Starting phenix.real_space_refine
on Wed Mar 12 08:15:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_21551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_21551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_21551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_21551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w62_21551/03_2025/6w62_21551.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 8}
          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: 4.79, per 1000 atoms: 0.65
  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: 2.30
  Conformation dependent library (CDL) restraints added in 815.4 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: 2.88
  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: 2.61

  Time building geometry restraints manager: 2.65 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.800
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.860
-------------------------------------------------------------------------------
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= 0.220
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.035   0.002   TRP A  79 
 HIS   0.004   0.001   HIS A 459 
 PHE   0.015   0.001   PHE A  51 
 TYR   0.012   0.001   TYR A 995 
 ARG   0.012   0.001   ARG A 715 

*********************** 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  : 0.881 
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: 0.8182 (mm) cc_final: 0.7961 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1889
  time to fit residues: 35.8081
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  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 GLN
** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 592 GLN
A 600 GLN
A 771 HIS
A 946 HIS
A 993 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.156098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.135589 restraints weight = 15709.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.139043 restraints weight = 9350.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.141360 restraints weight = 6595.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7573  Z= 0.294
  Angle     :  0.742   9.378  10346  Z= 0.386
  Chirality :  0.046   0.190   1183
  Planarity :  0.005   0.061   1236
  Dihedral  : 16.917 179.081   1356
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 11.22 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.29 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.27), residues: 900
  helix:  0.14 (0.24), residues: 456
  sheet: -2.48 (0.55), residues: 81
  loop : -3.16 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  79 
 HIS   0.005   0.002   HIS A 459 
 PHE   0.029   0.003   PHE A1047 
 TYR   0.014   0.002   TYR A 542 
 ARG   0.004   0.001   ARG A 652 

*********************** 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
  140 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8102 (mm-40)
REVERT: A  655 THR cc_start: 0.8411 (t) cc_final: 0.8164 (t)
REVERT: A  674 LEU cc_start: 0.7983 (pp) cc_final: 0.7631 (pp)
REVERT: A  758 MET cc_start: 0.7621 (tmm) cc_final: 0.7179 (tmm)
REVERT: A  880 LEU cc_start: 0.8343 (mm) cc_final: 0.8012 (mm)
REVERT: A  968 PRO cc_start: 0.8269 (Cg_exo) cc_final: 0.8050 (Cg_endo)
  outliers start: 13
  outliers final: 11
  residues processed: 134
  average time/residue: 0.1908
  time to fit residues: 35.0288
Evaluate side-chains
  112 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
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  375 THR
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  666 ASP
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 9 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 307 ASN
A 407 GLN
A 459 HIS
A 477 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.156710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.136339 restraints weight = 15992.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.139914 restraints weight = 9484.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.142253 restraints weight = 6570.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7573  Z= 0.240
  Angle     :  0.682   9.276  10346  Z= 0.354
  Chirality :  0.044   0.179   1183
  Planarity :  0.004   0.060   1236
  Dihedral  : 16.853 179.377   1356
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.22 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.26 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.27), residues: 900
  helix:  0.27 (0.24), residues: 449
  sheet: -2.46 (0.55), residues: 81
  loop : -3.18 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  79 
 HIS   0.011   0.002   HIS A 367 
 PHE   0.021   0.002   PHE A1047 
 TYR   0.013   0.002   TYR A 116 
 ARG   0.003   0.000   ARG A 439 

*********************** 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
  143 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7920 (mm-40)
REVERT: A   77 VAL cc_start: 0.8460 (t) cc_final: 0.8225 (p)
REVERT: A  758 MET cc_start: 0.7929 (tmm) cc_final: 0.7519 (tmm)
REVERT: A  802 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.3837 (tp)
REVERT: A  880 LEU cc_start: 0.8260 (mm) cc_final: 0.7942 (mm)
  outliers start: 25
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1580
  time to fit residues: 30.5597
Evaluate side-chains
  123 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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  375 THR
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  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  666 ASP
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  770 ASN
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 62 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.154528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.135857 restraints weight = 15362.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.139147 restraints weight = 8914.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.141378 restraints weight = 6140.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7573  Z= 0.313
  Angle     :  0.714   8.352  10346  Z= 0.374
  Chirality :  0.046   0.184   1183
  Planarity :  0.005   0.069   1236
  Dihedral  : 16.857 179.762   1356
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 14.71 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 900
  helix: -0.01 (0.23), residues: 457
  sheet: -2.48 (0.55), residues: 80
  loop : -3.15 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  79 
 HIS   0.013   0.002   HIS A 367 
 PHE   0.019   0.002   PHE A1047 
 TYR   0.018   0.002   TYR A 995 
 ARG   0.005   0.000   ARG A 439 

*********************** 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
  147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7382 (mp) cc_final: 0.6492 (mm)
REVERT: A   50 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7895 (mm-40)
REVERT: A   77 VAL cc_start: 0.8440 (t) cc_final: 0.8138 (p)
REVERT: A  758 MET cc_start: 0.8079 (tmm) cc_final: 0.7495 (tmm)
REVERT: A  802 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.4177 (tp)
REVERT: A  880 LEU cc_start: 0.8240 (mm) cc_final: 0.7910 (mm)
REVERT: A  927 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6783 (mtm)
  outliers start: 31
  outliers final: 19
  residues processed: 131
  average time/residue: 0.1657
  time to fit residues: 31.0545
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  : 0.757 
-------------------------------------------------------------------------------
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  375 THR
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  409 ASP
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  651 VAL
Chi-restraints excluded: chain A residue  666 ASP
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  927 MET
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 37 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 993 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.158731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.138974 restraints weight = 15688.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.142440 restraints weight = 9266.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.144799 restraints weight = 6443.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7573  Z= 0.194
  Angle     :  0.667   9.271  10346  Z= 0.341
  Chirality :  0.044   0.225   1183
  Planarity :  0.004   0.068   1236
  Dihedral  : 16.752 178.561   1356
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.68 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.28), residues: 900
  helix:  0.26 (0.24), residues: 453
  sheet: -2.39 (0.55), residues: 81
  loop : -2.98 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  79 
 HIS   0.015   0.001   HIS A 367 
 PHE   0.020   0.002   PHE A 476 
 TYR   0.019   0.002   TYR A 995 
 ARG   0.005   0.000   ARG A 715 

*********************** 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
  149 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7298 (mp) cc_final: 0.6454 (mm)
REVERT: A   50 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7959 (mm-40)
REVERT: A  758 MET cc_start: 0.8122 (tmm) cc_final: 0.7439 (tmm)
REVERT: A  803 SER cc_start: 0.7542 (m) cc_final: 0.7183 (m)
REVERT: A  880 LEU cc_start: 0.8214 (mm) cc_final: 0.7881 (mm)
REVERT: A  996 TYR cc_start: 0.6460 (m-80) cc_final: 0.5600 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1752
  time to fit residues: 34.4760
Evaluate side-chains
  130 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  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 53 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0060
   chunk 88 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   overall best weight:    2.1802

-------------------------------------------------------------------------------
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 407 GLN
A 993 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.154901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.134995 restraints weight = 15895.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.138353 restraints weight = 9485.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.140594 restraints weight = 6664.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7573  Z= 0.292
  Angle     :  0.716   8.912  10346  Z= 0.368
  Chirality :  0.046   0.252   1183
  Planarity :  0.004   0.071   1236
  Dihedral  : 16.758 179.638   1356
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.56 %
    Favored  : 88.44 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 17.83 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.28), residues: 900
  helix:  0.18 (0.24), residues: 453
  sheet: -2.53 (0.53), residues: 86
  loop : -3.00 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  79 
 HIS   0.004   0.001   HIS A 931 
 PHE   0.016   0.002   PHE A1047 
 TYR   0.013   0.002   TYR A 656 
 ARG   0.005   0.000   ARG A 715 

*********************** 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
  151 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ILE cc_start: 0.7451 (mp) cc_final: 0.6622 (mm)
REVERT: A   50 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7950 (mm-40)
REVERT: A  680 GLU cc_start: 0.6589 (pt0) cc_final: 0.6300 (tt0)
REVERT: A  758 MET cc_start: 0.8062 (tmm) cc_final: 0.7381 (tmm)
REVERT: A  802 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.4200 (tp)
REVERT: A  849 MET cc_start: 0.8230 (mmp) cc_final: 0.7073 (mmp)
REVERT: A  880 LEU cc_start: 0.8231 (mm) cc_final: 0.7884 (mm)
REVERT: A  913 MET cc_start: 0.4062 (mmm) cc_final: 0.3656 (tpp)
  outliers start: 34
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1552
  time to fit residues: 31.2617
Evaluate side-chains
  138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
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  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  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  802 LEU
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 90 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4319 r_free = 0.4319 target = 0.157972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.138324 restraints weight = 15765.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.141824 restraints weight = 9240.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.144254 restraints weight = 6367.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7573  Z= 0.208
  Angle     :  0.696  11.377  10346  Z= 0.351
  Chirality :  0.044   0.232   1183
  Planarity :  0.004   0.075   1236
  Dihedral  : 16.701 178.294   1356
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.47 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.28), residues: 900
  helix:  0.32 (0.24), residues: 456
  sheet: -2.53 (0.54), residues: 85
  loop : -3.04 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A  79 
 HIS   0.003   0.001   HIS A 952 
 PHE   0.043   0.002   PHE A 783 
 TYR   0.013   0.002   TYR A 116 
 ARG   0.004   0.000   ARG A 439 

*********************** 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
  144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7906 (mm-40)
REVERT: A   80 PHE cc_start: 0.7892 (m-80) cc_final: 0.7539 (m-80)
REVERT: A  758 MET cc_start: 0.8144 (tmm) cc_final: 0.7513 (tmm)
REVERT: A  802 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4021 (tp)
REVERT: A  803 SER cc_start: 0.7514 (m) cc_final: 0.7089 (m)
REVERT: A  880 LEU cc_start: 0.8129 (mm) cc_final: 0.7785 (mm)
REVERT: A  996 TYR cc_start: 0.6443 (m-80) cc_final: 0.5630 (t80)
  outliers start: 29
  outliers final: 22
  residues processed: 138
  average time/residue: 0.1624
  time to fit residues: 31.9241
Evaluate side-chains
  129 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
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  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  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  802 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 64 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
A 993 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.156862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.137783 restraints weight = 15500.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.141110 restraints weight = 9175.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.143382 restraints weight = 6375.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7573  Z= 0.227
  Angle     :  0.713  11.007  10346  Z= 0.358
  Chirality :  0.045   0.214   1183
  Planarity :  0.004   0.075   1236
  Dihedral  : 16.686 178.772   1356
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 20.21 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.28), residues: 900
  helix:  0.34 (0.24), residues: 454
  sheet: -2.46 (0.55), residues: 85
  loop : -3.04 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A  79 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.032   0.002   PHE A 783 
 TYR   0.014   0.002   TYR A 116 
 ARG   0.003   0.000   ARG A 439 

*********************** 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
  146 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7892 (mm-40)
REVERT: A  407 GLN cc_start: 0.7275 (mt0) cc_final: 0.6935 (mm-40)
REVERT: A  542 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.6263 (t80)
REVERT: A  758 MET cc_start: 0.8082 (tmm) cc_final: 0.7406 (tmm)
REVERT: A  802 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.4075 (tp)
  outliers start: 30
  outliers final: 24
  residues processed: 138
  average time/residue: 0.1598
  time to fit residues: 31.5296
Evaluate side-chains
  133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
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  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  542 TYR
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  707 TYR
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  802 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 84 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.4164

-------------------------------------------------------------------------------
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 = 0.4312 r_free = 0.4312 target = 0.157514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.137681 restraints weight = 16091.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.141166 restraints weight = 9463.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.143492 restraints weight = 6553.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7573  Z= 0.222
  Angle     :  0.717  11.366  10346  Z= 0.358
  Chirality :  0.046   0.240   1183
  Planarity :  0.004   0.079   1236
  Dihedral  : 16.655 178.480   1356
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.28), residues: 900
  helix:  0.37 (0.24), residues: 455
  sheet: -2.43 (0.55), residues: 85
  loop : -3.07 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.003   TRP A  79 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.030   0.002   PHE A 783 
 TYR   0.018   0.002   TYR A 995 
 ARG   0.004   0.000   ARG A 715 

*********************** 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
  139 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6560 (tpt) cc_final: 0.6178 (tpt)
REVERT: A   50 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7925 (mm-40)
REVERT: A  758 MET cc_start: 0.8090 (tmm) cc_final: 0.7475 (tmm)
REVERT: A  802 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4042 (tp)
REVERT: A  880 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7715 (mm)
  outliers start: 28
  outliers final: 23
  residues processed: 132
  average time/residue: 0.1641
  time to fit residues: 31.1472
Evaluate side-chains
  131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  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  452 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  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  707 TYR
Chi-restraints excluded: chain A residue  770 ASN
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  880 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
A 975 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 = 0.4321 r_free = 0.4321 target = 0.158335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.139005 restraints weight = 15787.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.142477 restraints weight = 9271.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.144733 restraints weight = 6388.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7573  Z= 0.213
  Angle     :  0.731  12.168  10346  Z= 0.364
  Chirality :  0.046   0.238   1183
  Planarity :  0.004   0.080   1236
  Dihedral  : 16.629 178.203   1356
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.51 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.28), residues: 900
  helix:  0.41 (0.24), residues: 456
  sheet: -2.43 (0.55), residues: 85
  loop : -3.13 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.089   0.003   TRP A  79 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.026   0.002   PHE A 783 
 TYR   0.022   0.002   TYR A 995 
 ARG   0.005   0.001   ARG A 439 

********************** 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: 28
    poor density    : 116
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.6512 (tpt) cc_final: 0.6236 (tpt)
REVERT: A   50 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7906 (mm-40)
REVERT: A   77 VAL cc_start: 0.8477 (t) cc_final: 0.8122 (p)
REVERT: A  304 MET cc_start: 0.5521 (ptp) cc_final: 0.5121 (ptp)
REVERT: A  542 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.6171 (t80)
REVERT: A  758 MET cc_start: 0.8077 (tmm) cc_final: 0.7472 (tmm)
REVERT: A  802 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.3929 (tp)
REVERT: A  803 SER cc_start: 0.7569 (m) cc_final: 0.7171 (m)
REVERT: A  880 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7742 (mm)
  outliers start: 28
  outliers final: 22
  residues processed: 136
  average time/residue: 0.1760
  time to fit residues: 33.8242
Evaluate side-chains
  135 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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  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  452 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  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  802 LEU
Chi-restraints excluded: chain A residue  880 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 85 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 407 GLN
A 993 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.160111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.140505 restraints weight = 15714.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.143991 restraints weight = 9272.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.146353 restraints weight = 6427.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7573  Z= 0.201
  Angle     :  0.734  12.379  10346  Z= 0.364
  Chirality :  0.046   0.320   1183
  Planarity :  0.004   0.079   1236
  Dihedral  : 16.578 177.990   1356
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.40 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 900
  helix:  0.46 (0.24), residues: 456
  sheet: -2.37 (0.55), residues: 85
  loop : -3.10 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.096   0.003   TRP A  79 
 HIS   0.003   0.001   HIS A 952 
 PHE   0.025   0.002   PHE A 783 
 TYR   0.026   0.002   TYR A 995 
 ARG   0.012   0.001   ARG A 960 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2573.43 seconds
wall clock time: 45 minutes 34.54 seconds (2734.54 seconds total)