Starting phenix.real_space_refine
on Tue Mar  3 14:50:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tnz_26024/03_2026/7tnz_26024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/03_2026/7tnz_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_2026/7tnz_26024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2026/7tnz_26024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2026/7tnz_26024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/03_2026/7tnz_26024.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.41, per 1000 atoms: 0.24
  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: 0.60
  Conformation dependent library (CDL) restraints added in 208.6 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: 0.70
  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: 1.07

  Time building geometry restraints manager: 0.79 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:             0.660
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.630
-------------------------------------------------------------------------------
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 : 8.24
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (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
 ARG   0.004   0.001   ARG A 502 
 TYR   0.017   0.003   TYR A 566 
 PHE   0.024   0.003   PHE A 856 
 TRP   0.011   0.003   TRP A 771 
 HIS   0.009   0.002   HIS A 444 

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

*********************** 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  : 0.233 
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: 0.7456 (p0) cc_final: 0.6938 (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: 0.0945
  time to fit residues: 16.8661
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  : 0.225 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 867 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.155617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111613 restraints weight = 7466.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.115692 restraints weight = 4711.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.118229 restraints weight = 3667.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119531 restraints weight = 3176.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.120711 restraints weight = 2935.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6157  Z= 0.123
  Angle     :  0.525   7.990   8413  Z= 0.264
  Chirality :  0.039   0.168    954
  Planarity :  0.004   0.040    991
  Dihedral  : 14.059  83.468   1116
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.21 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.18 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.32), residues: 676
  helix:  1.15 (0.29), residues: 324
  sheet: -4.00 (0.44), residues: 86
  loop : -2.77 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 575 
 TYR   0.010   0.001   TYR A 879 
 PHE   0.022   0.001   PHE A 616 
 TRP   0.008   0.001   TRP A 873 
 HIS   0.012   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6154)
  covalent geometry    : angle       0.52529 ( 8413)
  hydrogen bonds       : bond        0.03296 (  286)
  hydrogen bonds       : angle       3.63707 (  806)
  metal coordination   : bond        0.00169 (    3)

*********************** 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  : 0.222 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8235 (t80) cc_final: 0.7962 (t80)
REVERT: A  387 MET cc_start: 0.8756 (mmm) cc_final: 0.8518 (mmm)
REVERT: A  523 PHE cc_start: 0.8045 (t80) cc_final: 0.7488 (t80)
REVERT: A  547 LYS cc_start: 0.8328 (tppt) cc_final: 0.7936 (mmtm)
REVERT: A  550 ASP cc_start: 0.8653 (m-30) cc_final: 0.8381 (m-30)
REVERT: A  603 ASP cc_start: 0.8836 (t0) cc_final: 0.8242 (t0)
REVERT: A  625 ASN cc_start: 0.8636 (t0) cc_final: 0.8332 (t0)
REVERT: A  760 MET cc_start: 0.8681 (ttp) cc_final: 0.8444 (ttm)
REVERT: A  845 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.6836 (mtt90)
  outliers start: 11
  outliers final: 6
  residues processed: 105
  average time/residue: 0.0967
  time to fit residues: 12.9985
Evaluate side-chains
  88 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0000
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.7590

-------------------------------------------------------------------------------
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 557 HIS
A 726 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.148378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.104606 restraints weight = 7525.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108477 restraints weight = 4768.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110784 restraints weight = 3720.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112365 restraints weight = 3243.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.113053 restraints weight = 2981.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2520

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= 0.194
  Angle     :  0.580   7.547   8413  Z= 0.293
  Chirality :  0.041   0.206    954
  Planarity :  0.004   0.044    991
  Dihedral  : 14.145  75.278   1116
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.40 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.83 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.32), residues: 676
  helix:  1.29 (0.29), residues: 323
  sheet: -4.06 (0.45), residues: 85
  loop : -2.46 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 730 
 TYR   0.012   0.002   TYR A 717 
 PHE   0.018   0.002   PHE A 616 
 TRP   0.012   0.002   TRP A 873 
 HIS   0.007   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6154)
  covalent geometry    : angle       0.57959 ( 8413)
  hydrogen bonds       : bond        0.03816 (  286)
  hydrogen bonds       : angle       3.73884 (  806)
  metal coordination   : bond        0.00332 (    3)

*********************** 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
  114 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  523 PHE cc_start: 0.8029 (t80) cc_final: 0.7599 (t80)
REVERT: A  583 GLU cc_start: 0.8474 (mp0) cc_final: 0.8226 (mp0)
REVERT: A  603 ASP cc_start: 0.8915 (t0) cc_final: 0.8466 (t0)
REVERT: A  625 ASN cc_start: 0.8528 (t0) cc_final: 0.8263 (t0)
REVERT: A  695 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8588 (mt)
REVERT: A  760 MET cc_start: 0.8770 (ttp) cc_final: 0.8384 (ttm)
REVERT: A  845 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.6925 (mtt90)
  outliers start: 18
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0822
  time to fit residues: 11.9736
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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 42 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 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 = 0.3863 r_free = 0.3863 target = 0.162833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119150 restraints weight = 7748.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123288 restraints weight = 5095.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.125908 restraints weight = 4063.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.127182 restraints weight = 3564.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127803 restraints weight = 3315.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6157  Z= 0.106
  Angle     :  0.493   8.459   8413  Z= 0.250
  Chirality :  0.038   0.160    954
  Planarity :  0.004   0.048    991
  Dihedral  : 14.085  73.869   1116
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.10 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.33), residues: 676
  helix:  1.60 (0.29), residues: 323
  sheet: -3.98 (0.49), residues: 79
  loop : -2.37 (0.34), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.009   0.001   TYR A 246 
 PHE   0.029   0.001   PHE A 616 
 TRP   0.011   0.001   TRP A 873 
 HIS   0.008   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6154)
  covalent geometry    : angle       0.49340 ( 8413)
  hydrogen bonds       : bond        0.03179 (  286)
  hydrogen bonds       : angle       3.58987 (  806)
  metal coordination   : bond        0.00114 (    3)

*********************** 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: 20
    poor density    : 96
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7975 (mmmt)
REVERT: A  523 PHE cc_start: 0.7946 (t80) cc_final: 0.7582 (t80)
REVERT: A  550 ASP cc_start: 0.8728 (m-30) cc_final: 0.8363 (m-30)
REVERT: A  583 GLU cc_start: 0.8434 (mp0) cc_final: 0.8192 (mp0)
REVERT: A  603 ASP cc_start: 0.8854 (t0) cc_final: 0.8489 (t0)
REVERT: A  695 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8686 (mt)
REVERT: A  706 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6688 (mp)
REVERT: A  755 MET cc_start: 0.8399 (tpp) cc_final: 0.8167 (mmt)
REVERT: A  760 MET cc_start: 0.8776 (ttp) cc_final: 0.8431 (ttm)
REVERT: A  895 GLU cc_start: 0.7577 (tp30) cc_final: 0.7346 (mm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0772
  time to fit residues: 11.1854
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  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 PHE
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  562 ASP
Chi-restraints excluded: chain A residue  579 PHE
Chi-restraints excluded: chain A residue  629 ILE
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    0.4980
   chunk 40 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 19 optimal weight:    0.2980
   chunk 52 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117920 restraints weight = 7883.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121875 restraints weight = 5349.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124317 restraints weight = 4286.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.125574 restraints weight = 3784.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125975 restraints weight = 3507.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6157  Z= 0.120
  Angle     :  0.493   7.716   8413  Z= 0.249
  Chirality :  0.038   0.163    954
  Planarity :  0.004   0.050    991
  Dihedral  : 14.035  73.789   1116
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.78 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.33), residues: 676
  helix:  1.75 (0.29), residues: 323
  sheet: -3.97 (0.48), residues: 79
  loop : -2.22 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 811 
 TYR   0.009   0.001   TYR A 390 
 PHE   0.031   0.002   PHE A 616 
 TRP   0.010   0.002   TRP A 873 
 HIS   0.007   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6154)
  covalent geometry    : angle       0.49253 ( 8413)
  hydrogen bonds       : bond        0.03212 (  286)
  hydrogen bonds       : angle       3.54607 (  806)
  metal coordination   : bond        0.00145 (    3)

*********************** 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: 21
    poor density    : 84
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7892 (mmmt)
REVERT: A  523 PHE cc_start: 0.7797 (t80) cc_final: 0.7517 (t80)
REVERT: A  583 GLU cc_start: 0.8337 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  603 ASP cc_start: 0.8841 (t0) cc_final: 0.8500 (t0)
REVERT: A  695 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8612 (mt)
REVERT: A  706 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6581 (mp)
REVERT: A  755 MET cc_start: 0.8392 (tpp) cc_final: 0.8139 (mmt)
REVERT: A  760 MET cc_start: 0.8756 (ttp) cc_final: 0.8417 (ttm)
  outliers start: 21
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0759
  time to fit residues: 10.1494
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  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  272 PHE
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  579 PHE
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  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 19 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0870
   chunk 41 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.9760

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.117088 restraints weight = 7786.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.121267 restraints weight = 5130.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123738 restraints weight = 4090.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124926 restraints weight = 3602.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.125032 restraints weight = 3372.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6157  Z= 0.124
  Angle     :  0.503   8.585   8413  Z= 0.252
  Chirality :  0.039   0.151    954
  Planarity :  0.004   0.050    991
  Dihedral  : 14.053  73.777   1116
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.33), residues: 676
  helix:  1.75 (0.29), residues: 326
  sheet: -3.86 (0.51), residues: 79
  loop : -2.26 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 811 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.034   0.002   PHE A 616 
 TRP   0.015   0.002   TRP A 646 
 HIS   0.006   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6154)
  covalent geometry    : angle       0.50254 ( 8413)
  hydrogen bonds       : bond        0.03224 (  286)
  hydrogen bonds       : angle       3.55411 (  806)
  metal coordination   : bond        0.00169 (    3)

*********************** 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
  104 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (mmmt)
REVERT: A  523 PHE cc_start: 0.7824 (t80) cc_final: 0.7520 (t80)
REVERT: A  583 GLU cc_start: 0.8425 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  603 ASP cc_start: 0.8886 (t0) cc_final: 0.8501 (t0)
REVERT: A  695 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8656 (mt)
REVERT: A  706 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6637 (mp)
REVERT: A  755 MET cc_start: 0.8399 (tpp) cc_final: 0.8160 (mmt)
REVERT: A  760 MET cc_start: 0.8794 (ttp) cc_final: 0.8444 (ttm)
  outliers start: 23
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0746
  time to fit residues: 10.0496
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  : 0.231 
-------------------------------------------------------------------------------
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  562 ASP
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  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 34 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.175763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.133438 restraints weight = 7541.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.136336 restraints weight = 6137.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137989 restraints weight = 4811.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138644 restraints weight = 4242.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.138817 restraints weight = 3846.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3038

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= 0.138
  Angle     :  0.508   9.084   8413  Z= 0.258
  Chirality :  0.039   0.140    954
  Planarity :  0.004   0.056    991
  Dihedral  : 14.052  73.781   1116
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.34), residues: 676
  helix:  1.77 (0.29), residues: 326
  sheet: -3.55 (0.53), residues: 87
  loop : -2.29 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 811 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.022   0.001   PHE A 853 
 TRP   0.012   0.002   TRP A 873 
 HIS   0.004   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6154)
  covalent geometry    : angle       0.50839 ( 8413)
  hydrogen bonds       : bond        0.03337 (  286)
  hydrogen bonds       : angle       3.56709 (  806)
  metal coordination   : bond        0.00208 (    3)

*********************** 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
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7919 (mmmt)
REVERT: A  583 GLU cc_start: 0.8378 (mp0) cc_final: 0.8168 (mp0)
REVERT: A  603 ASP cc_start: 0.8825 (t0) cc_final: 0.8540 (t0)
REVERT: A  625 ASN cc_start: 0.8448 (t0) cc_final: 0.8153 (t0)
REVERT: A  664 ARG cc_start: 0.6663 (mpt180) cc_final: 0.6330 (mpt180)
REVERT: A  706 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6646 (mp)
REVERT: A  755 MET cc_start: 0.8403 (tpp) cc_final: 0.8155 (mmt)
REVERT: A  760 MET cc_start: 0.8749 (ttp) cc_final: 0.8381 (ttm)
REVERT: A  895 GLU cc_start: 0.7677 (tp30) cc_final: 0.7123 (mm-30)
  outliers start: 18
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0758
  time to fit residues: 9.9383
Evaluate side-chains
  89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  640 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 32 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.182461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138708 restraints weight = 7595.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.143383 restraints weight = 4865.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146367 restraints weight = 3797.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.147640 restraints weight = 3304.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.149044 restraints weight = 3068.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6157  Z= 0.109
  Angle     :  0.493   8.632   8413  Z= 0.249
  Chirality :  0.039   0.175    954
  Planarity :  0.004   0.055    991
  Dihedral  : 14.034  73.817   1116
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.59 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.34), residues: 676
  helix:  1.80 (0.29), residues: 329
  sheet: -3.45 (0.56), residues: 72
  loop : -2.21 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 811 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.039   0.001   PHE A 616 
 TRP   0.012   0.002   TRP A 873 
 HIS   0.004   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6154)
  covalent geometry    : angle       0.49300 ( 8413)
  hydrogen bonds       : bond        0.03189 (  286)
  hydrogen bonds       : angle       3.51681 (  806)
  metal coordination   : bond        0.00110 (    3)

*********************** 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
  98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7909 (mmmt)
REVERT: A  603 ASP cc_start: 0.8781 (t0) cc_final: 0.8532 (t0)
REVERT: A  755 MET cc_start: 0.8434 (tpp) cc_final: 0.8161 (mmt)
REVERT: A  760 MET cc_start: 0.8737 (ttp) cc_final: 0.8376 (ttm)
REVERT: A  895 GLU cc_start: 0.7641 (tp30) cc_final: 0.7329 (mm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0785
  time to fit residues: 9.8718
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  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  387 MET
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  579 PHE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    0.0670
   chunk 68 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.9924

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.181006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.136936 restraints weight = 7601.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.141635 restraints weight = 4887.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.144456 restraints weight = 3843.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.145984 restraints weight = 3346.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.146821 restraints weight = 3085.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6157  Z= 0.128
  Angle     :  0.514   8.491   8413  Z= 0.261
  Chirality :  0.040   0.190    954
  Planarity :  0.004   0.059    991
  Dihedral  : 14.033  73.785   1114
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.08 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.34), residues: 676
  helix:  1.72 (0.29), residues: 330
  sheet: -3.31 (0.52), residues: 91
  loop : -2.17 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 811 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.019   0.001   PHE A 853 
 TRP   0.011   0.002   TRP A 873 
 HIS   0.004   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6154)
  covalent geometry    : angle       0.51395 ( 8413)
  hydrogen bonds       : bond        0.03284 (  286)
  hydrogen bonds       : angle       3.59124 (  806)
  metal coordination   : bond        0.00171 (    3)

*********************** 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
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7827 (mmmt)
REVERT: A  603 ASP cc_start: 0.8763 (t0) cc_final: 0.8519 (t0)
REVERT: A  625 ASN cc_start: 0.8351 (t0) cc_final: 0.8122 (t0)
REVERT: A  760 MET cc_start: 0.8722 (ttp) cc_final: 0.8350 (ttm)
REVERT: A  895 GLU cc_start: 0.7660 (tp30) cc_final: 0.7335 (mm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0815
  time to fit residues: 9.5799
Evaluate side-chains
  90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  387 MET
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  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  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 40 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.175138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131605 restraints weight = 7539.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.136120 restraints weight = 4894.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.138926 restraints weight = 3858.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.140187 restraints weight = 3362.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.140187 restraints weight = 3125.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6157  Z= 0.137
  Angle     :  0.516   8.558   8413  Z= 0.261
  Chirality :  0.040   0.191    954
  Planarity :  0.004   0.059    991
  Dihedral  : 14.058  73.807   1114
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.08 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.34), residues: 676
  helix:  1.79 (0.29), residues: 327
  sheet: -3.34 (0.53), residues: 86
  loop : -2.17 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 602 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.050   0.002   PHE A 616 
 TRP   0.013   0.002   TRP A 873 
 HIS   0.014   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6154)
  covalent geometry    : angle       0.51627 ( 8413)
  hydrogen bonds       : bond        0.03368 (  286)
  hydrogen bonds       : angle       3.57153 (  806)
  metal coordination   : bond        0.00182 (    3)

********************** 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
  93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (mmmt)
REVERT: A  523 PHE cc_start: 0.7959 (t80) cc_final: 0.7646 (t80)
REVERT: A  603 ASP cc_start: 0.8833 (t0) cc_final: 0.8593 (t0)
REVERT: A  625 ASN cc_start: 0.8364 (t0) cc_final: 0.8079 (t0)
REVERT: A  755 MET cc_start: 0.8556 (tpp) cc_final: 0.8256 (mmt)
REVERT: A  760 MET cc_start: 0.8760 (ttp) cc_final: 0.8359 (ttm)
REVERT: A  853 PHE cc_start: 0.8318 (p90) cc_final: 0.7757 (p90)
REVERT: A  895 GLU cc_start: 0.7771 (tp30) cc_final: 0.7384 (mm-30)
  outliers start: 14
  outliers final: 13
  residues processed: 90
  average time/residue: 0.0784
  time to fit residues: 9.5939
Evaluate side-chains
  91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  387 MET
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  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  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 19 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.175669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.132085 restraints weight = 7503.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.136577 restraints weight = 4895.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.139302 restraints weight = 3871.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.140742 restraints weight = 3388.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141961 restraints weight = 3129.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6157  Z= 0.135
  Angle     :  0.524   8.519   8413  Z= 0.266
  Chirality :  0.040   0.191    954
  Planarity :  0.004   0.060    991
  Dihedral  : 14.060  73.800   1114
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.34), residues: 676
  helix:  1.78 (0.29), residues: 327
  sheet: -3.30 (0.54), residues: 86
  loop : -2.10 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 602 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.026   0.002   PHE A 685 
 TRP   0.012   0.002   TRP A 873 
 HIS   0.013   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6154)
  covalent geometry    : angle       0.52411 ( 8413)
  hydrogen bonds       : bond        0.03331 (  286)
  hydrogen bonds       : angle       3.58473 (  806)
  metal coordination   : bond        0.00184 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1154.52 seconds
wall clock time: 20 minutes 34.64 seconds (1234.64 seconds total)