Starting phenix.real_space_refine
on Sat May 10 10:42:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q74_18203/05_2025/8q74_18203.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Cu      1      5.60       5
     S      34      5.16       5
     C    3812      2.51       5
     N     988      2.21       5
     O    1108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5943
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 5942
          Classifications: {'peptide': 783}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CU': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3243  SG  CYS A 597      27.486  24.901  48.334  1.00140.08           S
  ATOM   3256  SG  CYS A 599      28.127  29.237  48.453  1.00142.78           S

  Time building chain proxies: 3.92, per 1000 atoms: 0.66
  Number of scatterers: 5943
  At special positions: 0
  Unit cell: (80.408, 86.3328, 141.349, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cu      1     28.99
     S      34     16.00
     O    1108      8.00
     N     988      7.00
     C    3812      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 823.2 milliseconds
  

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      53.6% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 209
      removed outlier: 4.285A  pdb=" N   ARG A 207 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 3.599A  pdb=" N   ALA A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 296
      removed outlier: 3.793A  pdb=" N   PHE A 286 " --> pdb=" O   TRP A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 297 through 300
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 317 through 332
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 6.499A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 377
      removed outlier: 3.696A  pdb=" N   LEU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 420
      removed outlier: 4.094A  pdb=" N   ILE A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 531
      removed outlier: 3.635A  pdb=" N   GLN A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
    Processing helix  chain 'A' and resid 546 through 567
      removed outlier: 3.520A  pdb=" N   TRP A 561 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 3.638A  pdb=" N   LEU A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 618
      removed outlier: 4.010A  pdb=" N   MET A 610 " --> pdb=" O   PRO A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 634
    Processing helix  chain 'A' and resid 682 through 693
      removed outlier: 4.373A  pdb=" N   THR A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 691 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 743 through 756
      removed outlier: 3.825A  pdb=" N   GLU A 747 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 768
    Processing helix  chain 'A' and resid 782 through 794
    Processing helix  chain 'A' and resid 804 through 816
    Processing helix  chain 'A' and resid 825 through 839
    Processing helix  chain 'A' and resid 849 through 851
      No H-bonds generated for 'chain 'A' and resid 849 through 851'
    Processing helix  chain 'A' and resid 852 through 859
    Processing helix  chain 'A' and resid 869 through 876
      removed outlier: 3.900A  pdb=" N   ILE A 873 " --> pdb=" O   THR A 869 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 922
      removed outlier: 4.123A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR A 890 " --> pdb=" O   GLU A 886 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 915 " --> pdb=" O   GLY A 911 " (cutoff:3.500A)
      Proline residue:  A 918  - end of helix
    Processing helix  chain 'A' and resid 924 through 929
    Processing helix  chain 'A' and resid 933 through 954
      removed outlier: 4.146A  pdb=" N   ALA A 939 " --> pdb=" O   TRP A 935 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A 940 " --> pdb=" O   LEU A 936 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 941 " --> pdb=" O   ALA A 937 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 954 " --> pdb=" O   CYS A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 958
    Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312
      removed outlier: 3.628A  pdb=" N   VAL A 311 " --> pdb=" O   MET A 315 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   MET A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425
    Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455
      removed outlier: 4.082A  pdb=" N   CYS A 504 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821
      removed outlier: 8.929A  pdb=" N   PHE A 821 " --> pdb=" O   SER A 797 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET A 799 " --> pdb=" O   PHE A 821 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA A 637 " --> pdb=" O   ALA A 844 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    831 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: 1.59

  Time building geometry restraints manager: 1.73 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: 1893
        1.34 -     1.46: 801
        1.46 -     1.57: 3309
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6057
  Sorted by residual:
  bond pdb=" CA  CYS A 597 "
       pdb=" C   CYS A 597 "
    ideal  model  delta    sigma   weight residual
    1.524  1.474  0.050 1.26e-02 6.30e+03 1.59e+01
  bond pdb=" CA  CYS A 599 "
       pdb=" C   CYS A 599 "
    ideal  model  delta    sigma   weight residual
    1.527  1.495  0.032 1.30e-02 5.92e+03 5.93e+00
  bond pdb=" CA  MET A 352 "
       pdb=" C   MET A 352 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.28e-02 6.10e+03 4.59e+00
  bond pdb=" N   ALA A 600 "
       pdb=" CA  ALA A 600 "
    ideal  model  delta    sigma   weight residual
    1.458  1.433  0.026 1.26e-02 6.30e+03 4.14e+00
  bond pdb=" CA  ASP A 353 "
       pdb=" C   ASP A 353 "
    ideal  model  delta    sigma   weight residual
    1.525  1.499  0.026 1.37e-02 5.33e+03 3.62e+00
  ... (remaining 6052 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 7903
        2.42 -     4.85: 279
        4.85 -     7.27: 38
        7.27 -     9.69: 4
        9.69 -    12.12: 2
  Bond angle restraints: 8226
  Sorted by residual:
  angle pdb=" N   ALA A 600 "
        pdb=" CA  ALA A 600 "
        pdb=" C   ALA A 600 "
      ideal   model   delta    sigma   weight residual
     111.69  103.10    8.59 1.23e+00 6.61e-01 4.88e+01
  angle pdb=" C   THR A 656 "
        pdb=" N   LYS A 657 "
        pdb=" CA  LYS A 657 "
      ideal   model   delta    sigma   weight residual
     122.11  112.10   10.01 1.59e+00 3.96e-01 3.97e+01
  angle pdb=" N   VAL A 311 "
        pdb=" CA  VAL A 311 "
        pdb=" C   VAL A 311 "
      ideal   model   delta    sigma   weight residual
     113.53  108.53    5.00 9.80e-01 1.04e+00 2.60e+01
  angle pdb=" C   LYS A 657 "
        pdb=" N   VAL A 658 "
        pdb=" CA  VAL A 658 "
      ideal   model   delta    sigma   weight residual
     120.13  128.17   -8.04 1.58e+00 4.01e-01 2.59e+01
  angle pdb=" N   TRP A 335 "
        pdb=" CA  TRP A 335 "
        pdb=" C   TRP A 335 "
      ideal   model   delta    sigma   weight residual
     113.43  107.54    5.89 1.26e+00 6.30e-01 2.18e+01
  ... (remaining 8221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3320
       17.59 -    35.18: 277
       35.18 -    52.77: 34
       52.77 -    70.36: 13
       70.36 -    87.95: 8
  Dihedral angle restraints: 3652
    sinusoidal: 1403
      harmonic: 2249
  Sorted by residual:
  dihedral pdb=" CA  PRO A 250 "
           pdb=" C   PRO A 250 "
           pdb=" N   PRO A 251 "
           pdb=" CA  PRO A 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.23   40.77     0      5.00e+00 4.00e-02 6.65e+01
  dihedral pdb=" CA  ASN A 721 "
           pdb=" C   ASN A 721 "
           pdb=" N   VAL A 722 "
           pdb=" CA  VAL A 722 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.73  -35.27     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  GLY A 724 "
           pdb=" C   GLY A 724 "
           pdb=" N   LYS A 725 "
           pdb=" CA  LYS A 725 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.04  -26.96     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 3649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 705
       0.048 -    0.096: 209
       0.096 -    0.144: 50
       0.144 -    0.192: 8
       0.192 -    0.240: 2
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CB  ILE A 704 "
            pdb=" CA  ILE A 704 "
            pdb=" CG1 ILE A 704 "
            pdb=" CG2 ILE A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  THR A 656 "
            pdb=" N   THR A 656 "
            pdb=" C   THR A 656 "
            pdb=" CB  THR A 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CB  ILE A 662 "
            pdb=" CA  ILE A 662 "
            pdb=" CG1 ILE A 662 "
            pdb=" CG2 ILE A 662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1041
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 662 "   -0.050 5.00e-02 4.00e+02   7.66e-02 9.38e+00
        pdb=" N   PRO A 663 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 663 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 663 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 570 "   -0.047 5.00e-02 4.00e+02   7.02e-02 7.88e+00
        pdb=" N   PRO A 571 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 571 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 571 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 740 "    0.043 5.00e-02 4.00e+02   6.53e-02 6.83e+00
        pdb=" N   PRO A 741 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 741 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 741 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1038 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 11
        2.29 -     2.94: 2791
        2.94 -     3.59: 9756
        3.59 -     4.25: 14043
        4.25 -     4.90: 22453
  Nonbonded interactions: 49054
  Sorted by model distance:
  nonbonded pdb=" CE  MET A 352 "
            pdb="CU    CU A1001 "
     model   vdw
     1.633 2.660
  nonbonded pdb=" SG  CYS A 597 "
            pdb="CU    CU A1001 "
     model   vdw
     2.079 2.600
  nonbonded pdb=" SD  MET A 352 "
            pdb="CU    CU A1001 "
     model   vdw
     2.087 2.600
  nonbonded pdb=" O   VAL A 687 "
            pdb=" OG1 THR A 690 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OE1 GLU A 476 "
            pdb=" N   MET A 478 "
     model   vdw
     2.183 3.120
  ... (remaining 49049 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=0.00 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:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.010
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
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      :  0.005   0.124   6058  Z= 0.287
  Angle     :  1.020  12.117   8226  Z= 0.613
  Chirality :  0.048   0.240    974
  Planarity :  0.008   0.077   1041
  Dihedral  : 14.005  87.951   2204
  Min Nonbonded Distance : 1.633

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 15.88 %
    Favored  : 83.23 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.23 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.30), residues: 781
  helix:  0.65 (0.28), residues: 366
  sheet: -3.40 (0.73), residues: 30
  loop : -3.90 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 558 
 HIS   0.009   0.001   HIS A 473 
 PHE   0.020   0.002   PHE A 582 
 TYR   0.028   0.002   TYR A 689 
 ARG   0.008   0.001   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19672 (  283)
  hydrogen bonds       : angle       6.81073 (  831)
  covalent geometry    : bond        0.00436 ( 6057)
  covalent geometry    : angle       1.02032 ( 8226)
  Misc. bond           : bond        0.12434 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9357 (m-80) cc_final: 0.9065 (m-80)
REVERT: A  315 MET cc_start: 0.9055 (ppp) cc_final: 0.8799 (tmm)
REVERT: A  319 MET cc_start: 0.8325 (mpp) cc_final: 0.8016 (mtp)
REVERT: A  331 PHE cc_start: 0.7861 (m-80) cc_final: 0.7285 (m-80)
REVERT: A  686 ILE cc_start: 0.9548 (mt) cc_final: 0.9235 (mt)
REVERT: A  790 LEU cc_start: 0.9583 (mt) cc_final: 0.9329 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1563
  time to fit residues: 17.2370
Evaluate side-chains
  46 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 32 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0870
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0010
   overall best weight:    0.8966

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 448 GLN
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.102528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.065074 restraints weight = 24011.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.067010 restraints weight = 10364.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.067887 restraints weight = 6638.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6058  Z= 0.169
  Angle     :  0.848   9.330   8226  Z= 0.437
  Chirality :  0.047   0.176    974
  Planarity :  0.006   0.066   1041
  Dihedral  :  6.507  38.672    826
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 18.23
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 15.24 %
    Favored  : 83.99 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.17 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.31), residues: 781
  helix:  0.92 (0.27), residues: 383
  sheet: -3.03 (0.76), residues: 31
  loop : -3.67 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 558 
 HIS   0.012   0.002   HIS A 473 
 PHE   0.029   0.002   PHE A 293 
 TYR   0.017   0.002   TYR A 253 
 ARG   0.006   0.001   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05643 (  283)
  hydrogen bonds       : angle       5.29049 (  831)
  covalent geometry    : bond        0.00358 ( 6057)
  covalent geometry    : angle       0.84839 ( 8226)
  Misc. bond           : bond        0.00090 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TRP cc_start: 0.8167 (m100) cc_final: 0.7958 (m-10)
REVERT: A  315 MET cc_start: 0.9103 (ppp) cc_final: 0.8826 (tmm)
REVERT: A  319 MET cc_start: 0.8391 (mpp) cc_final: 0.8117 (mpp)
REVERT: A  601 LEU cc_start: 0.9174 (mm) cc_final: 0.8855 (mm)
REVERT: A  689 TYR cc_start: 0.8981 (p90) cc_final: 0.8628 (p90)
REVERT: A  799 MET cc_start: 0.8997 (ppp) cc_final: 0.8421 (ppp)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1281
  time to fit residues: 11.6616
Evaluate side-chains
  50 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  899 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 48 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.101210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060387 restraints weight = 24052.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062170 restraints weight = 10792.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.063072 restraints weight = 7187.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6058  Z= 0.180
  Angle     :  0.787   8.562   8226  Z= 0.409
  Chirality :  0.047   0.234    974
  Planarity :  0.006   0.062   1041
  Dihedral  :  6.286  35.383    826
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.85 %
    Favored  : 84.38 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.48 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.30), residues: 781
  helix:  1.01 (0.27), residues: 389
  sheet: -2.25 (0.85), residues: 21
  loop : -3.54 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.021   0.002   PHE A 331 
 TYR   0.015   0.001   TYR A 253 
 ARG   0.004   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05354 (  283)
  hydrogen bonds       : angle       5.07049 (  831)
  covalent geometry    : bond        0.00396 ( 6057)
  covalent geometry    : angle       0.78708 ( 8226)
  Misc. bond           : bond        0.00033 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8504 (mpp) cc_final: 0.8220 (mpp)
REVERT: A  331 PHE cc_start: 0.8856 (m-80) cc_final: 0.8438 (m-80)
REVERT: A  689 TYR cc_start: 0.9111 (p90) cc_final: 0.8679 (p90)
REVERT: A  799 MET cc_start: 0.8922 (ppp) cc_final: 0.8562 (ppp)
REVERT: A  845 MET cc_start: 0.8119 (ptm) cc_final: 0.7533 (ptm)
  outliers start: 19
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1317
  time to fit residues: 12.3576
Evaluate side-chains
  55 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:   40.0000
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.102120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.062418 restraints weight = 24386.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.064326 restraints weight = 10640.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.065181 restraints weight = 6872.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6058  Z= 0.144
  Angle     :  0.755  11.414   8226  Z= 0.386
  Chirality :  0.046   0.201    974
  Planarity :  0.005   0.061   1041
  Dihedral  :  6.178  37.541    826
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.57 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.79 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.30), residues: 781
  helix:  1.27 (0.27), residues: 395
  sheet: -2.09 (0.85), residues: 21
  loop : -3.66 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.011   0.002   PHE A 254 
 TYR   0.021   0.001   TYR A 689 
 ARG   0.002   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04504 (  283)
  hydrogen bonds       : angle       4.78317 (  831)
  covalent geometry    : bond        0.00313 ( 6057)
  covalent geometry    : angle       0.75542 ( 8226)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9437 (t80) cc_final: 0.9228 (t80)
REVERT: A  315 MET cc_start: 0.9276 (tmm) cc_final: 0.8986 (tmm)
REVERT: A  319 MET cc_start: 0.8416 (mpp) cc_final: 0.8136 (mpp)
REVERT: A  331 PHE cc_start: 0.8840 (m-80) cc_final: 0.8459 (m-80)
REVERT: A  689 TYR cc_start: 0.9094 (p90) cc_final: 0.8631 (p90)
REVERT: A  705 MET cc_start: 0.8723 (ppp) cc_final: 0.8285 (ppp)
REVERT: A  799 MET cc_start: 0.8949 (ppp) cc_final: 0.8682 (tmm)
REVERT: A  845 MET cc_start: 0.8116 (ptm) cc_final: 0.7523 (ptm)
REVERT: A  881 MET cc_start: 0.9282 (tpp) cc_final: 0.9030 (tmm)
  outliers start: 19
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1640
  time to fit residues: 16.0108
Evaluate side-chains
  53 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0570
   chunk 28 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 53 optimal weight:   50.0000
   chunk 68 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7502

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

Flipped N/Q/H residues before XYZ refinement:
** A 473 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.102347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.063236 restraints weight = 24037.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.065133 restraints weight = 10323.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.066091 restraints weight = 6710.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6058  Z= 0.134
  Angle     :  0.718   8.720   8226  Z= 0.369
  Chirality :  0.045   0.145    974
  Planarity :  0.005   0.059   1041
  Dihedral  :  5.992  38.310    826
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.32 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.80 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.31), residues: 781
  helix:  1.41 (0.27), residues: 396
  sheet: -1.81 (0.90), residues: 21
  loop : -3.59 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.011   0.001   PHE A 710 
 TYR   0.021   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  283)
  hydrogen bonds       : angle       4.63158 (  831)
  covalent geometry    : bond        0.00286 ( 6057)
  covalent geometry    : angle       0.71786 ( 8226)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9470 (t80) cc_final: 0.9254 (t80)
REVERT: A  319 MET cc_start: 0.8419 (mpp) cc_final: 0.8143 (mpp)
REVERT: A  331 PHE cc_start: 0.8842 (m-80) cc_final: 0.8513 (m-80)
REVERT: A  657 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6795 (mmtt)
REVERT: A  689 TYR cc_start: 0.9084 (p90) cc_final: 0.8706 (p90)
REVERT: A  705 MET cc_start: 0.8672 (ppp) cc_final: 0.8150 (ppp)
REVERT: A  799 MET cc_start: 0.8932 (ppp) cc_final: 0.8666 (tmm)
REVERT: A  845 MET cc_start: 0.8103 (ptm) cc_final: 0.7518 (ptm)
REVERT: A  863 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8432 (tt)
  outliers start: 19
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1423
  time to fit residues: 12.6575
Evaluate side-chains
  58 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:   30.0000
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:   30.0000
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 837 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.101639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.061383 restraints weight = 24211.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063220 restraints weight = 10732.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.064120 restraints weight = 7095.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6058  Z= 0.165
  Angle     :  0.744  10.715   8226  Z= 0.378
  Chirality :  0.045   0.143    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  5.927  38.779    826
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.93 %
    Favored  : 86.17 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.10 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.31), residues: 781
  helix:  1.49 (0.27), residues: 390
  sheet: -2.14 (0.88), residues: 31
  loop : -3.62 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.012   0.002   PHE A 395 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  283)
  hydrogen bonds       : angle       4.75637 (  831)
  covalent geometry    : bond        0.00364 ( 6057)
  covalent geometry    : angle       0.74388 ( 8226)
  Misc. bond           : bond        0.00041 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 44
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9474 (t80) cc_final: 0.9210 (t80)
REVERT: A  315 MET cc_start: 0.9266 (tmm) cc_final: 0.8965 (tmm)
REVERT: A  319 MET cc_start: 0.8500 (mpp) cc_final: 0.8201 (mpp)
REVERT: A  331 PHE cc_start: 0.8870 (m-80) cc_final: 0.8500 (m-80)
REVERT: A  689 TYR cc_start: 0.9203 (p90) cc_final: 0.8765 (p90)
REVERT: A  705 MET cc_start: 0.8694 (ppp) cc_final: 0.8235 (ppp)
REVERT: A  799 MET cc_start: 0.8942 (ppp) cc_final: 0.8691 (tmm)
REVERT: A  845 MET cc_start: 0.8184 (ptm) cc_final: 0.7564 (ptm)
  outliers start: 23
  outliers final: 18
  residues processed: 63
  average time/residue: 0.1604
  time to fit residues: 14.2972
Evaluate side-chains
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:   40.0000
   chunk 31 optimal weight:   30.0000
   chunk 54 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:   50.0000
   chunk 55 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 536 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.099615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.058933 restraints weight = 24535.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.060637 restraints weight = 11213.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.061535 restraints weight = 7498.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6058  Z= 0.238
  Angle     :  0.798  12.445   8226  Z= 0.410
  Chirality :  0.046   0.142    974
  Planarity :  0.005   0.057   1041
  Dihedral  :  5.999  38.938    826
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 18.98
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.44 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.26 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.31), residues: 781
  helix:  1.22 (0.26), residues: 387
  sheet: -2.65 (0.85), residues: 33
  loop : -3.48 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.002   HIS A 473 
 PHE   0.019   0.002   PHE A 395 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.004   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05625 (  283)
  hydrogen bonds       : angle       5.16877 (  831)
  covalent geometry    : bond        0.00526 ( 6057)
  covalent geometry    : angle       0.79798 ( 8226)
  Misc. bond           : bond        0.00103 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 43
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 MET cc_start: 0.9350 (ptp) cc_final: 0.9092 (mpp)
REVERT: A  319 MET cc_start: 0.8518 (mpp) cc_final: 0.8221 (mpp)
REVERT: A  331 PHE cc_start: 0.8936 (m-80) cc_final: 0.8462 (m-80)
REVERT: A  689 TYR cc_start: 0.9297 (p90) cc_final: 0.8870 (p90)
REVERT: A  705 MET cc_start: 0.8846 (ppp) cc_final: 0.8444 (ppp)
REVERT: A  799 MET cc_start: 0.8971 (ppp) cc_final: 0.8687 (tmm)
REVERT: A  845 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7604 (ptm)
  outliers start: 29
  outliers final: 24
  residues processed: 64
  average time/residue: 0.1504
  time to fit residues: 13.7392
Evaluate side-chains
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 42
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  845 MET
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  947 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 14 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:   30.0000
   chunk 49 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.101753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061691 restraints weight = 24503.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.063499 restraints weight = 10802.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.064472 restraints weight = 7091.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6058  Z= 0.141
  Angle     :  0.749  12.658   8226  Z= 0.381
  Chirality :  0.046   0.361    974
  Planarity :  0.005   0.066   1041
  Dihedral  :  5.989  39.133    826
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.68 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.80 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.31), residues: 781
  helix:  1.36 (0.27), residues: 393
  sheet: -2.71 (0.72), residues: 41
  loop : -3.70 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 558 
 HIS   0.010   0.001   HIS A 473 
 PHE   0.010   0.001   PHE A 303 
 TYR   0.019   0.001   TYR A 689 
 ARG   0.002   0.000   ARG A 785 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04546 (  283)
  hydrogen bonds       : angle       4.74040 (  831)
  covalent geometry    : bond        0.00301 ( 6057)
  covalent geometry    : angle       0.74882 ( 8226)
  Misc. bond           : bond        0.00008 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9802 (mmtm) cc_final: 0.9353 (tppt)
REVERT: A  292 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9093 (ptp)
REVERT: A  315 MET cc_start: 0.9322 (tmm) cc_final: 0.9090 (tmm)
REVERT: A  331 PHE cc_start: 0.8856 (m-80) cc_final: 0.8426 (m-80)
REVERT: A  689 TYR cc_start: 0.9203 (p90) cc_final: 0.8778 (p90)
REVERT: A  705 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8546 (ppp)
REVERT: A  799 MET cc_start: 0.8971 (ppp) cc_final: 0.8708 (tmm)
REVERT: A  845 MET cc_start: 0.8096 (ptm) cc_final: 0.7818 (ptt)
  outliers start: 18
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1537
  time to fit residues: 13.7199
Evaluate side-chains
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 24 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:   40.0000
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.101757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061789 restraints weight = 24448.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.063673 restraints weight = 10727.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.064535 restraints weight = 6998.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6058  Z= 0.146
  Angle     :  0.763  12.653   8226  Z= 0.388
  Chirality :  0.046   0.349    974
  Planarity :  0.005   0.072   1041
  Dihedral  :  5.855  38.796    826
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.55 %
    Favored  : 86.56 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.80 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.31), residues: 781
  helix:  1.35 (0.27), residues: 393
  sheet: -2.44 (0.84), residues: 23
  loop : -3.56 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.010   0.001   PHE A 395 
 TYR   0.019   0.001   TYR A 689 
 ARG   0.001   0.000   ARG A 785 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  283)
  hydrogen bonds       : angle       4.77110 (  831)
  covalent geometry    : bond        0.00317 ( 6057)
  covalent geometry    : angle       0.76274 ( 8226)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9279 (tmm) cc_final: 0.9047 (tmm)
REVERT: A  331 PHE cc_start: 0.8848 (m-80) cc_final: 0.8446 (m-80)
REVERT: A  610 MET cc_start: 0.8920 (ttp) cc_final: 0.8703 (ttp)
REVERT: A  689 TYR cc_start: 0.9263 (p90) cc_final: 0.8846 (p90)
REVERT: A  705 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8527 (ppp)
REVERT: A  799 MET cc_start: 0.8992 (ppp) cc_final: 0.8732 (tmm)
REVERT: A  845 MET cc_start: 0.7974 (ptm) cc_final: 0.7773 (ptm)
  outliers start: 18
  outliers final: 13
  residues processed: 59
  average time/residue: 0.1539
  time to fit residues: 13.3413
Evaluate side-chains
  60 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 70 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:   50.0000
   chunk 24 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.102551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.063607 restraints weight = 24430.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.065561 restraints weight = 10585.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.066495 restraints weight = 6807.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6058  Z= 0.134
  Angle     :  0.749  11.557   8226  Z= 0.380
  Chirality :  0.045   0.280    974
  Planarity :  0.005   0.077   1041
  Dihedral  :  5.800  39.194    826
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.29 %
    Favored  : 86.81 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.88 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.31), residues: 781
  helix:  1.41 (0.27), residues: 393
  sheet: -2.39 (0.70), residues: 31
  loop : -3.59 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 335 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.015   0.001   PHE A 291 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.001   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04150 (  283)
  hydrogen bonds       : angle       4.67152 (  831)
  covalent geometry    : bond        0.00288 ( 6057)
  covalent geometry    : angle       0.74925 ( 8226)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9259 (tmm) cc_final: 0.8838 (tmm)
REVERT: A  319 MET cc_start: 0.7842 (mtp) cc_final: 0.7313 (ttp)
REVERT: A  331 PHE cc_start: 0.8872 (m-80) cc_final: 0.8543 (m-80)
REVERT: A  689 TYR cc_start: 0.9224 (p90) cc_final: 0.8796 (p90)
REVERT: A  705 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8502 (ppp)
REVERT: A  799 MET cc_start: 0.8989 (ppp) cc_final: 0.8729 (tmm)
REVERT: A  845 MET cc_start: 0.8002 (ptm) cc_final: 0.7779 (ptm)
  outliers start: 12
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1862
  time to fit residues: 15.6394
Evaluate side-chains
  58 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0370
   chunk 74 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.1820

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.102177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.062695 restraints weight = 24946.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.064512 restraints weight = 10818.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.065595 restraints weight = 7065.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6058  Z= 0.145
  Angle     :  0.763  13.776   8226  Z= 0.389
  Chirality :  0.045   0.269    974
  Planarity :  0.005   0.079   1041
  Dihedral  :  5.736  39.255    826
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.68 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.18 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.31), residues: 781
  helix:  1.40 (0.27), residues: 393
  sheet: -2.22 (0.83), residues: 23
  loop : -3.51 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.006   0.000   ARG A 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  283)
  hydrogen bonds       : angle       4.77550 (  831)
  covalent geometry    : bond        0.00318 ( 6057)
  covalent geometry    : angle       0.76342 ( 8226)
  Misc. bond           : bond        0.00001 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2926.89 seconds
wall clock time: 51 minutes 49.80 seconds (3109.80 seconds total)