: 900
  helix:  0.41 (0.24), residues: 456
  sheet: -2.29 (0.56), residues: 80
  loop : -3.09 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  22 
 TYR   0.013   0.002   TYR A 116 
 PHE   0.030   0.002   PHE A1047 
 TRP   0.032   0.002   TRP A  79 
 HIS   0.005   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7573)
  covalent geometry    : angle       0.68664 (10346)
  hydrogen bonds       : bond        0.04700 (  371)
  hydrogen bonds       : angle       4.68514 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8136 (mm-40)
REVERT: A   77 VAL cc_start: 0.8289 (t) cc_final: 0.8008 (p)
REVERT: A   80 PHE cc_start: 0.8000 (m-80) cc_final: 0.7742 (m-80)
REVERT: A  674 LEU cc_start: 0.8031 (pp) cc_final: 0.7738 (pp)
REVERT: A  758 MET cc_start: 0.7519 (tmm) cc_final: 0.7214 (tmm)
REVERT: A  880 LEU cc_start: 0.8310 (mm) cc_final: 0.8011 (mm)
REVERT: A  968 PRO cc_start: 0.8382 (Cg_exo) cc_final: 0.8164 (Cg_endo)
  outliers start: 11
  outliers final: 9
  residues processed: 132
  average time/residue: 0.0726
  time to fit residues: 13.3826
Evaluate side-chains
  114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  770 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 600 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.156706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.136585 restraints weight = 15842.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.140058 restraints weight = 9241.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.142421 restraints weight = 6426.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.143884 restraints weight = 4959.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.145022 restraints weight = 4160.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7573  Z= 0.201
  Angle     :  0.709   8.928  10346  Z= 0.370
  Chirality :  0.045   0.180   1183
  Planarity :  0.004   0.063   1236
  Dihedral  : 16.859 179.763   1356
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 11.11 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.82 %
    Favored  : 82.32 %
  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: -2.04 (0.27), residues: 900
  helix:  0.25 (0.24), residues: 451
  sheet: -2.44 (0.55), residues: 81
  loop : -3.23 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 439 
 TYR   0.020   0.002   TYR A 116 
 PHE   0.020   0.002   PHE A1047 
 TRP   0.029   0.002   TRP A  79 
 HIS   0.013   0.002   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7573)
  covalent geometry    : angle       0.70925 (10346)
  hydrogen bonds       : bond        0.04675 (  371)
  hydrogen bonds       : angle       4.70064 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7887 (mm-40)
REVERT: A   77 VAL cc_start: 0.8477 (t) cc_final: 0.8170 (p)
REVERT: A   80 PHE cc_start: 0.8030 (m-80) cc_final: 0.7787 (m-80)
REVERT: A  758 MET cc_start: 0.7949 (tmm) cc_final: 0.7526 (tmm)
REVERT: A  802 LEU cc_start: 0.5201 (OUTLIER) cc_final: 0.3873 (tp)
REVERT: A  880 LEU cc_start: 0.8367 (mm) cc_final: 0.8003 (mm)
  outliers start: 26
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0689
  time to fit residues: 13.4751
Evaluate side-chains
  127 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 862 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.151808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.131407 restraints weight = 15860.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.134737 restraints weight = 9301.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.137056 restraints weight = 6507.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.138577 restraints weight = 5029.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.139502 restraints weight = 4208.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7573  Z= 0.246
  Angle     :  0.764   8.382  10346  Z= 0.397
  Chirality :  0.048   0.227   1183
  Planarity :  0.005   0.068   1236
  Dihedral  : 16.921 179.314   1356
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 12.22 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 14.56 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.27), residues: 900
  helix: -0.09 (0.23), residues: 452
  sheet: -2.45 (0.54), residues: 81
  loop : -3.21 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 715 
 TYR   0.015   0.002   TYR A1048 
 PHE   0.019   0.002   PHE A1047 
 TRP   0.027   0.003   TRP A  79 
 HIS   0.014   0.002   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7573)
  covalent geometry    : angle       0.76423 (10346)
  hydrogen bonds       : bond        0.04999 (  371)
  hydrogen bonds       : angle       4.87814 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7443 (mp) cc_final: 0.6577 (mm)
REVERT: A   50 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7883 (mm-40)
REVERT: A   77 VAL cc_start: 0.8500 (t) cc_final: 0.8168 (p)
REVERT: A   80 PHE cc_start: 0.8089 (m-80) cc_final: 0.7794 (m-80)
REVERT: A  476 PHE cc_start: 0.6992 (m-80) cc_final: 0.6601 (m-80)
REVERT: A  487 LYS cc_start: 0.5521 (pttt) cc_final: 0.5260 (ptmt)
REVERT: A  758 MET cc_start: 0.8013 (tmm) cc_final: 0.7288 (tmm)
REVERT: A  880 LEU cc_start: 0.8291 (mm) cc_final: 0.7946 (mm)
  outliers start: 35
  outliers final: 22
  residues processed: 136
  average time/residue: 0.0669
  time to fit residues: 12.9278
Evaluate side-chains
  128 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1057 ASP
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 HIS
A 407 GLN
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.157188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.137424 restraints weight = 15797.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.140795 restraints weight = 9305.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.143142 restraints weight = 6509.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.144751 restraints weight = 5038.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.145634 restraints weight = 4165.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7573  Z= 0.153
  Angle     :  0.687   9.333  10346  Z= 0.351
  Chirality :  0.044   0.204   1183
  Planarity :  0.004   0.067   1236
  Dihedral  : 16.762 178.697   1356
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.98 %
    Favored  : 78.16 %
  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: -1.98 (0.27), residues: 900
  helix:  0.19 (0.24), residues: 452
  sheet: -2.40 (0.54), residues: 86
  loop : -3.05 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 715 
 TYR   0.012   0.002   TYR A 116 
 PHE   0.020   0.002   PHE A 476 
 TRP   0.026   0.002   TRP A  79 
 HIS   0.013   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7573)
  covalent geometry    : angle       0.68670 (10346)
  hydrogen bonds       : bond        0.04287 (  371)
  hydrogen bonds       : angle       4.56011 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7318 (mp) cc_final: 0.6476 (mm)
REVERT: A   50 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7854 (mm-40)
REVERT: A  758 MET cc_start: 0.8161 (tmm) cc_final: 0.7447 (tmm)
REVERT: A  880 LEU cc_start: 0.8164 (mm) cc_final: 0.7815 (mm)
REVERT: A  996 TYR cc_start: 0.6497 (m-80) cc_final: 0.5561 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0638
  time to fit residues: 12.5583
Evaluate side-chains
  133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.151595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.131198 restraints weight = 15834.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.134506 restraints weight = 9407.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.136784 restraints weight = 6625.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.138227 restraints weight = 5162.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.138953 restraints weight = 4339.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7573  Z= 0.240
  Angle     :  0.765   8.801  10346  Z= 0.396
  Chirality :  0.048   0.212   1183
  Planarity :  0.005   0.071   1236
  Dihedral  : 16.851 179.614   1356
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 17.38 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.27), residues: 900
  helix: -0.09 (0.23), residues: 452
  sheet: -2.51 (0.53), residues: 86
  loop : -3.13 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 715 
 TYR   0.027   0.002   TYR A 995 
 PHE   0.016   0.002   PHE A1047 
 TRP   0.018   0.003   TRP A  79 
 HIS   0.005   0.002   HIS A 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 7573)
  covalent geometry    : angle       0.76541 (10346)
  hydrogen bonds       : bond        0.04958 (  371)
  hydrogen bonds       : angle       4.82835 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 114
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7552 (mp) cc_final: 0.6729 (mm)
REVERT: A   50 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7800 (mm-40)
REVERT: A   77 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8353 (p)
REVERT: A  680 GLU cc_start: 0.6639 (pt0) cc_final: 0.6364 (tt0)
REVERT: A  758 MET cc_start: 0.8107 (tmm) cc_final: 0.7312 (tmm)
REVERT: A  880 LEU cc_start: 0.8282 (mm) cc_final: 0.7935 (mm)
  outliers start: 41
  outliers final: 25
  residues processed: 140
  average time/residue: 0.0634
  time to fit residues: 12.9164
Evaluate side-chains
  132 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1057 ASP
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 91 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
A 477 ASN
A 993 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.154853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.135122 restraints weight = 15827.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.138401 restraints weight = 9522.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.140574 restraints weight = 6723.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.142054 restraints weight = 5255.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.142951 restraints weight = 4414.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7573  Z= 0.184
  Angle     :  0.732  10.387  10346  Z= 0.371
  Chirality :  0.046   0.238   1183
  Planarity :  0.004   0.069   1236
  Dihedral  : 16.793 178.854   1356
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 19.02 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.27), residues: 900
  helix:  0.03 (0.23), residues: 451
  sheet: -2.46 (0.54), residues: 86
  loop : -3.11 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 715 
 TYR   0.019   0.002   TYR A 996 
 PHE   0.020   0.002   PHE A  80 
 TRP   0.026   0.002   TRP A  79 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7573)
  covalent geometry    : angle       0.73234 (10346)
  hydrogen bonds       : bond        0.04437 (  371)
  hydrogen bonds       : angle       4.66822 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7763 (mm-40)
REVERT: A   77 VAL cc_start: 0.8657 (t) cc_final: 0.8279 (p)
REVERT: A  680 GLU cc_start: 0.6524 (pt0) cc_final: 0.6231 (tt0)
REVERT: A  758 MET cc_start: 0.8112 (tmm) cc_final: 0.7418 (tmm)
REVERT: A  880 LEU cc_start: 0.8163 (mm) cc_final: 0.7853 (mm)
REVERT: A  996 TYR cc_start: 0.6435 (m-80) cc_final: 0.5558 (t80)
  outliers start: 36
  outliers final: 27
  residues processed: 141
  average time/residue: 0.0710
  time to fit residues: 14.3464
Evaluate side-chains
  133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0060
   chunk 7 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5354

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

Flipped N/Q/H residues before XYZ refinement:
A 993 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.160247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.140497 restraints weight = 15980.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.144126 restraints weight = 9224.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.146519 restraints weight = 6292.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.148082 restraints weight = 4815.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.149272 restraints weight = 3985.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7573  Z= 0.131
  Angle     :  0.715  12.751  10346  Z= 0.353
  Chirality :  0.044   0.251   1183
  Planarity :  0.004   0.074   1236
  Dihedral  : 16.699 177.167   1356
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.25 %
    Favored  : 75.04 %
  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 (0.28), residues: 900
  helix:  0.45 (0.24), residues: 450
  sheet: -2.47 (0.54), residues: 85
  loop : -3.11 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 779 
 TYR   0.013   0.001   TYR A 116 
 PHE   0.032   0.002   PHE A 783 
 TRP   0.051   0.003   TRP A  79 
 HIS   0.004   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7573)
  covalent geometry    : angle       0.71480 (10346)
  hydrogen bonds       : bond        0.03959 (  371)
  hydrogen bonds       : angle       4.39947 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   50 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7778 (mm-40)
REVERT: A  542 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6104 (t80)
REVERT: A  650 ILE cc_start: 0.6341 (pt) cc_final: 0.6137 (pt)
REVERT: A  656 TYR cc_start: 0.6258 (p90) cc_final: 0.5800 (p90)
REVERT: A  680 GLU cc_start: 0.6426 (pt0) cc_final: 0.6174 (tt0)
REVERT: A  758 MET cc_start: 0.8126 (tmm) cc_final: 0.7576 (tmm)
REVERT: A  878 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7510 (mtpt)
REVERT: A  880 LEU cc_start: 0.8186 (mm) cc_final: 0.7834 (mm)
REVERT: A  996 TYR cc_start: 0.6249 (m-80) cc_final: 0.5599 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 138
  average time/residue: 0.0708
  time to fit residues: 13.7013
Evaluate side-chains
  128 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.154823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.136438 restraints weight = 15608.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.139707 restraints weight = 9041.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.141875 restraints weight = 6228.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.143306 restraints weight = 4784.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.144117 restraints weight = 3983.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7573  Z= 0.209
  Angle     :  0.789  10.939  10346  Z= 0.404
  Chirality :  0.048   0.248   1183
  Planarity :  0.005   0.074   1236
  Dihedral  : 16.780 179.461   1356
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.95 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.28), residues: 900
  helix:  0.18 (0.24), residues: 453
  sheet: -2.50 (0.53), residues: 86
  loop : -3.07 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 715 
 TYR   0.018   0.002   TYR A 995 
 PHE   0.052   0.003   PHE A 783 
 TRP   0.057   0.003   TRP A  79 
 HIS   0.006   0.002   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7573)
  covalent geometry    : angle       0.78877 (10346)
  hydrogen bonds       : bond        0.04763 (  371)
  hydrogen bonds       : angle       4.64650 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   50 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7823 (mm-40)
REVERT: A   77 VAL cc_start: 0.8619 (t) cc_final: 0.8308 (p)
REVERT: A  542 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6282 (t80)
REVERT: A  650 ILE cc_start: 0.6496 (pt) cc_final: 0.6285 (pt)
REVERT: A  680 GLU cc_start: 0.6482 (pt0) cc_final: 0.6134 (tt0)
REVERT: A  758 MET cc_start: 0.8020 (tmm) cc_final: 0.7203 (tmm)
REVERT: A  880 LEU cc_start: 0.8201 (mm) cc_final: 0.7887 (mm)
  outliers start: 29
  outliers final: 22
  residues processed: 132
  average time/residue: 0.0722
  time to fit residues: 13.5873
Evaluate side-chains
  126 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 60 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 88 optimal weight:    0.3980
   chunk 84 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 91 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.159050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.140018 restraints weight = 15540.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.143429 restraints weight = 9164.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.145680 restraints weight = 6330.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.147257 restraints weight = 4884.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.147990 restraints weight = 4029.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7573  Z= 0.147
  Angle     :  0.755  12.451  10346  Z= 0.377
  Chirality :  0.046   0.234   1183
  Planarity :  0.005   0.076   1236
  Dihedral  : 16.682 177.656   1356
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.95 %
    Favored  : 75.19 %
  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: -1.92 (0.28), residues: 900
  helix:  0.35 (0.24), residues: 449
  sheet: -2.42 (0.53), residues: 86
  loop : -3.15 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 779 
 TYR   0.021   0.002   TYR A 995 
 PHE   0.045   0.002   PHE A 783 
 TRP   0.087   0.004   TRP A  79 
 HIS   0.004   0.001   HIS A 952 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7573)
  covalent geometry    : angle       0.75526 (10346)
  hydrogen bonds       : bond        0.04201 (  371)
  hydrogen bonds       : angle       4.48553 ( 1061)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   50 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7757 (mm-40)
REVERT: A   77 VAL cc_start: 0.8481 (t) cc_final: 0.8143 (p)
REVERT: A  466 ILE cc_start: 0.8082 (pt) cc_final: 0.7651 (tt)
REVERT: A  542 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6036 (t80)
REVERT: A  650 ILE cc_start: 0.6333 (pt) cc_final: 0.6093 (pt)
REVERT: A  680 GLU cc_start: 0.6345 (pt0) cc_final: 0.6121 (tt0)
REVERT: A  758 MET cc_start: 0.8126 (tmm) cc_final: 0.7488 (tmm)
REVERT: A  840 GLU cc_start: 0.8516 (mp0) cc_final: 0.8305 (mp0)
REVERT: A  880 LEU cc_start: 0.8100 (mm) cc_final: 0.7858 (mm)
  outliers start: 26
  outliers final: 21
  residues processed: 138
  average time/residue: 0.0708
  time to fit residues: 13.9195
Evaluate side-chains
  134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  703 VAL
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue 1046 MET
Chi-restraints excluded: chain A residue 1059 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0870
   chunk 73 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 993 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.158732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.139745 restraints weight = 15526.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.143055 restraints weight = 9161.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.145280 restraints weight = 6389.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.146558 restraints weight = 4932.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.147768 restraints weight = 4172.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7573  Z= 0.151
  Angle     :  0.754  12.224  10346  Z= 0.379
  Chirality :  0.046   0.332   1183
  Planarity :  0.005   0.074   1236
  Dihedral  : 16.650 178.260   1356
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.69 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.28), residues: 900
  helix:  0.36 (0.24), residues: 453
  sheet: -2.34 (0.53), residues: 86
  loop : -3.10 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 960 
 TYR   0.028   0.002   TYR A 995 
 PHE   0.043   0.002   PHE A 783 
 TRP   0.103   0.004   TRP A  79 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7573)
  covalent geometry    : angle       0.75357 (10346)
  hydrogen bonds       : bond        0.04268 (  371)
  hydrogen bonds       : angle       4.48526 ( 1061)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1278.69 seconds
wall clock time: 22 minutes 52.07 seconds (1372.07 seconds total)