Starting phenix.real_space_refine
on Thu Jun  5 14:13:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tnz_26024/06_2025/7tnz_26024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/06_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_26024/06_2025/7tnz_26024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/06_2025/7tnz_26024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/06_2025/7tnz_26024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/06_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-5710/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
          Unusual residues: {'5GP%rna3p': 1}
          Classifications: {'RNA': 11, 'RNA_mixed': 1}
          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: 5.33, per 1000 atoms: 0.89
  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: 1.69
  Conformation dependent library (CDL) restraints added in 854.0 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: 2.15
  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: 2.28

  Time building geometry restraints manager: 1.99 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: 5899
        1.23 -     2.46: 2220
        2.46 -     3.70: 271
        3.70 -     4.93: 18
        4.93 -     6.16: 5
  Bond angle restraints: 8413
  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 8408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 3440
       17.67 -    35.35: 254
       35.35 -    53.02: 58
       53.02 -    70.70: 41
       70.70 -    88.37: 14
  Dihedral angle restraints: 3807
    sinusoidal: 1812
      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 3804 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 393
       0.040 -    0.080: 282
       0.080 -    0.120: 217
       0.120 -    0.159: 54
       0.159 -    0.199: 8
  Chirality restraints: 954
  Sorted by residual:
  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
  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     -2.49   -2.68    0.19 2.00e-01 2.50e+01 9.00e-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:             18.230
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.300
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:             0.020
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.150
-------------------------------------------------------------------------------
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      :  0.012   0.275   6157  Z= 0.832
  Angle     :  1.168   6.161   8413  Z= 0.855
  Chirality :  0.069   0.199    954
  Planarity :  0.004   0.032    991
  Dihedral  : 15.338  88.374   2511
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09624 (  286)
  hydrogen bonds       : angle       4.62379 (  806)
  metal coordination   : bond        0.24247 (    3)
  covalent geometry    : bond        0.01095 ( 6154)
  covalent geometry    : angle       1.16828 ( 8413)

*********************** 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  : 0.703 
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: 0.2154
  time to fit residues: 38.1737
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  : 0.709 
-------------------------------------------------------------------------------
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 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.153307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109195 restraints weight = 7403.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.113160 restraints weight = 4708.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115655 restraints weight = 3692.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6157  Z= 0.142
  Angle     :  0.539   8.179   8413  Z= 0.272
  Chirality :  0.039   0.165    954
  Planarity :  0.004   0.041    991
  Dihedral  : 14.076  83.402   1116
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.07 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.86 %
    Favored  : 87.34 %
  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: -1.54 (0.32), residues: 676
  helix:  1.12 (0.29), residues: 324
  sheet: -3.98 (0.47), residues: 81
  loop : -2.79 (0.32), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 873 
 HIS   0.011   0.001   HIS A 280 
 PHE   0.021   0.001   PHE A 616 
 TYR   0.009   0.001   TYR A 879 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  286)
  hydrogen bonds       : angle       3.67028 (  806)
  metal coordination   : bond        0.00462 (    3)
  covalent geometry    : bond        0.00335 ( 6154)
  covalent geometry    : angle       0.53913 ( 8413)

*********************** 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
  108 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  387 MET cc_start: 0.8778 (mmm) cc_final: 0.8550 (mmm)
REVERT: A  523 PHE cc_start: 0.8045 (t80) cc_final: 0.7505 (t80)
REVERT: A  547 LYS cc_start: 0.8397 (tppt) cc_final: 0.7949 (mmtm)
REVERT: A  603 ASP cc_start: 0.8867 (t0) cc_final: 0.8263 (t0)
REVERT: A  625 ASN cc_start: 0.8678 (t0) cc_final: 0.8323 (t0)
REVERT: A  760 MET cc_start: 0.8698 (ttp) cc_final: 0.8454 (ttm)
REVERT: A  845 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.6852 (mtt90)
  outliers start: 11
  outliers final: 6
  residues processed: 105
  average time/residue: 0.2223
  time to fit residues: 30.9046
Evaluate side-chains
  91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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  903 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 HIS
A 557 HIS
A 726 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.148214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.104714 restraints weight = 7514.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108559 restraints weight = 4763.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.111022 restraints weight = 3734.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6157  Z= 0.213
  Angle     :  0.592   7.595   8413  Z= 0.300
  Chirality :  0.042   0.208    954
  Planarity :  0.004   0.046    991
  Dihedral  : 14.140  77.259   1116
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.54 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.49 %
    Favored  : 83.72 %
  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: -1.36 (0.32), residues: 676
  helix:  1.22 (0.29), residues: 323
  sheet: -4.16 (0.43), residues: 85
  loop : -2.48 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 873 
 HIS   0.006   0.002   HIS A 623 
 PHE   0.018   0.002   PHE A 616 
 TYR   0.013   0.002   TYR A 717 
 ARG   0.003   0.001   ARG A 730 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  286)
  hydrogen bonds       : angle       3.78124 (  806)
  metal coordination   : bond        0.00342 (    3)
  covalent geometry    : bond        0.00499 ( 6154)
  covalent geometry    : angle       0.59225 ( 8413)

*********************** 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
  110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  435 ASP cc_start: 0.8640 (t0) cc_final: 0.8435 (t0)
REVERT: A  523 PHE cc_start: 0.8050 (t80) cc_final: 0.7570 (t80)
REVERT: A  583 GLU cc_start: 0.8513 (mp0) cc_final: 0.8228 (mp0)
REVERT: A  603 ASP cc_start: 0.8901 (t0) cc_final: 0.8335 (t0)
REVERT: A  695 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8602 (mt)
REVERT: A  760 MET cc_start: 0.8779 (ttp) cc_final: 0.8402 (ttm)
REVERT: A  845 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7313 (mtt90)
  outliers start: 17
  outliers final: 9
  residues processed: 107
  average time/residue: 0.2281
  time to fit residues: 32.9771
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
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  640 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  706 ILE
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0170
   chunk 10 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    0.2980
   overall best weight:    0.9620

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.158811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.117012 restraints weight = 7768.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120879 restraints weight = 5206.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123331 restraints weight = 4173.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6157  Z= 0.128
  Angle     :  0.515   8.262   8413  Z= 0.262
  Chirality :  0.039   0.176    954
  Planarity :  0.004   0.047    991
  Dihedral  : 14.097  73.824   1116
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.40 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.13 %
    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: -1.03 (0.33), residues: 676
  helix:  1.51 (0.29), residues: 323
  sheet: -4.06 (0.48), residues: 79
  loop : -2.38 (0.34), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 623 
 PHE   0.027   0.001   PHE A 616 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  286)
  hydrogen bonds       : angle       3.63010 (  806)
  metal coordination   : bond        0.00158 (    3)
  covalent geometry    : bond        0.00297 ( 6154)
  covalent geometry    : angle       0.51532 ( 8413)

*********************** 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
  116 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7865 (mmmt)
REVERT: A  523 PHE cc_start: 0.7915 (t80) cc_final: 0.7575 (t80)
REVERT: A  547 LYS cc_start: 0.8635 (tppt) cc_final: 0.8149 (mmtm)
REVERT: A  550 ASP cc_start: 0.8703 (m-30) cc_final: 0.8388 (m-30)
REVERT: A  603 ASP cc_start: 0.8777 (t0) cc_final: 0.8485 (t0)
REVERT: A  625 ASN cc_start: 0.8429 (t0) cc_final: 0.8206 (t0)
REVERT: A  695 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8736 (mt)
REVERT: A  755 MET cc_start: 0.8396 (tpp) cc_final: 0.8160 (mmt)
REVERT: A  760 MET cc_start: 0.8783 (ttp) cc_final: 0.8408 (ttm)
REVERT: A  845 ARG cc_start: 0.7583 (mtt-85) cc_final: 0.7075 (mtt90)
  outliers start: 23
  outliers final: 14
  residues processed: 110
  average time/residue: 0.2182
  time to fit residues: 32.6347
Evaluate side-chains
  100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
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  458 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  827 GLU
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:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.111900 restraints weight = 7658.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.115487 restraints weight = 5311.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.117357 restraints weight = 4312.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6157  Z= 0.212
  Angle     :  0.573   8.495   8413  Z= 0.295
  Chirality :  0.041   0.157    954
  Planarity :  0.005   0.060    991
  Dihedral  : 14.158  73.798   1116
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.84 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 16.28 %
    Favored  : 79.44 %
  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: -1.13 (0.33), residues: 676
  helix:  1.36 (0.29), residues: 327
  sheet: -3.84 (0.47), residues: 93
  loop : -2.35 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 873 
 HIS   0.009   0.002   HIS A 623 
 PHE   0.035   0.002   PHE A 853 
 TYR   0.009   0.001   TYR A 390 
 ARG   0.004   0.000   ARG A 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  286)
  hydrogen bonds       : angle       3.79594 (  806)
  metal coordination   : bond        0.00350 (    3)
  covalent geometry    : bond        0.00495 ( 6154)
  covalent geometry    : angle       0.57344 ( 8413)

*********************** 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
  106 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (mmmt)
REVERT: A  523 PHE cc_start: 0.7815 (t80) cc_final: 0.7515 (t80)
REVERT: A  550 ASP cc_start: 0.8691 (m-30) cc_final: 0.8367 (m-30)
REVERT: A  579 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.5006 (t80)
REVERT: A  603 ASP cc_start: 0.8846 (t0) cc_final: 0.8526 (t0)
REVERT: A  625 ASN cc_start: 0.8454 (t0) cc_final: 0.8125 (t0)
REVERT: A  755 MET cc_start: 0.8455 (tpp) cc_final: 0.8209 (mmt)
REVERT: A  760 MET cc_start: 0.8824 (ttp) cc_final: 0.8387 (ttm)
REVERT: A  845 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7109 (mtt90)
  outliers start: 26
  outliers final: 18
  residues processed: 98
  average time/residue: 0.1816
  time to fit residues: 23.8752
Evaluate side-chains
  95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  412 VAL
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  520 CYS
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain A residue  640 VAL
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  827 GLU
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:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0980
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.160029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118968 restraints weight = 7596.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122832 restraints weight = 5143.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.125271 restraints weight = 4117.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6157  Z= 0.105
  Angle     :  0.507   8.122   8413  Z= 0.257
  Chirality :  0.039   0.170    954
  Planarity :  0.004   0.053    991
  Dihedral  : 14.064  73.864   1116
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.43 %
    Favored  : 79.44 %
  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: -0.73 (0.34), residues: 676
  helix:  1.67 (0.29), residues: 326
  sheet: -3.91 (0.51), residues: 79
  loop : -2.14 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 512 
 HIS   0.010   0.001   HIS A 623 
 PHE   0.032   0.001   PHE A 616 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  286)
  hydrogen bonds       : angle       3.57741 (  806)
  metal coordination   : bond        0.00076 (    3)
  covalent geometry    : bond        0.00237 ( 6154)
  covalent geometry    : angle       0.50739 ( 8413)

*********************** 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: 19
    poor density    : 86
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7812 (t80) cc_final: 0.7543 (t80)
REVERT: A  550 ASP cc_start: 0.8690 (m-30) cc_final: 0.8361 (m-30)
REVERT: A  579 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.5053 (t80)
REVERT: A  603 ASP cc_start: 0.8827 (t0) cc_final: 0.8536 (t0)
REVERT: A  695 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8678 (mt)
REVERT: A  755 MET cc_start: 0.8542 (tpp) cc_final: 0.8307 (mmt)
REVERT: A  760 MET cc_start: 0.8788 (ttp) cc_final: 0.8410 (ttm)
REVERT: A  845 ARG cc_start: 0.7628 (mtt-85) cc_final: 0.7109 (mtt90)
  outliers start: 19
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1981
  time to fit residues: 27.0236
Evaluate side-chains
  91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  632 LEU
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  827 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0270
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.1644

-------------------------------------------------------------------------------
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 = 0.159270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115869 restraints weight = 7848.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119997 restraints weight = 5143.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122495 restraints weight = 4098.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6157  Z= 0.144
  Angle     :  0.545   8.391   8413  Z= 0.274
  Chirality :  0.040   0.240    954
  Planarity :  0.004   0.056    991
  Dihedral  : 14.066  73.774   1114
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.75 %
    Favored  : 78.12 %
  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: -0.80 (0.34), residues: 676
  helix:  1.60 (0.29), residues: 329
  sheet: -3.96 (0.50), residues: 79
  loop : -2.21 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 873 
 HIS   0.011   0.001   HIS A 623 
 PHE   0.036   0.002   PHE A 616 
 TYR   0.011   0.001   TYR A 390 
 ARG   0.008   0.000   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  286)
  hydrogen bonds       : angle       3.62192 (  806)
  metal coordination   : bond        0.00207 (    3)
  covalent geometry    : bond        0.00339 ( 6154)
  covalent geometry    : angle       0.54548 ( 8413)

*********************** 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
  101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7924 (t80) cc_final: 0.7649 (t80)
REVERT: A  550 ASP cc_start: 0.8786 (m-30) cc_final: 0.8430 (m-30)
REVERT: A  603 ASP cc_start: 0.8926 (t0) cc_final: 0.8587 (t0)
REVERT: A  625 ASN cc_start: 0.8405 (t0) cc_final: 0.8107 (t0)
REVERT: A  628 THR cc_start: 0.7145 (t) cc_final: 0.6853 (t)
REVERT: A  664 ARG cc_start: 0.6566 (mpt180) cc_final: 0.6355 (mpp80)
REVERT: A  760 MET cc_start: 0.8803 (ttp) cc_final: 0.8431 (ttm)
REVERT: A  845 ARG cc_start: 0.7652 (mtt-85) cc_final: 0.7078 (mtt90)
  outliers start: 19
  outliers final: 14
  residues processed: 98
  average time/residue: 0.2209
  time to fit residues: 29.2633
Evaluate side-chains
  95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  387 MET
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  640 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  827 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.162008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118738 restraints weight = 7743.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122955 restraints weight = 5104.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125180 restraints weight = 4047.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6157  Z= 0.114
  Angle     :  0.515   8.756   8413  Z= 0.262
  Chirality :  0.040   0.171    954
  Planarity :  0.004   0.057    991
  Dihedral  : 14.045  73.830   1114
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.57 %
    Favored  : 77.80 %
  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: -0.69 (0.33), residues: 676
  helix:  1.73 (0.29), residues: 323
  sheet: -3.79 (0.54), residues: 66
  loop : -2.29 (0.35), residues: 287

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   0.024   0.001   PHE A 616 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  286)
  hydrogen bonds       : angle       3.57110 (  806)
  metal coordination   : bond        0.00117 (    3)
  covalent geometry    : bond        0.00264 ( 6154)
  covalent geometry    : angle       0.51516 ( 8413)

*********************** 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
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.7891 (t80) cc_final: 0.7647 (t80)
REVERT: A  550 ASP cc_start: 0.8760 (m-30) cc_final: 0.8413 (m-30)
REVERT: A  603 ASP cc_start: 0.8904 (t0) cc_final: 0.8641 (t0)
REVERT: A  664 ARG cc_start: 0.6553 (mpt180) cc_final: 0.6336 (mpp80)
REVERT: A  706 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6596 (mp)
REVERT: A  760 MET cc_start: 0.8806 (ttp) cc_final: 0.8447 (ttm)
REVERT: A  845 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7075 (mtt90)
REVERT: A  895 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6972 (mm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 95
  average time/residue: 0.2465
  time to fit residues: 32.7079
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
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  387 MET
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  759 LYS
Chi-restraints excluded: chain A residue  827 GLU
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:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   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 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 = 0.3970 r_free = 0.3970 target = 0.173069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.131376 restraints weight = 7539.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.133708 restraints weight = 5715.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.134993 restraints weight = 4745.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6157  Z= 0.168
  Angle     :  0.559   8.864   8413  Z= 0.282
  Chirality :  0.041   0.178    954
  Planarity :  0.004   0.059    991
  Dihedral  : 14.122  73.754   1114
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.41 %
    Favored  : 77.30 %
  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:  1.68 (0.29), residues: 322
  sheet: -3.55 (0.49), residues: 92
  loop : -2.27 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 873 
 HIS   0.008   0.001   HIS A 280 
 PHE   0.023   0.002   PHE A 616 
 TYR   0.011   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 730 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03656 (  286)
  hydrogen bonds       : angle       3.64215 (  806)
  metal coordination   : bond        0.00238 (    3)
  covalent geometry    : bond        0.00396 ( 6154)
  covalent geometry    : angle       0.55853 ( 8413)

*********************** 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: 20
    poor density    : 79
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A  523 PHE cc_start: 0.7796 (t80) cc_final: 0.7408 (t80)
REVERT: A  550 ASP cc_start: 0.8730 (m-30) cc_final: 0.8380 (m-30)
REVERT: A  603 ASP cc_start: 0.8931 (t0) cc_final: 0.8663 (t0)
REVERT: A  625 ASN cc_start: 0.8448 (t0) cc_final: 0.8147 (t0)
REVERT: A  664 ARG cc_start: 0.6759 (mpt180) cc_final: 0.6540 (mpp80)
REVERT: A  706 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6733 (mp)
REVERT: A  760 MET cc_start: 0.8800 (ttp) cc_final: 0.8405 (ttm)
REVERT: A  845 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7184 (mtt90)
  outliers start: 20
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1773
  time to fit residues: 22.7156
Evaluate side-chains
  95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  564 LEU
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  718 VAL
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:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0970
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0870
   chunk 64 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.183152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139612 restraints weight = 7612.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.144454 restraints weight = 4869.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.147453 restraints weight = 3804.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6157  Z= 0.105
  Angle     :  0.523   8.137   8413  Z= 0.267
  Chirality :  0.039   0.185    954
  Planarity :  0.004   0.061    991
  Dihedral  : 14.079  73.882   1114
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 20.56 %
    Favored  : 76.97 %
  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: -0.64 (0.34), residues: 676
  helix:  1.80 (0.29), residues: 324
  sheet: -3.68 (0.48), residues: 83
  loop : -2.17 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 623 
 PHE   0.048   0.001   PHE A 616 
 TYR   0.011   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  286)
  hydrogen bonds       : angle       3.55337 (  806)
  metal coordination   : bond        0.00079 (    3)
  covalent geometry    : bond        0.00237 ( 6154)
  covalent geometry    : angle       0.52293 ( 8413)

********************** 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
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A  523 PHE cc_start: 0.7732 (t80) cc_final: 0.7396 (t80)
REVERT: A  755 MET cc_start: 0.8575 (tpp) cc_final: 0.8279 (mmt)
REVERT: A  760 MET cc_start: 0.8740 (ttp) cc_final: 0.8341 (ttm)
REVERT: A  845 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.7180 (mtt90)
  outliers start: 15
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1835
  time to fit residues: 23.7864
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  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  387 MET
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  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:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.173118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.131409 restraints weight = 7653.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.132478 restraints weight = 6051.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.134157 restraints weight = 4912.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6157  Z= 0.173
  Angle     :  0.574   8.841   8413  Z= 0.292
  Chirality :  0.041   0.203    954
  Planarity :  0.004   0.058    991
  Dihedral  : 14.110  73.773   1114
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.72 %
    Favored  : 76.64 %
  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 (0.34), residues: 676
  helix:  1.72 (0.29), residues: 324
  sheet: -3.47 (0.50), residues: 92
  loop : -2.18 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 873 
 HIS   0.014   0.002   HIS A 623 
 PHE   0.050   0.002   PHE A 471 
 TYR   0.011   0.001   TYR A 390 
 ARG   0.008   0.000   ARG A 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  286)
  hydrogen bonds       : angle       3.63098 (  806)
  metal coordination   : bond        0.00269 (    3)
  covalent geometry    : bond        0.00409 ( 6154)
  covalent geometry    : angle       0.57376 ( 8413)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2519.70 seconds
wall clock time: 46 minutes 16.12 seconds (2776.12 seconds total)