Starting phenix.real_space_refine
on Tue Mar 11 16:37:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2025/7tnz_26024.cif"
  }
  resolution = 3.54
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      24      5.49       5
     S      33      5.16       5
     C    3724      2.51       5
     N    1026      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5986
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5472
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 651}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 260
          Classifications: {'RNA': 12}
          Modifications used: {'rna3p': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 11}
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 253
          Classifications: {'RNA': 12}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4548  SG  CYS A 810      61.041  58.191  17.936  1.00 89.32           S
  ATOM   4987  SG  CYS A 864      59.505  57.429  14.128  1.00 94.72           S
  ATOM   5026  SG  CYS A 869      62.267  55.718  15.502  1.00 96.38           S

  Time building chain proxies: 3.98, per 1000 atoms: 0.66
  Number of scatterers: 5986
  At special positions: 0
  Unit cell: (96.12, 85.44, 82.236, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      33     16.00
     P      24     15.00
     O    1178      8.00
     N    1026      7.00
     C    3724      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: 1.52
  Conformation dependent library (CDL) restraints added in 785.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "


  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      49.4% alpha, 7.5% beta
      11 base pairs and 17 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 250
      removed outlier: 3.838A  pdb=" N   LEU A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 283
      removed outlier: 3.799A  pdb=" N   LYS A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 314
      removed outlier: 3.861A  pdb=" N   GLN A 305 " --> pdb=" O   PRO A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 341
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.988A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.961A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 381 through 397
      removed outlier: 4.450A  pdb=" N   GLY A 397 " --> pdb=" O   GLN A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 435
      removed outlier: 4.078A  pdb=" N   ASP A 425 " --> pdb=" O   ASP A 421 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 4.129A  pdb=" N   LEU A 449 " --> pdb=" O   ASN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 490
      removed outlier: 3.863A  pdb=" N   ILE A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 529 through 558
    Processing helix  chain 'A' and resid 559 through 576
      removed outlier: 3.765A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 603
      removed outlier: 3.938A  pdb=" N   LYS A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 649
    Processing helix  chain 'A' and resid 674 through 684
    Processing helix  chain 'A' and resid 720 through 729
    Processing helix  chain 'A' and resid 744 through 770
      removed outlier: 4.144A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A 756 " --> pdb=" O   GLN A 752 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A 759 " --> pdb=" O   MET A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
    Processing helix  chain 'A' and resid 836 through 840
      removed outlier: 3.812A  pdb=" N   GLU A 840 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 891
      No H-bonds generated for 'chain 'A' and resid 889 through 891'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 409
      removed outlier: 7.910A  pdb=" N   THR A 409 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   ILE A 262 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295
    Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.787A  pdb=" N   GLN A 457 " --> pdb=" O   CYS A 738 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   PHE A 459 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 632 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLY A 659 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 807 through 809
    Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832
    Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 845
    Processing sheet with id=AA7, first strand: chain 'A' and resid 874 through 878
    Processing sheet with id=AA8, first strand: chain 'A' and resid 893 through 895

    258 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      17 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1657
        1.33 -     1.45: 1010
        1.45 -     1.57: 3395
        1.57 -     1.69: 45
        1.69 -     1.82: 47
  Bond restraints: 6154
  Sorted by residual:
  bond pdb=" O3' 5GP B   1 "
       pdb=" P     G B   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.718 -0.111 1.50e-02 4.44e+03 5.48e+01
  bond pdb=" N   VAL A 414 "
       pdb=" CA  VAL A 414 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.06e-02 8.90e+03 1.04e+01
  bond pdb=" N   ILE A 704 "
       pdb=" CA  ILE A 704 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.040 1.25e-02 6.40e+03 1.03e+01
  bond pdb=" CA  ALA A 700 "
       pdb=" CB  ALA A 700 "
    ideal  model  delta    sigma   weight residual
    1.530  1.481  0.049 1.56e-02 4.11e+03 9.69e+00
  bond pdb=" CA  SER A 437 "
       pdb=" CB  SER A 437 "
    ideal  model  delta    sigma   weight residual
    1.537  1.494  0.043 1.38e-02 5.25e+03 9.58e+00
  ... (remaining 6149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 5902
        1.23 -     2.46: 2222
        2.46 -     3.70: 269
        3.70 -     4.93: 17
        4.93 -     6.16: 4
  Bond angle restraints: 8414
  Sorted by residual:
  angle pdb=" C3' 5GP B   1 "
        pdb=" O3' 5GP B   1 "
        pdb=" P     G B   2 "
      ideal   model   delta    sigma   weight residual
     120.20  114.04    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" N   SER A 743 "
        pdb=" CA  SER A 743 "
        pdb=" C   SER A 743 "
      ideal   model   delta    sigma   weight residual
     114.04  109.57    4.47 1.24e+00 6.50e-01 1.30e+01
  angle pdb=" C   THR A 347 "
        pdb=" N   PRO A 348 "
        pdb=" CA  PRO A 348 "
      ideal   model   delta    sigma   weight residual
     119.24  122.81   -3.57 1.04e+00 9.25e-01 1.18e+01
  angle pdb=" N   ALA A 684 "
        pdb=" CA  ALA A 684 "
        pdb=" C   ALA A 684 "
      ideal   model   delta    sigma   weight residual
     112.93  109.14    3.79 1.12e+00 7.97e-01 1.14e+01
  angle pdb=" O   ILE A 499 "
        pdb=" C   ILE A 499 "
        pdb=" N   GLN A 500 "
      ideal   model   delta    sigma   weight residual
     121.85  124.37   -2.52 7.60e-01 1.73e+00 1.10e+01
  ... (remaining 8409 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 3442
       17.67 -    35.35: 254
       35.35 -    53.02: 58
       53.02 -    70.70: 41
       70.70 -    88.37: 14
  Dihedral angle restraints: 3809
    sinusoidal: 1814
      harmonic: 1995
  Sorted by residual:
  dihedral pdb=" CA  ARG A 859 "
           pdb=" C   ARG A 859 "
           pdb=" N   ALA A 860 "
           pdb=" CA  ALA A 860 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.64  -20.36     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CB  GLU A 621 "
           pdb=" CG  GLU A 621 "
           pdb=" CD  GLU A 621 "
           pdb=" OE1 GLU A 621 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.94  -87.94     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU A 591 "
           pdb=" CG  GLU A 591 "
           pdb=" CD  GLU A 591 "
           pdb=" OE1 GLU A 591 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.22   86.22     1      3.00e+01 1.11e-03 9.96e+00
  ... (remaining 3806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 400
       0.041 -    0.082: 294
       0.082 -    0.123: 207
       0.123 -    0.164: 48
       0.164 -    0.204: 5
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" C3' 5GP B   1 "
            pdb=" C2' 5GP B   1 "
            pdb=" C4' 5GP B   1 "
            pdb=" O3' 5GP B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  PHE A 856 "
            pdb=" N   PHE A 856 "
            pdb=" C   PHE A 856 "
            pdb=" CB  PHE A 856 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" CA  ILE A 360 "
            pdb=" N   ILE A 360 "
            pdb=" C   ILE A 360 "
            pdb=" CB  ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.54e-01
  ... (remaining 951 not shown)

  Planarity restraints: 991
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  11 "   -0.015 2.00e-02 2.50e+03   1.30e-02 3.81e+00
        pdb=" N1    C B  11 "    0.029 2.00e-02 2.50e+03
        pdb=" C2    C B  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2    C B  11 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    C B  11 "    0.014 2.00e-02 2.50e+03
        pdb=" C4    C B  11 "    0.001 2.00e-02 2.50e+03
        pdb=" N4    C B  11 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    C B  11 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6    C B  11 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   9 "   -0.015 2.00e-02 2.50e+03   9.11e-03 2.49e+00
        pdb=" N9    G B   9 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G B   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G B   9 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    G B   9 "    0.008 2.00e-02 2.50e+03
        pdb=" C6    G B   9 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G B   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" N1    G B   9 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2    G B   9 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G B   9 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B   9 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    G B   9 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 527 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" C   ASP A 527 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASP A 527 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 528 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 988 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 879
        2.79 -     3.32: 6134
        3.32 -     3.84: 9707
        3.84 -     4.37: 11552
        4.37 -     4.90: 19112
  Nonbonded interactions: 47384
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 558 "
            pdb=" ND2 ASN A 608 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   THR A 697 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LYS A 379 "
            pdb=" OP1   G B   5 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" N   ASP A 701 "
            pdb=" OD1 ASP A 701 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   CYS A 374 "
            pdb=" OG1 THR A 377 "
     model   vdw
     2.342 3.040
  ... (remaining 47379 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.160
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
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      :  0.011   0.111   6154  Z= 0.707
  Angle     :  1.165   6.161   8414  Z= 0.855
  Chirality :  0.068   0.204    954
  Planarity :  0.004   0.032    991
  Dihedral  : 15.334  88.374   2513
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.80 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.45 %
    Favored  : 95.89 %
  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: -2.66 (0.29), residues: 676
  helix:  0.17 (0.27), residues: 317
  sheet: -4.32 (0.44), residues: 70
  loop : -3.39 (0.28), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP A 771 
 HIS   0.009   0.002   HIS A 444 
 PHE   0.024   0.003   PHE A 856 
 TYR   0.017   0.003   TYR A 566 
 ARG   0.004   0.001   ARG A 502 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp)
REVERT: A  369 MET cc_start: 0.7175 (mtt) cc_final: 0.6896 (mtp)
REVERT: A  459 PHE cc_start: 0.8451 (m-80) cc_final: 0.8059 (m-10)
REVERT: A  481 ASP cc_start: 0.7992 (m-30) cc_final: 0.7644 (m-30)
REVERT: A  523 PHE cc_start: 0.8105 (t80) cc_final: 0.7344 (t80)
REVERT: A  550 ASP cc_start: 0.8932 (m-30) cc_final: 0.8731 (m-30)
REVERT: A  562 ASP cc_start: 0.7457 (p0) cc_final: 0.6939 (p0)
REVERT: A  603 ASP cc_start: 0.8497 (t0) cc_final: 0.8012 (t0)
REVERT: A  620 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8377 (mt-10)
REVERT: A  625 ASN cc_start: 0.8627 (t0) cc_final: 0.8307 (t0)
REVERT: A  759 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7737 (mttt)
REVERT: A  845 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7155 (mtt90)
  outliers start: 4
  outliers final: 1
  residues processed: 141
  average time/residue: 0.2177
  time to fit residues: 38.6762
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  706 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
A 299 GLN
A 341 ASN
A 354 ASN
A 500 GLN
A 678 GLN
** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 GLN
A 867 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.153741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109629 restraints weight = 7394.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113594 restraints weight = 4734.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.116178 restraints weight = 3703.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6154  Z= 0.218
  Angle     :  0.538   7.947   8414  Z= 0.271
  Chirality :  0.039   0.163    954
  Planarity :  0.004   0.040    991
  Dihedral  : 14.107  83.533   1118
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.92 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.18 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.53 (0.32), residues: 676
  helix:  1.12 (0.29), residues: 324
  sheet: -3.97 (0.47), residues: 81
  loop : -2.78 (0.32), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 873 
 HIS   0.011   0.001   HIS A 280 
 PHE   0.020   0.001   PHE A 616 
 TYR   0.010   0.001   TYR A 879 
 ARG   0.003   0.000   ARG A 575 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8348 (t80) cc_final: 0.8110 (t80)
REVERT: A  523 PHE cc_start: 0.8039 (t80) cc_final: 0.7482 (t80)
REVERT: A  547 LYS cc_start: 0.8461 (tppt) cc_final: 0.7954 (mmtm)
REVERT: A  603 ASP cc_start: 0.8874 (t0) cc_final: 0.8283 (t0)
REVERT: A  625 ASN cc_start: 0.8672 (t0) cc_final: 0.8315 (t0)
REVERT: A  760 MET cc_start: 0.8704 (ttp) cc_final: 0.8438 (ttm)
REVERT: A  845 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.6849 (mtt90)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1920
  time to fit residues: 26.5713
Evaluate side-chains
  91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0980
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0570
   chunk 49 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 726 GLN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.157295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.113742 restraints weight = 7433.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118005 restraints weight = 4620.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120802 restraints weight = 3566.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6154  Z= 0.147
  Angle     :  0.497   6.698   8414  Z= 0.249
  Chirality :  0.038   0.164    954
  Planarity :  0.004   0.047    991
  Dihedral  : 14.072  73.856   1118
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.10 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.66 %
    Favored  : 84.54 %
  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: -1.11 (0.32), residues: 676
  helix:  1.47 (0.29), residues: 324
  sheet: -3.75 (0.48), residues: 81
  loop : -2.58 (0.33), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 873 
 HIS   0.006   0.001   HIS A 623 
 PHE   0.018   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 879 
 ARG   0.002   0.000   ARG A 575 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7992 (t80) cc_final: 0.7486 (t80)
REVERT: A  547 LYS cc_start: 0.8373 (tppt) cc_final: 0.7891 (mmtm)
REVERT: A  583 GLU cc_start: 0.8548 (mp0) cc_final: 0.8310 (mp0)
REVERT: A  603 ASP cc_start: 0.8895 (t0) cc_final: 0.8408 (t0)
REVERT: A  760 MET cc_start: 0.8721 (ttp) cc_final: 0.8519 (ttm)
  outliers start: 17
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1915
  time to fit residues: 28.0377
Evaluate side-chains
  95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  443 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.183920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.139149 restraints weight = 7699.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.144046 restraints weight = 4908.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.146778 restraints weight = 3818.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6154  Z= 0.191
  Angle     :  0.508   9.002   8414  Z= 0.255
  Chirality :  0.039   0.170    954
  Planarity :  0.004   0.045    991
  Dihedral  : 14.031  73.750   1118
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.40 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.80 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.91 (0.33), residues: 676
  helix:  1.57 (0.29), residues: 324
  sheet: -3.75 (0.48), residues: 81
  loop : -2.36 (0.34), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 623 
 PHE   0.020   0.001   PHE A 853 
 TYR   0.008   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 466 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7828 (t80) cc_final: 0.7563 (t80)
REVERT: A  583 GLU cc_start: 0.8396 (mp0) cc_final: 0.8185 (mp0)
REVERT: A  603 ASP cc_start: 0.8792 (t0) cc_final: 0.8446 (t0)
REVERT: A  706 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6361 (mt)
REVERT: A  760 MET cc_start: 0.8698 (ttp) cc_final: 0.8415 (ttm)
  outliers start: 18
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1794
  time to fit residues: 25.4100
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 59 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.176962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.132471 restraints weight = 7439.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137083 restraints weight = 4857.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.139914 restraints weight = 3830.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6154  Z= 0.225
  Angle     :  0.520   8.217   8414  Z= 0.263
  Chirality :  0.040   0.149    954
  Planarity :  0.004   0.050    991
  Dihedral  : 14.073  73.794   1118
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.95 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.81 (0.33), residues: 676
  helix:  1.65 (0.29), residues: 326
  sheet: -3.98 (0.48), residues: 79
  loop : -2.24 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 873 
 HIS   0.009   0.001   HIS A 623 
 PHE   0.012   0.001   PHE A 856 
 TYR   0.011   0.001   TYR A 246 
 ARG   0.002   0.000   ARG A 730 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7834 (t80) cc_final: 0.7516 (t80)
REVERT: A  583 GLU cc_start: 0.8435 (mp0) cc_final: 0.8180 (mp0)
REVERT: A  603 ASP cc_start: 0.8845 (t0) cc_final: 0.8503 (t0)
REVERT: A  706 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6669 (mp)
REVERT: A  760 MET cc_start: 0.8763 (ttp) cc_final: 0.8427 (ttm)
  outliers start: 18
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1670
  time to fit residues: 22.4763
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    0.0570
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
A 557 HIS
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.139946 restraints weight = 7494.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.141409 restraints weight = 6665.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143579 restraints weight = 4989.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6154  Z= 0.197
  Angle     :  0.507   7.261   8414  Z= 0.258
  Chirality :  0.039   0.141    954
  Planarity :  0.004   0.052    991
  Dihedral  : 14.073  73.794   1118
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.78 %
    Favored  : 79.61 %
  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: -0.70 (0.33), residues: 676
  helix:  1.67 (0.29), residues: 328
  sheet: -3.74 (0.53), residues: 72
  loop : -2.25 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 873 
 HIS   0.005   0.001   HIS A 623 
 PHE   0.011   0.001   PHE A 856 
 TYR   0.008   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 559 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7733 (t80) cc_final: 0.7424 (t80)
REVERT: A  583 GLU cc_start: 0.8433 (mp0) cc_final: 0.8130 (mp0)
REVERT: A  603 ASP cc_start: 0.8901 (t0) cc_final: 0.8546 (t0)
REVERT: A  706 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6651 (mp)
REVERT: A  760 MET cc_start: 0.8768 (ttp) cc_final: 0.8421 (ttm)
  outliers start: 22
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1849
  time to fit residues: 24.5916
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0980
   chunk 64 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.184412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.139898 restraints weight = 7540.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.144763 restraints weight = 4815.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.147742 restraints weight = 3762.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6154  Z= 0.162
  Angle     :  0.499   6.991   8414  Z= 0.254
  Chirality :  0.039   0.162    954
  Planarity :  0.004   0.056    991
  Dihedral  : 14.087  73.822   1118
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.93 %
    Favored  : 79.28 %
  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: -0.59 (0.34), residues: 676
  helix:  1.73 (0.29), residues: 330
  sheet: -3.64 (0.55), residues: 72
  loop : -2.21 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 623 
 PHE   0.009   0.001   PHE A 655 
 TYR   0.008   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 466 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A  603 ASP cc_start: 0.8813 (t0) cc_final: 0.8528 (t0)
REVERT: A  760 MET cc_start: 0.8719 (ttp) cc_final: 0.8387 (ttm)
  outliers start: 17
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1768
  time to fit residues: 23.5230
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.159149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116579 restraints weight = 7749.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.120572 restraints weight = 5079.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.123093 restraints weight = 4026.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6154  Z= 0.243
  Angle     :  0.551   7.428   8414  Z= 0.279
  Chirality :  0.040   0.221    954
  Planarity :  0.004   0.056    991
  Dihedral  : 14.073  73.757   1116
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.93 %
    Favored  : 79.28 %
  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: -0.71 (0.33), residues: 676
  helix:  1.64 (0.29), residues: 329
  sheet: -3.95 (0.51), residues: 73
  loop : -2.15 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 873 
 HIS   0.009   0.001   HIS A 280 
 PHE   0.031   0.002   PHE A 471 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 730 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.8074 (t80) cc_final: 0.7733 (t80)
REVERT: A  603 ASP cc_start: 0.8930 (t0) cc_final: 0.8552 (t0)
REVERT: A  625 ASN cc_start: 0.8423 (t0) cc_final: 0.8151 (t0)
REVERT: A  760 MET cc_start: 0.8768 (ttp) cc_final: 0.8395 (ttm)
  outliers start: 17
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1775
  time to fit residues: 22.4247
Evaluate side-chains
  94 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0070
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.162180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.119831 restraints weight = 7730.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.123920 restraints weight = 5037.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.126307 restraints weight = 3973.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6154  Z= 0.170
  Angle     :  0.529  10.781   8414  Z= 0.266
  Chirality :  0.039   0.167    954
  Planarity :  0.004   0.061    991
  Dihedral  : 14.073  73.843   1116
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.09 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.60 (0.34), residues: 676
  helix:  1.66 (0.29), residues: 331
  sheet: -3.84 (0.52), residues: 73
  loop : -2.05 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 280 
 PHE   0.039   0.002   PHE A 616 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.005   0.000   ARG A 664 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.8024 (t80) cc_final: 0.7720 (t80)
REVERT: A  603 ASP cc_start: 0.8924 (t0) cc_final: 0.8601 (t0)
REVERT: A  760 MET cc_start: 0.8766 (ttp) cc_final: 0.8417 (ttm)
  outliers start: 17
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1741
  time to fit residues: 22.2151
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0060
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.161675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120317 restraints weight = 7705.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124170 restraints weight = 5157.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.126729 restraints weight = 4133.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6154  Z= 0.162
  Angle     :  0.529  11.067   8414  Z= 0.265
  Chirality :  0.039   0.190    954
  Planarity :  0.004   0.062    991
  Dihedral  : 14.064  73.806   1116
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.26 %
    Favored  : 78.95 %
  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: -0.55 (0.34), residues: 676
  helix:  1.70 (0.29), residues: 331
  sheet: -3.78 (0.53), residues: 73
  loop : -2.03 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 873 
 HIS   0.007   0.001   HIS A 280 
 PHE   0.033   0.001   PHE A 471 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.004   0.000   ARG A 664 

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

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

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1352 Ramachandran restraints generated.
    676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7985 (t80) cc_final: 0.7672 (t80)
REVERT: A  760 MET cc_start: 0.8737 (ttp) cc_final: 0.8388 (ttm)
  outliers start: 17
  outliers final: 16
  residues processed: 94
  average time/residue: 0.1686
  time to fit residues: 21.4854
Evaluate side-chains
  93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  903 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.119104 restraints weight = 7769.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123056 restraints weight = 5244.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125493 restraints weight = 4172.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6154  Z= 0.176
  Angle     :  0.534   9.845   8414  Z= 0.269
  Chirality :  0.039   0.198    954
  Planarity :  0.004   0.061    991
  Dihedral  : 14.052  73.776   1116
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.42 %
    Favored  : 78.95 %
  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: -0.49 (0.34), residues: 676
  helix:  1.71 (0.29), residues: 331
  sheet: -3.73 (0.54), residues: 73
  loop : -1.96 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 873 
 HIS   0.007   0.001   HIS A 280 
 PHE   0.050   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 664 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2088.31 seconds
wall clock time: 37 minutes 15.15 seconds (2235.15 seconds total)