Starting phenix.real_space_refine
on Fri Oct 10 13:28:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q74_18203/10_2025/8q74_18203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q74_18203/10_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_18203/10_2025/8q74_18203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q74_18203/10_2025/8q74_18203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q74_18203/10_2025/8q74_18203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q74_18203/10_2025/8q74_18203.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.57, per 1000 atoms: 0.26
  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: 0.57
  Conformation dependent library (CDL) restraints added in 432.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.18
  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: 0.74

  Time building geometry restraints manager: 0.71 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:             2.140
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.260
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.560
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG A 322 
 TYR   0.028   0.002   TYR A 689 
 PHE   0.020   0.002   PHE A 582 
 TRP   0.023   0.002   TRP A 558 
 HIS   0.009   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 6057)
  covalent geometry    : angle       1.02032 ( 8226)
  hydrogen bonds       : bond        0.19672 (  283)
  hydrogen bonds       : angle       6.81073 (  831)
  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  : 0.265 
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: 0.0690
  time to fit residues: 7.6263
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  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 721 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.100220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.059678 restraints weight = 24265.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061418 restraints weight = 11082.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.062320 restraints weight = 7386.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.062690 restraints weight = 6169.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.062911 restraints weight = 5747.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6058  Z= 0.235
  Angle     :  0.880  10.113   8226  Z= 0.458
  Chirality :  0.048   0.169    974
  Planarity :  0.006   0.067   1041
  Dihedral  :  6.641  38.937    826
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 16.26 %
    Favored  : 82.97 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.94 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -2.07 (0.30), residues: 781
  helix:  0.73 (0.27), residues: 381
  sheet: -3.08 (0.75), residues: 31
  loop : -3.73 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 322 
 TYR   0.016   0.002   TYR A 253 
 PHE   0.022   0.003   PHE A 293 
 TRP   0.024   0.002   TRP A 558 
 HIS   0.012   0.002   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 6057)
  covalent geometry    : angle       0.88000 ( 8226)
  hydrogen bonds       : bond        0.06278 (  283)
  hydrogen bonds       : angle       5.63461 (  831)
  Misc. bond           : bond        0.00132 (    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
  61 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8535 (mpp) cc_final: 0.8241 (mpp)
REVERT: A  331 PHE cc_start: 0.8162 (m-10) cc_final: 0.7517 (m-80)
REVERT: A  601 LEU cc_start: 0.9242 (mm) cc_final: 0.8929 (mm)
REVERT: A  689 TYR cc_start: 0.9120 (p90) cc_final: 0.8759 (p90)
REVERT: A  799 MET cc_start: 0.8983 (ppp) cc_final: 0.8299 (ppp)
  outliers start: 14
  outliers final: 13
  residues processed: 55
  average time/residue: 0.0551
  time to fit residues: 4.6391
Evaluate side-chains
  53 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  368 VAL
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  648 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 54 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4184 r_free = 0.4184 target = 0.101361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.061290 restraints weight = 23765.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.063129 restraints weight = 10555.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.064006 restraints weight = 6929.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 73)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.064515 restraints weight = 5768.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.064648 restraints weight = 5273.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2014

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= 0.161
  Angle     :  0.787   8.736   8226  Z= 0.408
  Chirality :  0.046   0.220    974
  Planarity :  0.006   0.063   1041
  Dihedral  :  6.413  36.443    826
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.21 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.56 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -1.72 (0.30), residues: 781
  helix:  1.06 (0.27), residues: 384
  sheet: -2.68 (0.81), residues: 31
  loop : -3.67 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 322 
 TYR   0.015   0.001   TYR A 689 
 PHE   0.026   0.002   PHE A 293 
 TRP   0.015   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6057)
  covalent geometry    : angle       0.78655 ( 8226)
  hydrogen bonds       : bond        0.05366 (  283)
  hydrogen bonds       : angle       5.10640 (  831)
  Misc. bond           : bond        0.00026 (    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
  68 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9319 (m-80) cc_final: 0.8671 (m-80)
REVERT: A  315 MET cc_start: 0.9277 (tmm) cc_final: 0.9011 (tmm)
REVERT: A  319 MET cc_start: 0.8421 (mpp) cc_final: 0.8115 (mpp)
REVERT: A  331 PHE cc_start: 0.8133 (m-10) cc_final: 0.7565 (m-80)
REVERT: A  689 TYR cc_start: 0.8991 (p90) cc_final: 0.8609 (p90)
REVERT: A  799 MET cc_start: 0.8933 (ppp) cc_final: 0.8496 (ppp)
REVERT: A  845 MET cc_start: 0.7894 (ptp) cc_final: 0.7674 (ppp)
  outliers start: 19
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0561
  time to fit residues: 5.6046
Evaluate side-chains
  55 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 53 optimal weight:   50.0000
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:   30.0000
   chunk 65 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
A 721 ASN
A 837 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.099680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.059292 restraints weight = 24205.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061027 restraints weight = 10963.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.061917 restraints weight = 7352.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.062292 restraints weight = 6079.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.062375 restraints weight = 5635.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6058  Z= 0.215
  Angle     :  0.816  10.814   8226  Z= 0.418
  Chirality :  0.047   0.202    974
  Planarity :  0.006   0.062   1041
  Dihedral  :  6.350  37.603    826
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 19.90
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.98 %
    Favored  : 84.25 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.79 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -1.73 (0.30), residues: 781
  helix:  1.02 (0.26), residues: 384
  sheet: -2.53 (0.85), residues: 31
  loop : -3.65 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 322 
 TYR   0.022   0.002   TYR A 253 
 PHE   0.019   0.002   PHE A 286 
 TRP   0.014   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 6057)
  covalent geometry    : angle       0.81640 ( 8226)
  hydrogen bonds       : bond        0.05490 (  283)
  hydrogen bonds       : angle       5.18290 (  831)
  Misc. bond           : bond        0.00071 (    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
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 41
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 PHE cc_start: 0.9270 (m-80) cc_final: 0.9063 (m-80)
REVERT: A  319 MET cc_start: 0.8485 (mpp) cc_final: 0.8183 (mpp)
REVERT: A  331 PHE cc_start: 0.8258 (m-10) cc_final: 0.7737 (m-80)
REVERT: A  657 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6835 (mmtt)
REVERT: A  705 MET cc_start: 0.8910 (ppp) cc_final: 0.8499 (ppp)
REVERT: A  799 MET cc_start: 0.8967 (ppp) cc_final: 0.8677 (tmm)
REVERT: A  845 MET cc_start: 0.8184 (ptp) cc_final: 0.7777 (ppp)
REVERT: A  881 MET cc_start: 0.9068 (tmm) cc_final: 0.8777 (tmm)
  outliers start: 24
  outliers final: 15
  residues processed: 62
  average time/residue: 0.0623
  time to fit residues: 5.5635
Evaluate side-chains
  56 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
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  296 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  479 ILE
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4180 r_free = 0.4180 target = 0.101402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061558 restraints weight = 24819.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063431 restraints weight = 10831.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.064427 restraints weight = 7104.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.064713 restraints weight = 5814.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.065014 restraints weight = 5446.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2730

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= 0.145
  Angle     :  0.762   9.289   8226  Z= 0.392
  Chirality :  0.046   0.171    974
  Planarity :  0.005   0.060   1041
  Dihedral  :  6.201  38.055    826
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.44 %
    Favored  : 85.79 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.64 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -1.56 (0.30), residues: 781
  helix:  1.21 (0.27), residues: 390
  sheet: -2.36 (0.86), residues: 31
  loop : -3.72 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 322 
 TYR   0.015   0.001   TYR A 689 
 PHE   0.012   0.002   PHE A 293 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6057)
  covalent geometry    : angle       0.76170 ( 8226)
  hydrogen bonds       : bond        0.04681 (  283)
  hydrogen bonds       : angle       4.92977 (  831)
  Misc. bond           : bond        0.00008 (    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
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9268 (tmm) cc_final: 0.9000 (tmm)
REVERT: A  319 MET cc_start: 0.8390 (mpp) cc_final: 0.8092 (mpp)
REVERT: A  331 PHE cc_start: 0.8238 (m-10) cc_final: 0.7662 (m-80)
REVERT: A  579 MET cc_start: 0.9196 (pmm) cc_final: 0.8909 (pmm)
REVERT: A  705 MET cc_start: 0.8834 (ppp) cc_final: 0.8254 (ppp)
REVERT: A  799 MET cc_start: 0.8962 (ppp) cc_final: 0.8686 (tmm)
REVERT: A  845 MET cc_start: 0.7994 (ptp) cc_final: 0.7637 (ppp)
  outliers start: 17
  outliers final: 14
  residues processed: 60
  average time/residue: 0.0669
  time to fit residues: 5.7848
Evaluate side-chains
  53 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  303 PHE
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  557 THR
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  902 ILE
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 26 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    0.1980
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 53 optimal weight:   50.0000
   chunk 11 optimal weight:    0.0970
   chunk 57 optimal weight:    6.9990
   chunk 14 optimal weight:    0.1980
   chunk 43 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.101301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061083 restraints weight = 24725.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.062962 restraints weight = 10882.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063897 restraints weight = 7200.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.064344 restraints weight = 5934.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.064588 restraints weight = 5491.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6058  Z= 0.160
  Angle     :  0.764  10.345   8226  Z= 0.391
  Chirality :  0.045   0.144    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  6.105  38.022    826
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 12.80 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.80 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -1.52 (0.31), residues: 781
  helix:  1.25 (0.27), residues: 391
  sheet: -2.31 (0.89), residues: 31
  loop : -3.73 (0.28), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.041   0.002   TYR A 689 
 PHE   0.016   0.002   PHE A 293 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6057)
  covalent geometry    : angle       0.76420 ( 8226)
  hydrogen bonds       : bond        0.04704 (  283)
  hydrogen bonds       : angle       4.93642 (  831)
  Misc. bond           : bond        0.00017 (    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
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 41
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9256 (tmm) cc_final: 0.8952 (tmm)
REVERT: A  319 MET cc_start: 0.8449 (mpp) cc_final: 0.8155 (mpp)
REVERT: A  331 PHE cc_start: 0.8329 (m-10) cc_final: 0.7680 (m-80)
REVERT: A  657 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7025 (mmtt)
REVERT: A  705 MET cc_start: 0.8882 (ppp) cc_final: 0.8373 (ppp)
REVERT: A  799 MET cc_start: 0.8963 (ppp) cc_final: 0.8690 (tmm)
REVERT: A  845 MET cc_start: 0.8127 (ptp) cc_final: 0.7606 (ppp)
REVERT: A  863 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8292 (tt)
  outliers start: 23
  outliers final: 17
  residues processed: 58
  average time/residue: 0.0699
  time to fit residues: 5.7896
Evaluate side-chains
  61 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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  303 PHE
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  478 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN
A 536 GLN
A 587 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.100610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.059950 restraints weight = 24684.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.061778 restraints weight = 11165.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.062642 restraints weight = 7424.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.063120 restraints weight = 6221.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.063258 restraints weight = 5743.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3159

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= 0.179
  Angle     :  0.767  10.920   8226  Z= 0.396
  Chirality :  0.045   0.143    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  6.063  38.239    826
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.44 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.64 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.31), residues: 781
  helix:  1.17 (0.27), residues: 393
  sheet: -2.70 (0.74), residues: 41
  loop : -3.78 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 322 
 TYR   0.019   0.001   TYR A 689 
 PHE   0.020   0.002   PHE A 293 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6057)
  covalent geometry    : angle       0.76745 ( 8226)
  hydrogen bonds       : bond        0.04973 (  283)
  hydrogen bonds       : angle       5.05023 (  831)
  Misc. bond           : bond        0.00042 (    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
  68 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 42
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8492 (mpp) cc_final: 0.8185 (mpp)
REVERT: A  330 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7589 (tm-30)
REVERT: A  657 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7142 (mmtt)
REVERT: A  705 MET cc_start: 0.8968 (ppp) cc_final: 0.8560 (ppp)
REVERT: A  799 MET cc_start: 0.8958 (ppp) cc_final: 0.8667 (tmm)
REVERT: A  845 MET cc_start: 0.8225 (ptp) cc_final: 0.7636 (ppp)
REVERT: A  863 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8277 (tt)
  outliers start: 26
  outliers final: 21
  residues processed: 63
  average time/residue: 0.0608
  time to fit residues: 5.5417
Evaluate side-chains
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 41
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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  303 PHE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  330 GLN
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  417 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
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
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 18 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.101834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.061291 restraints weight = 24299.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063190 restraints weight = 10795.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.064155 restraints weight = 7139.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.064535 restraints weight = 5937.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.064762 restraints weight = 5537.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6058  Z= 0.148
  Angle     :  0.768  12.474   8226  Z= 0.393
  Chirality :  0.047   0.409    974
  Planarity :  0.005   0.065   1041
  Dihedral  :  5.994  38.508    826
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.57 %
    Favored  : 85.53 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.88 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.31), residues: 781
  helix:  1.18 (0.27), residues: 393
  sheet: -2.76 (0.74), residues: 41
  loop : -3.78 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 322 
 TYR   0.045   0.001   TYR A 689 
 PHE   0.020   0.002   PHE A 331 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6057)
  covalent geometry    : angle       0.76784 ( 8226)
  hydrogen bonds       : bond        0.04696 (  283)
  hydrogen bonds       : angle       4.92719 (  831)
  Misc. bond           : bond        0.00004 (    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
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 43
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9804 (mmtm) cc_final: 0.9322 (tppt)
REVERT: A  315 MET cc_start: 0.9278 (tmm) cc_final: 0.9008 (tmm)
REVERT: A  319 MET cc_start: 0.8440 (mpp) cc_final: 0.8145 (mpp)
REVERT: A  657 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7263 (mmtt)
REVERT: A  705 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8505 (ppp)
REVERT: A  799 MET cc_start: 0.8960 (ppp) cc_final: 0.8670 (tmm)
REVERT: A  845 MET cc_start: 0.8202 (ptp) cc_final: 0.7675 (ppp)
REVERT: A  863 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8231 (tt)
  outliers start: 24
  outliers final: 19
  residues processed: 62
  average time/residue: 0.0606
  time to fit residues: 5.2703
Evaluate side-chains
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  303 PHE
Chi-restraints excluded: chain A residue  324 LEU
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  478 MET
Chi-restraints excluded: chain A residue  488 LYS
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
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  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
Chi-restraints excluded: chain A residue  947 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 73 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0170
   chunk 66 optimal weight:    8.9990
   overall best weight:    3.6424

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.098885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.058319 restraints weight = 24924.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.060020 restraints weight = 11388.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.060944 restraints weight = 7625.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061310 restraints weight = 6345.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 66)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.061548 restraints weight = 5904.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   6058  Z= 0.273
  Angle     :  0.866  16.885   8226  Z= 0.445
  Chirality :  0.048   0.342    974
  Planarity :  0.006   0.069   1041
  Dihedral  :  6.118  38.465    826
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 22.23
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 14.60 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 18.95 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.30), residues: 781
  helix:  0.81 (0.27), residues: 387
  sheet: -2.64 (0.86), residues: 33
  loop : -3.59 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 322 
 TYR   0.035   0.002   TYR A 689 
 PHE   0.021   0.002   PHE A 303 
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.002   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 6057)
  covalent geometry    : angle       0.86598 ( 8226)
  hydrogen bonds       : bond        0.05983 (  283)
  hydrogen bonds       : angle       5.46702 (  831)
  Misc. bond           : bond        0.00119 (    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
  68 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 38
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9278 (tmm) cc_final: 0.8934 (tmm)
REVERT: A  319 MET cc_start: 0.8506 (mpp) cc_final: 0.8207 (mpp)
REVERT: A  331 PHE cc_start: 0.8296 (m-80) cc_final: 0.7899 (m-80)
REVERT: A  610 MET cc_start: 0.8954 (ttp) cc_final: 0.8720 (ttp)
REVERT: A  705 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8573 (ppp)
REVERT: A  799 MET cc_start: 0.8985 (ppp) cc_final: 0.8690 (tmm)
REVERT: A  845 MET cc_start: 0.8348 (ptp) cc_final: 0.7937 (ptp)
REVERT: A  863 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (tt)
  outliers start: 30
  outliers final: 26
  residues processed: 62
  average time/residue: 0.0637
  time to fit residues: 5.6932
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 36
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  324 LEU
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  488 LYS
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  657 LYS
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  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
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue  948 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 53 optimal weight:   50.0000
   chunk 70 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0370
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4186 r_free = 0.4186 target = 0.102030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061362 restraints weight = 24683.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.063295 restraints weight = 10705.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.064276 restraints weight = 7035.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.064663 restraints weight = 5840.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.064907 restraints weight = 5399.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6058  Z= 0.149
  Angle     :  0.799  14.710   8226  Z= 0.407
  Chirality :  0.046   0.305    974
  Planarity :  0.006   0.073   1041
  Dihedral  :  6.011  38.503    826
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.70 %
    Favored  : 85.40 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.03 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.31), residues: 781
  helix:  0.97 (0.27), residues: 393
  sheet: -2.60 (0.84), residues: 33
  loop : -3.70 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 882 
 TYR   0.030   0.001   TYR A 689 
 PHE   0.011   0.002   PHE A 293 
 TRP   0.009   0.001   TRP A 335 
 HIS   0.012   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6057)
  covalent geometry    : angle       0.79877 ( 8226)
  hydrogen bonds       : bond        0.04914 (  283)
  hydrogen bonds       : angle       5.06997 (  831)
  Misc. bond           : bond        0.00013 (    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
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 40
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9787 (mmtm) cc_final: 0.9297 (tppt)
REVERT: A  315 MET cc_start: 0.9290 (tmm) cc_final: 0.9026 (tmm)
REVERT: A  331 PHE cc_start: 0.8223 (m-80) cc_final: 0.7871 (m-80)
REVERT: A  705 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8640 (ppp)
REVERT: A  799 MET cc_start: 0.8968 (ppp) cc_final: 0.8670 (tmm)
REVERT: A  845 MET cc_start: 0.8197 (ptp) cc_final: 0.7945 (ptp)
  outliers start: 23
  outliers final: 19
  residues processed: 60
  average time/residue: 0.0691
  time to fit residues: 5.7931
Evaluate side-chains
  59 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  284 CYS
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  333 ILE
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  584 LEU
Chi-restraints excluded: chain A residue  657 LYS
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  902 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0070
   chunk 5 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 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 = 0.4213 r_free = 0.4213 target = 0.103345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063399 restraints weight = 24727.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.065411 restraints weight = 10627.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.066341 restraints weight = 6877.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.066812 restraints weight = 5703.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.066812 restraints weight = 5216.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6058  Z= 0.142
  Angle     :  0.791  13.567   8226  Z= 0.398
  Chirality :  0.046   0.288    974
  Planarity :  0.006   0.076   1041
  Dihedral  :  5.868  38.795    826
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.93 %
    Favored  : 86.17 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.26 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.31), residues: 781
  helix:  1.11 (0.27), residues: 395
  sheet: -2.51 (0.83), residues: 33
  loop : -3.60 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 347 
 TYR   0.034   0.001   TYR A 689 
 PHE   0.011   0.001   PHE A 293 
 TRP   0.011   0.001   TRP A 335 
 HIS   0.017   0.002   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6057)
  covalent geometry    : angle       0.79056 ( 8226)
  hydrogen bonds       : bond        0.04299 (  283)
  hydrogen bonds       : angle       4.85997 (  831)
  Misc. bond           : bond        0.00037 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1759.11 seconds
wall clock time: 30 minutes 52.76 seconds (1852.76 seconds total)