Starting phenix.real_space_refine
on Wed Mar  4 01:53:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k8a_22724/03_2026/7k8a_22724.map"
  }
  resolution = 3.65
  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
-------------------------------------------------------------------------------
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=   0.181
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5513 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3570      2.51       5
     N     913      2.21       5
     O    1002      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  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: 5513
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 723, 5513
          Classifications: {'peptide': 723}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 37, 'TRANS': 685}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 1.42, per 1000 atoms: 0.26
  Number of scatterers: 5513
  At special positions: 0
  Unit cell: (92.22, 99.64, 100.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1002      8.00
     N     913      7.00
     C    3570      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: 0.53
  Conformation dependent library (CDL) restraints added in 229.7 milliseconds
  

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      71.1% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
      removed outlier: 3.661A  pdb=" N   TRP A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE A  12 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 31
      removed outlier: 4.589A  pdb=" N   VAL A  16 " --> pdb=" O   PHE A  12 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 36
      No H-bonds generated for 'chain 'A' and resid 34 through 36'
    Processing helix  chain 'A' and resid 48 through 62
      removed outlier: 3.914A  pdb=" N   ALA A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 4.347A  pdb=" N   SER A  67 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   HIS A  68 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 64 through 68'
    Processing helix  chain 'A' and resid 83 through 101
      removed outlier: 4.169A  pdb=" N   GLN A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 143 through 160
      removed outlier: 3.566A  pdb=" N   ILE A 147 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 170 through 206
      removed outlier: 3.734A  pdb=" N   LEU A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   GLY A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU A 184 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
    Processing helix  chain 'A' and resid 207 through 233
      Proline residue:  A 214  - end of helix
    Processing helix  chain 'A' and resid 241 through 271
      removed outlier: 3.529A  pdb=" N   VAL A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 286
    Processing helix  chain 'A' and resid 286 through 302
      removed outlier: 3.774A  pdb=" N   SER A 301 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 309 through 342
      removed outlier: 4.998A  pdb=" N   ALA A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ALA A 336 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 400
      removed outlier: 4.254A  pdb=" N   ARG A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 415
      Proline residue:  A 407  - end of helix
      removed outlier: 3.678A  pdb=" N   VAL A 410 " --> pdb=" O   ALA A 406 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 471 through 483
    Processing helix  chain 'A' and resid 493 through 497
    Processing helix  chain 'A' and resid 525 through 534
      removed outlier: 3.503A  pdb=" N   LYS A 529 " --> pdb=" O   ASP A 525 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASP A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 563
    Processing helix  chain 'A' and resid 563 through 583
      removed outlier: 3.530A  pdb=" N   MET A 567 " --> pdb=" O   LYS A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 612
    Processing helix  chain 'A' and resid 616 through 621
    Processing helix  chain 'A' and resid 630 through 660
      removed outlier: 3.536A  pdb=" N   PHE A 649 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 692
      removed outlier: 4.275A  pdb=" N   ALA A 673 " --> pdb=" O   ARG A 669 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR A 674 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU A 678 " --> pdb=" O   THR A 674 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 681 " --> pdb=" O   ARG A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 722
      removed outlier: 3.791A  pdb=" N   ILE A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 732
    Processing helix  chain 'A' and resid 733 through 737
      removed outlier: 3.624A  pdb=" N   TRP A 737 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 747
      removed outlier: 4.402A  pdb=" N   VAL A 745 " --> pdb=" O   TRP A 741 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110
      removed outlier: 3.967A  pdb=" N   THR A 133 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518
      removed outlier: 3.523A  pdb=" N   ILE A 516 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A 518 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)

    360 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1661
        1.34 -     1.46: 864
        1.46 -     1.58: 3045
        1.58 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 5624
  Sorted by residual:
  bond pdb=" N   ASP A  78 "
       pdb=" CA  ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.458  1.413  0.045 1.33e-02 5.65e+03 1.16e+01
  bond pdb=" CA  THR A  74 "
       pdb=" C   THR A  74 "
    ideal  model  delta    sigma   weight residual
    1.519  1.558 -0.039 1.28e-02 6.10e+03 9.24e+00
  bond pdb=" CA  ASP A  78 "
       pdb=" C   ASP A  78 "
    ideal  model  delta    sigma   weight residual
    1.524  1.483  0.041 1.43e-02 4.89e+03 8.40e+00
  bond pdb=" C   THR A  74 "
       pdb=" N   PRO A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.38e+00
  bond pdb=" C   VAL A 302 "
       pdb=" N   PRO A 303 "
    ideal  model  delta    sigma   weight residual
    1.337  1.361 -0.024 1.11e-02 8.12e+03 4.82e+00
  ... (remaining 5619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 7413
        2.20 -     4.41: 176
        4.41 -     6.61: 50
        6.61 -     8.82: 13
        8.82 -    11.02: 1
  Bond angle restraints: 7653
  Sorted by residual:
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     110.70  117.53   -6.83 1.22e+00 6.72e-01 3.13e+01
  angle pdb=" N   LEU A  73 "
        pdb=" CA  LEU A  73 "
        pdb=" C   LEU A  73 "
      ideal   model   delta    sigma   weight residual
     109.46  116.61   -7.15 1.66e+00 3.63e-01 1.86e+01
  angle pdb=" C   PRO A  75 "
        pdb=" N   PRO A  76 "
        pdb=" CA  PRO A  76 "
      ideal   model   delta    sigma   weight residual
     119.84  114.51    5.33 1.25e+00 6.40e-01 1.82e+01
  angle pdb=" C   ILE A 719 "
        pdb=" N   ARG A 720 "
        pdb=" CA  ARG A 720 "
      ideal   model   delta    sigma   weight residual
     122.38  115.10    7.28 1.81e+00 3.05e-01 1.62e+01
  angle pdb=" N   PHE A 649 "
        pdb=" CA  PHE A 649 "
        pdb=" CB  PHE A 649 "
      ideal   model   delta    sigma   weight residual
     110.28  116.18   -5.90 1.55e+00 4.16e-01 1.45e+01
  ... (remaining 7648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3073
       17.99 -    35.98: 235
       35.98 -    53.97: 45
       53.97 -    71.96: 3
       71.96 -    89.95: 4
  Dihedral angle restraints: 3360
    sinusoidal: 1302
      harmonic: 2058
  Sorted by residual:
  dihedral pdb=" N   PHE A 649 "
           pdb=" C   PHE A 649 "
           pdb=" CA  PHE A 649 "
           pdb=" CB  PHE A 649 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.31  -16.51     0      2.50e+00 1.60e-01 4.36e+01
  dihedral pdb=" C   PHE A 649 "
           pdb=" N   PHE A 649 "
           pdb=" CA  PHE A 649 "
           pdb=" CB  PHE A 649 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.03   16.43     0      2.50e+00 1.60e-01 4.32e+01
  dihedral pdb=" CA  PHE A 722 "
           pdb=" C   PHE A 722 "
           pdb=" N   LEU A 723 "
           pdb=" CA  LEU A 723 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.25  -24.75     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 3357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 905
       0.135 -    0.270: 8
       0.270 -    0.405: 0
       0.405 -    0.540: 0
       0.540 -    0.675: 1
  Chirality restraints: 914
  Sorted by residual:
  chirality pdb=" CA  PHE A 649 "
            pdb=" N   PHE A 649 "
            pdb=" C   PHE A 649 "
            pdb=" CB  PHE A 649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CB  ILE A 137 "
            pdb=" CA  ILE A 137 "
            pdb=" CG1 ILE A 137 "
            pdb=" CG2 ILE A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.77e-01
  chirality pdb=" CA  ILE A 135 "
            pdb=" N   ILE A 135 "
            pdb=" C   ILE A 135 "
            pdb=" CB  ILE A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 911 not shown)

  Planarity restraints: 967
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 406 "   -0.050 5.00e-02 4.00e+02   7.47e-02 8.92e+00
        pdb=" N   PRO A 407 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 417 "    0.029 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A 418 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 649 "    0.016 2.00e-02 2.50e+03   1.29e-02 2.91e+00
        pdb=" CG  PHE A 649 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 649 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 649 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 649 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 649 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 649 "    0.001 2.00e-02 2.50e+03
  ... (remaining 964 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 936
        2.76 -     3.30: 5906
        3.30 -     3.83: 9048
        3.83 -     4.37: 10106
        4.37 -     4.90: 16840
  Nonbonded interactions: 42836
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 142 "
            pdb=" OE2 GLU A 146 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" O   MET A 610 "
            pdb=" OH  TYR A 622 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" O   VAL A 513 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR A 680 "
            pdb=" NH2 ARG A 720 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   GLY A 426 "
            pdb=" OH  TYR A 431 "
     model   vdw
     2.306 3.040
  ... (remaining 42831 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.180
  Find NCS groups from input model:        0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5519
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      :  0.004   0.045   5624  Z= 0.226
  Angle     :  0.918  11.022   7653  Z= 0.501
  Chirality :  0.052   0.675    914
  Planarity :  0.006   0.075    967
  Dihedral  : 13.382  89.947   2036
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.19 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.15 %
  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: -1.30 (0.30), residues: 719
  helix: -0.15 (0.24), residues: 457
  sheet: -3.15 (0.69), residues: 31
  loop : -1.78 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  63 
 TYR   0.025   0.002   TYR A 151 
 PHE   0.029   0.002   PHE A 649 
 TRP   0.023   0.002   TRP A 737 
 HIS   0.005   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5624)
  covalent geometry    : angle       0.91844 ( 7653)
  hydrogen bonds       : bond        0.13154 (  360)
  hydrogen bonds       : angle       5.64963 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7275 (tp-100)
REVERT: A  147 ILE cc_start: 0.8233 (pt) cc_final: 0.7432 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0644
  time to fit residues: 11.3620
Evaluate side-chains
  117 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    7.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 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 = 0.4740 r_free = 0.4740 target = 0.268096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.250589 restraints weight = 9401.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.256272 restraints weight = 7654.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.259094 restraints weight = 3818.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.259676 restraints weight = 2510.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.259662 restraints weight = 2159.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5573
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5624  Z= 0.156
  Angle     :  0.770   8.052   7653  Z= 0.383
  Chirality :  0.044   0.184    914
  Planarity :  0.006   0.068    967
  Dihedral  :  5.242  23.007    769
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.87 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.39 %
    Favored  : 86.39 %
  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: -1.11 (0.30), residues: 719
  helix:  0.11 (0.24), residues: 459
  sheet: -3.10 (0.69), residues: 39
  loop : -1.93 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 264 
 TYR   0.018   0.002   TYR A 151 
 PHE   0.019   0.002   PHE A 265 
 TRP   0.016   0.001   TRP A 737 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5624)
  covalent geometry    : angle       0.76981 ( 7653)
  hydrogen bonds       : bond        0.04847 (  360)
  hydrogen bonds       : angle       4.92987 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   65 ARG cc_start: 0.6597 (mpt-90) cc_final: 0.6332 (mpt-90)
REVERT: A  128 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7104 (tp-100)
REVERT: A  273 TYR cc_start: 0.6174 (m-10) cc_final: 0.4654 (m-10)
  outliers start: 13
  outliers final: 8
  residues processed: 124
  average time/residue: 0.0715
  time to fit residues: 11.9359
Evaluate side-chains
  121 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  648 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0470
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    2.5284

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.266216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.249813 restraints weight = 9229.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.251977 restraints weight = 5622.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.254605 restraints weight = 4336.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.255897 restraints weight = 2934.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.256133 restraints weight = 2605.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5623
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5624  Z= 0.151
  Angle     :  0.750   8.403   7653  Z= 0.372
  Chirality :  0.044   0.174    914
  Planarity :  0.006   0.056    967
  Dihedral  :  5.145  22.008    767
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.15 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 14.63 %
    Favored  : 81.80 %
  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: -0.99 (0.31), residues: 719
  helix:  0.21 (0.24), residues: 461
  sheet: -3.08 (0.69), residues: 42
  loop : -1.88 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 534 
 TYR   0.018   0.002   TYR A 151 
 PHE   0.019   0.002   PHE A 449 
 TRP   0.016   0.001   TRP A 737 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5624)
  covalent geometry    : angle       0.74996 ( 7653)
  hydrogen bonds       : bond        0.04495 (  360)
  hydrogen bonds       : angle       4.82485 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.7484 (tp-100) cc_final: 0.6972 (tp-100)
REVERT: A  273 TYR cc_start: 0.6248 (m-10) cc_final: 0.4760 (m-10)
  outliers start: 21
  outliers final: 14
  residues processed: 130
  average time/residue: 0.0706
  time to fit residues: 12.3842
Evaluate side-chains
  130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  721 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 26 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    3.8106

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.262971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.245621 restraints weight = 9192.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.250856 restraints weight = 8221.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.252506 restraints weight = 4078.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.254955 restraints weight = 2745.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.254705 restraints weight = 2105.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.4622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5624  Z= 0.180
  Angle     :  0.778   8.391   7653  Z= 0.388
  Chirality :  0.046   0.363    914
  Planarity :  0.006   0.043    967
  Dihedral  :  5.274  22.612    767
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.70 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 16.16 %
    Favored  : 78.57 %
  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: -0.98 (0.31), residues: 719
  helix:  0.20 (0.24), residues: 460
  sheet: -3.39 (0.69), residues: 34
  loop : -1.83 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 534 
 TYR   0.017   0.002   TYR A 151 
 PHE   0.018   0.002   PHE A 389 
 TRP   0.013   0.002   TRP A 737 
 HIS   0.006   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5624)
  covalent geometry    : angle       0.77786 ( 7653)
  hydrogen bonds       : bond        0.04637 (  360)
  hydrogen bonds       : angle       4.92875 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.7049 (mpt-90) cc_final: 0.6748 (mpt-90)
REVERT: A  128 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7079 (tp-100)
REVERT: A  631 MET cc_start: 0.6843 (tpt) cc_final: 0.6457 (mmm)
REVERT: A  742 MET cc_start: -0.1677 (tpt) cc_final: -0.3124 (tpt)
  outliers start: 31
  outliers final: 26
  residues processed: 131
  average time/residue: 0.0765
  time to fit residues: 13.2065
Evaluate side-chains
  140 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  721 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 70 optimal weight:   30.0000
   chunk 17 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 492 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.267480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.249546 restraints weight = 9371.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.253162 restraints weight = 5968.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.255655 restraints weight = 4088.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.257193 restraints weight = 3009.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.258468 restraints weight = 2346.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.4647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5574
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5624  Z= 0.135
  Angle     :  0.709   6.952   7653  Z= 0.347
  Chirality :  0.043   0.216    914
  Planarity :  0.005   0.040    967
  Dihedral  :  4.990  21.076    767
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.73 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 17.86 %
    Favored  : 77.21 %
  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: -0.73 (0.31), residues: 719
  helix:  0.43 (0.24), residues: 466
  sheet: -3.00 (0.71), residues: 42
  loop : -1.87 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 720 
 TYR   0.019   0.001   TYR A 151 
 PHE   0.020   0.001   PHE A 265 
 TRP   0.008   0.001   TRP A 498 
 HIS   0.002   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5624)
  covalent geometry    : angle       0.70913 ( 7653)
  hydrogen bonds       : bond        0.04139 (  360)
  hydrogen bonds       : angle       4.72742 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.6964 (mpt-90) cc_final: 0.6761 (mpt-90)
REVERT: A  128 GLN cc_start: 0.7379 (tp-100) cc_final: 0.7138 (tp40)
REVERT: A  273 TYR cc_start: 0.6169 (m-10) cc_final: 0.4990 (m-10)
REVERT: A  333 VAL cc_start: 0.5882 (OUTLIER) cc_final: 0.5645 (t)
REVERT: A  482 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6562 (tp)
REVERT: A  631 MET cc_start: 0.6810 (tpt) cc_final: 0.6515 (mmm)
REVERT: A  693 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.6000 (m-10)
REVERT: A  742 MET cc_start: -0.1617 (tpt) cc_final: -0.3051 (tpt)
  outliers start: 29
  outliers final: 20
  residues processed: 130
  average time/residue: 0.0798
  time to fit residues: 13.6639
Evaluate side-chains
  135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  693 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0030
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0060
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    0.6608

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 492 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.268761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.251472 restraints weight = 9330.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.256804 restraints weight = 7680.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.259206 restraints weight = 3908.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.261505 restraints weight = 2401.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.261616 restraints weight = 1853.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.4673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5506
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5624  Z= 0.131
  Angle     :  0.706   7.776   7653  Z= 0.343
  Chirality :  0.044   0.366    914
  Planarity :  0.005   0.041    967
  Dihedral  :  4.818  20.650    767
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.45 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 18.03 %
    Favored  : 76.87 %
  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: -0.44 (0.31), residues: 719
  helix:  0.69 (0.25), residues: 462
  sheet: -3.01 (0.70), residues: 42
  loop : -1.78 (0.40), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 534 
 TYR   0.019   0.001   TYR A 151 
 PHE   0.018   0.001   PHE A 265 
 TRP   0.009   0.001   TRP A 498 
 HIS   0.001   0.000   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5624)
  covalent geometry    : angle       0.70647 ( 7653)
  hydrogen bonds       : bond        0.03926 (  360)
  hydrogen bonds       : angle       4.61983 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.6883 (mpt-90) cc_final: 0.6606 (mpt-90)
REVERT: A  134 PHE cc_start: 0.7603 (p90) cc_final: 0.7365 (p90)
REVERT: A  273 TYR cc_start: 0.6060 (m-10) cc_final: 0.4912 (m-10)
REVERT: A  333 VAL cc_start: 0.5927 (OUTLIER) cc_final: 0.5715 (t)
REVERT: A  631 MET cc_start: 0.6821 (tpt) cc_final: 0.6536 (mmm)
REVERT: A  742 MET cc_start: -0.1882 (tpt) cc_final: -0.3237 (tpt)
  outliers start: 30
  outliers final: 23
  residues processed: 131
  average time/residue: 0.0736
  time to fit residues: 12.7714
Evaluate side-chains
  133 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0370
   chunk 22 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0070
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7680

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.269569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.252212 restraints weight = 9288.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.256044 restraints weight = 5780.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.258624 restraints weight = 3929.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.260249 restraints weight = 2826.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.261549 restraints weight = 2191.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5624  Z= 0.129
  Angle     :  0.715  10.619   7653  Z= 0.343
  Chirality :  0.043   0.246    914
  Planarity :  0.005   0.042    967
  Dihedral  :  4.694  19.514    767
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.73 %
    Favored  : 75.51 %
  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: -0.24 (0.32), residues: 719
  helix:  0.85 (0.25), residues: 463
  sheet: -3.08 (0.77), residues: 36
  loop : -1.75 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 534 
 TYR   0.018   0.001   TYR A 151 
 PHE   0.016   0.001   PHE A 265 
 TRP   0.010   0.001   TRP A 498 
 HIS   0.001   0.000   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5624)
  covalent geometry    : angle       0.71464 ( 7653)
  hydrogen bonds       : bond        0.03830 (  360)
  hydrogen bonds       : angle       4.58756 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 TYR cc_start: 0.6027 (m-10) cc_final: 0.5066 (m-10)
REVERT: A  631 MET cc_start: 0.6755 (tpt) cc_final: 0.6500 (mmm)
REVERT: A  742 MET cc_start: -0.1625 (tpt) cc_final: -0.3039 (tpt)
  outliers start: 28
  outliers final: 22
  residues processed: 127
  average time/residue: 0.0750
  time to fit residues: 12.4576
Evaluate side-chains
  127 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.267981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.251216 restraints weight = 9160.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.256483 restraints weight = 7697.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.258427 restraints weight = 3920.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.261348 restraints weight = 2484.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.261135 restraints weight = 1678.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5529
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5624  Z= 0.136
  Angle     :  0.737   8.838   7653  Z= 0.354
  Chirality :  0.044   0.396    914
  Planarity :  0.005   0.042    967
  Dihedral  :  4.700  20.106    767
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.73 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 19.90 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.25 (0.32), residues: 719
  helix:  0.85 (0.25), residues: 463
  sheet: -3.22 (0.69), residues: 42
  loop : -1.66 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 534 
 TYR   0.016   0.001   TYR A 151 
 PHE   0.017   0.001   PHE A 649 
 TRP   0.010   0.001   TRP A 498 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5624)
  covalent geometry    : angle       0.73695 ( 7653)
  hydrogen bonds       : bond        0.03881 (  360)
  hydrogen bonds       : angle       4.56693 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.6683 (mpt-90) cc_final: 0.6441 (mpt-90)
REVERT: A  273 TYR cc_start: 0.5935 (m-10) cc_final: 0.5018 (m-10)
REVERT: A  631 MET cc_start: 0.6814 (tpt) cc_final: 0.6500 (mmm)
REVERT: A  742 MET cc_start: -0.1738 (tpt) cc_final: -0.3057 (tpt)
  outliers start: 26
  outliers final: 26
  residues processed: 119
  average time/residue: 0.0796
  time to fit residues: 12.3362
Evaluate side-chains
  130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  542 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0270
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    5.0046

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.259308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.241526 restraints weight = 9102.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.246787 restraints weight = 8226.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.248763 restraints weight = 4182.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.250613 restraints weight = 2664.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.250921 restraints weight = 2067.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5772
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5624  Z= 0.217
  Angle     :  0.848   8.416   7653  Z= 0.427
  Chirality :  0.047   0.376    914
  Planarity :  0.006   0.042    967
  Dihedral  :  5.471  23.107    767
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.84 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.24 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.31), residues: 719
  helix:  0.28 (0.24), residues: 466
  sheet: -3.61 (0.70), residues: 34
  loop : -1.96 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 534 
 TYR   0.018   0.002   TYR A  44 
 PHE   0.025   0.003   PHE A 389 
 TRP   0.011   0.002   TRP A 498 
 HIS   0.007   0.002   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 5624)
  covalent geometry    : angle       0.84790 ( 7653)
  hydrogen bonds       : bond        0.05085 (  360)
  hydrogen bonds       : angle       5.09442 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5309 (tmm) cc_final: 0.4828 (ppp)
REVERT: A  271 GLU cc_start: 0.5553 (mt-10) cc_final: 0.4896 (mt-10)
REVERT: A  273 TYR cc_start: 0.6343 (m-10) cc_final: 0.5240 (m-10)
REVERT: A  480 LYS cc_start: 0.6435 (mmtm) cc_final: 0.5473 (mttm)
REVERT: A  579 MET cc_start: 0.6013 (mmm) cc_final: 0.5726 (mmm)
REVERT: A  604 MET cc_start: 0.5958 (tmm) cc_final: 0.5609 (tmm)
REVERT: A  631 MET cc_start: 0.7216 (tpt) cc_final: 0.6685 (mmm)
REVERT: A  664 THR cc_start: 0.3568 (OUTLIER) cc_final: 0.2465 (m)
REVERT: A  742 MET cc_start: -0.1846 (tpt) cc_final: -0.3095 (tpt)
  outliers start: 26
  outliers final: 22
  residues processed: 128
  average time/residue: 0.0751
  time to fit residues: 12.6300
Evaluate side-chains
  130 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN
A 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.265488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.247662 restraints weight = 9108.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.253473 restraints weight = 7813.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.255390 restraints weight = 3832.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.257609 restraints weight = 2455.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.257621 restraints weight = 1919.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5647
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5624  Z= 0.146
  Angle     :  0.759   8.470   7653  Z= 0.370
  Chirality :  0.044   0.305    914
  Planarity :  0.005   0.056    967
  Dihedral  :  5.096  21.688    767
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.59 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.26 %
    Favored  : 74.66 %
  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 (0.31), residues: 719
  helix:  0.49 (0.25), residues: 461
  sheet: -3.43 (0.73), residues: 42
  loop : -1.85 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  63 
 TYR   0.016   0.002   TYR A 151 
 PHE   0.021   0.002   PHE A 265 
 TRP   0.011   0.001   TRP A 498 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5624)
  covalent geometry    : angle       0.75886 ( 7653)
  hydrogen bonds       : bond        0.04278 (  360)
  hydrogen bonds       : angle       4.83705 ( 1053)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 GLU cc_start: 0.5348 (mt-10) cc_final: 0.4873 (mt-10)
REVERT: A  273 TYR cc_start: 0.6236 (m-10) cc_final: 0.5031 (m-10)
REVERT: A  419 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.4922 (pp)
REVERT: A  480 LYS cc_start: 0.6149 (mmtm) cc_final: 0.5032 (mttm)
REVERT: A  604 MET cc_start: 0.5745 (tmm) cc_final: 0.5406 (tmm)
REVERT: A  631 MET cc_start: 0.7027 (tpt) cc_final: 0.6625 (mmm)
REVERT: A  742 MET cc_start: -0.1894 (tpt) cc_final: -0.3190 (tpt)
  outliers start: 24
  outliers final: 23
  residues processed: 125
  average time/residue: 0.0768
  time to fit residues: 12.4881
Evaluate side-chains
  135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ARG
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  309 GLN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  452 PHE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  498 TRP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  567 MET
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 59 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0020
   chunk 65 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.2990

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN
A 440 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.266439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.249060 restraints weight = 9177.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.254539 restraints weight = 8137.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.256452 restraints weight = 3924.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.258563 restraints weight = 2580.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.258809 restraints weight = 1932.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5595
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5624  Z= 0.138
  Angle     :  0.749   8.430   7653  Z= 0.361
  Chirality :  0.043   0.278    914
  Planarity :  0.005   0.043    967
  Dihedral  :  4.914  19.631    767
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.77 %
    Favored  : 74.15 %
  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: -0.55 (0.32), residues: 719
  helix:  0.61 (0.25), residues: 461
  sheet: -3.38 (0.73), residues: 42
  loop : -1.74 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 534 
 TYR   0.015   0.001   TYR A 151 
 PHE   0.020   0.002   PHE A 265 
 TRP   0.010   0.001   TRP A 498 
 HIS   0.002   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5624)
  covalent geometry    : angle       0.74912 ( 7653)
  hydrogen bonds       : bond        0.04049 (  360)
  hydrogen bonds       : angle       4.74037 ( 1053)

===============================================================================
Job complete
usr+sys time: 1031.70 seconds
wall clock time: 18 minutes 24.79 seconds (1104.79 seconds total)