Starting phenix.real_space_refine
on Tue Feb 11 14:41:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q74_18203/02_2025/8q74_18203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q74_18203/02_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_18203/02_2025/8q74_18203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q74_18203/02_2025/8q74_18203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q74_18203/02_2025/8q74_18203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q74_18203/02_2025/8q74_18203.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5943
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 5942
          Classifications: {'peptide': 783}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CU': 1}
          Classifications: {'undetermined': 1}

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

  Time building chain proxies: 4.42, per 1000 atoms: 0.74
  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: 2.00
  Conformation dependent library (CDL) restraints added in 932.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      53.6% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 209
      removed outlier: 4.285A  pdb=" N   ARG A 207 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 3.599A  pdb=" N   ALA A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 296
      removed outlier: 3.793A  pdb=" N   PHE A 286 " --> pdb=" O   TRP A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 297 through 300
    Processing helix  chain 'A' and resid 302 through 308
    Processing helix  chain 'A' and resid 317 through 332
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 6.499A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 377
      removed outlier: 3.696A  pdb=" N   LEU A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 420
      removed outlier: 4.094A  pdb=" N   ILE A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 531
      removed outlier: 3.635A  pdb=" N   GLN A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
    Processing helix  chain 'A' and resid 546 through 567
      removed outlier: 3.520A  pdb=" N   TRP A 561 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 594
      removed outlier: 3.638A  pdb=" N   LEU A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 618
      removed outlier: 4.010A  pdb=" N   MET A 610 " --> pdb=" O   PRO A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 634
    Processing helix  chain 'A' and resid 682 through 693
      removed outlier: 4.373A  pdb=" N   THR A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 691 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 743 through 756
      removed outlier: 3.825A  pdb=" N   GLU A 747 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 768
    Processing helix  chain 'A' and resid 782 through 794
    Processing helix  chain 'A' and resid 804 through 816
    Processing helix  chain 'A' and resid 825 through 839
    Processing helix  chain 'A' and resid 849 through 851
      No H-bonds generated for 'chain 'A' and resid 849 through 851'
    Processing helix  chain 'A' and resid 852 through 859
    Processing helix  chain 'A' and resid 869 through 876
      removed outlier: 3.900A  pdb=" N   ILE A 873 " --> pdb=" O   THR A 869 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 922
      removed outlier: 4.123A  pdb=" N   ILE A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR A 890 " --> pdb=" O   GLU A 886 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A 913 " --> pdb=" O   ALA A 909 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 915 " --> pdb=" O   GLY A 911 " (cutoff:3.500A)
      Proline residue:  A 918  - end of helix
    Processing helix  chain 'A' and resid 924 through 929
    Processing helix  chain 'A' and resid 933 through 954
      removed outlier: 4.146A  pdb=" N   ALA A 939 " --> pdb=" O   TRP A 935 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A 940 " --> pdb=" O   LEU A 936 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 941 " --> pdb=" O   ALA A 937 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 954 " --> pdb=" O   CYS A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 958
    Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312
      removed outlier: 3.628A  pdb=" N   VAL A 311 " --> pdb=" O   MET A 315 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   MET A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425
    Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455
      removed outlier: 4.082A  pdb=" N   CYS A 504 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821
      removed outlier: 8.929A  pdb=" N   PHE A 821 " --> pdb=" O   SER A 797 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET A 799 " --> pdb=" O   PHE A 821 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA A 637 " --> pdb=" O   ALA A 844 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    831 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.90 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:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.700
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.380
-------------------------------------------------------------------------------
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      :  0.004   0.071   6057  Z= 0.291
  Angle     :  1.020  12.117   8226  Z= 0.613
  Chirality :  0.048   0.240    974
  Planarity :  0.008   0.077   1041
  Dihedral  : 14.005  87.951   2204
  Min Nonbonded Distance : 1.633

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

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

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

*********************** 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  : 0.780 
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: 0.1554
  time to fit residues: 17.1339
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  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 32 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0870
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0010
   overall best weight:    0.8966

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

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

Total number of N/Q/H flips: 3

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6057  Z= 0.240
  Angle     :  0.848   9.330   8226  Z= 0.437
  Chirality :  0.047   0.176    974
  Planarity :  0.006   0.066   1041
  Dihedral  :  6.507  38.672    826
  Min Nonbonded Distance : 2.339

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

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

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

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

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TRP cc_start: 0.8167 (m100) cc_final: 0.7958 (m-10)
REVERT: A  315 MET cc_start: 0.9103 (ppp) cc_final: 0.8826 (tmm)
REVERT: A  319 MET cc_start: 0.8391 (mpp) cc_final: 0.8117 (mpp)
REVERT: A  601 LEU cc_start: 0.9174 (mm) cc_final: 0.8855 (mm)
REVERT: A  689 TYR cc_start: 0.8981 (p90) cc_final: 0.8628 (p90)
REVERT: A  799 MET cc_start: 0.8997 (ppp) cc_final: 0.8421 (ppp)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1409
  time to fit residues: 12.8132
Evaluate side-chains
  50 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  899 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 48 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.7986

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

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

Total number of N/Q/H flips: 1

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6057  Z= 0.263
  Angle     :  0.787   8.562   8226  Z= 0.409
  Chirality :  0.047   0.234    974
  Planarity :  0.006   0.062   1041
  Dihedral  :  6.286  35.383    826
  Min Nonbonded Distance : 2.116

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

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

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

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

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8504 (mpp) cc_final: 0.8220 (mpp)
REVERT: A  331 PHE cc_start: 0.8856 (m-80) cc_final: 0.8438 (m-80)
REVERT: A  689 TYR cc_start: 0.9111 (p90) cc_final: 0.8679 (p90)
REVERT: A  799 MET cc_start: 0.8922 (ppp) cc_final: 0.8562 (ppp)
REVERT: A  845 MET cc_start: 0.8119 (ptm) cc_final: 0.7533 (ptm)
  outliers start: 19
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1254
  time to fit residues: 11.8023
Evaluate side-chains
  55 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:   40.0000
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.102496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062720 restraints weight = 24376.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.064588 restraints weight = 10719.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.065579 restraints weight = 6988.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6057  Z= 0.203
  Angle     :  0.750  10.819   8226  Z= 0.383
  Chirality :  0.046   0.182    974
  Planarity :  0.005   0.061   1041
  Dihedral  :  6.167  37.995    826
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.32 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.64 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.31), residues: 781
  helix:  1.31 (0.27), residues: 395
  sheet: -2.09 (0.85), residues: 21
  loop : -3.66 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.011   0.002   PHE A 710 
 TYR   0.022   0.001   TYR A 689 
 ARG   0.002   0.000   ARG A 269 

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

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

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

  1562 Ramachandran restraints generated.
    781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9444 (t80) cc_final: 0.9224 (t80)
REVERT: A  315 MET cc_start: 0.9273 (tmm) cc_final: 0.8991 (tmm)
REVERT: A  319 MET cc_start: 0.8411 (mpp) cc_final: 0.8132 (mpp)
REVERT: A  331 PHE cc_start: 0.8823 (m-80) cc_final: 0.8439 (m-80)
REVERT: A  657 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6739 (mmtt)
REVERT: A  689 TYR cc_start: 0.9021 (p90) cc_final: 0.8784 (p90)
REVERT: A  705 MET cc_start: 0.8729 (ppp) cc_final: 0.8507 (ppp)
REVERT: A  799 MET cc_start: 0.8935 (ppp) cc_final: 0.8682 (tmm)
REVERT: A  845 MET cc_start: 0.8112 (ptm) cc_final: 0.7524 (ptm)
REVERT: A  881 MET cc_start: 0.9256 (tpp) cc_final: 0.9016 (tmm)
  outliers start: 19
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1487
  time to fit residues: 13.6257
Evaluate side-chains
  55 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 28 optimal weight:   30.0000
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 837 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.102465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.063208 restraints weight = 24228.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.065078 restraints weight = 10369.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.066027 restraints weight = 6762.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6057  Z= 0.192
  Angle     :  0.716   9.620   8226  Z= 0.367
  Chirality :  0.045   0.147    974
  Planarity :  0.005   0.059   1041
  Dihedral  :  5.947  38.509    826
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.32 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.80 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.31), residues: 781
  helix:  1.44 (0.27), residues: 393
  sheet: -2.14 (0.89), residues: 31
  loop : -3.69 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.011   0.001   PHE A 710 
 TYR   0.020   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

*********************** 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: 18
    poor density    : 44
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9486 (t80) cc_final: 0.9250 (t80)
REVERT: A  319 MET cc_start: 0.8437 (mpp) cc_final: 0.8163 (mpp)
REVERT: A  331 PHE cc_start: 0.8857 (m-80) cc_final: 0.8521 (m-80)
REVERT: A  689 TYR cc_start: 0.9134 (p90) cc_final: 0.8669 (p90)
REVERT: A  705 MET cc_start: 0.8725 (ppp) cc_final: 0.8214 (ppp)
REVERT: A  799 MET cc_start: 0.8934 (ppp) cc_final: 0.8621 (tmm)
REVERT: A  845 MET cc_start: 0.8120 (ptm) cc_final: 0.7532 (ptm)
REVERT: A  863 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8443 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 59
  average time/residue: 0.1426
  time to fit residues: 12.3101
Evaluate side-chains
  53 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4145 r_free = 0.4145 target = 0.099849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059361 restraints weight = 24447.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061117 restraints weight = 11124.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.061878 restraints weight = 7413.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6057  Z= 0.349
  Angle     :  0.796  10.595   8226  Z= 0.408
  Chirality :  0.046   0.158    974
  Planarity :  0.005   0.057   1041
  Dihedral  :  6.027  38.951    826
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.44 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.26 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.30), residues: 781
  helix:  1.33 (0.26), residues: 383
  sheet: -2.67 (0.85), residues: 33
  loop : -3.53 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 558 
 HIS   0.012   0.002   HIS A 473 
 PHE   0.019   0.002   PHE A 395 
 TYR   0.017   0.002   TYR A 253 
 ARG   0.004   0.001   ARG A 322 

*********************** 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
  69 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 41
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.9444 (t80) cc_final: 0.9171 (t80)
REVERT: A  315 MET cc_start: 0.9268 (tmm) cc_final: 0.8938 (tmm)
REVERT: A  319 MET cc_start: 0.8554 (mpp) cc_final: 0.8268 (mpp)
REVERT: A  331 PHE cc_start: 0.8927 (m-80) cc_final: 0.8477 (m-80)
REVERT: A  689 TYR cc_start: 0.9282 (p90) cc_final: 0.8834 (p90)
REVERT: A  705 MET cc_start: 0.8757 (ppp) cc_final: 0.8320 (ppp)
REVERT: A  799 MET cc_start: 0.8944 (ppp) cc_final: 0.8696 (tmm)
REVERT: A  845 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7613 (ptm)
  outliers start: 28
  outliers final: 21
  residues processed: 62
  average time/residue: 0.1515
  time to fit residues: 13.3347
Evaluate side-chains
  61 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 39
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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  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  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  845 MET
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  947 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:   40.0000
   chunk 31 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 30 optimal weight:   50.0000
   chunk 55 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 536 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.100012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.059217 restraints weight = 24589.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.060922 restraints weight = 11231.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.061825 restraints weight = 7573.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6057  Z= 0.316
  Angle     :  0.774  11.538   8226  Z= 0.401
  Chirality :  0.046   0.142    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  6.047  39.000    826
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 17.98
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.96 %
    Favored  : 85.15 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.57 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.31), residues: 781
  helix:  1.23 (0.27), residues: 386
  sheet: -2.64 (0.86), residues: 33
  loop : -3.60 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.018   0.002   PHE A 303 
 TYR   0.016   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

*********************** 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
  67 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 42
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8505 (mpp) cc_final: 0.8212 (mpp)
REVERT: A  331 PHE cc_start: 0.8904 (m-80) cc_final: 0.8427 (m-80)
REVERT: A  689 TYR cc_start: 0.9256 (p90) cc_final: 0.8834 (p90)
REVERT: A  705 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8462 (ppp)
REVERT: A  799 MET cc_start: 0.8948 (ppp) cc_final: 0.8670 (tmm)
REVERT: A  845 MET cc_start: 0.8237 (ptm) cc_final: 0.7656 (ptm)
REVERT: A  863 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8443 (tt)
  outliers start: 25
  outliers final: 21
  residues processed: 60
  average time/residue: 0.1395
  time to fit residues: 12.4223
Evaluate side-chains
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 42
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  601 LEU
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  885 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:   40.0000
   chunk 14 optimal weight:    0.9980
   chunk 44 optimal weight:    0.2980
   chunk 58 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 32 optimal weight:   50.0000
   chunk 49 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.105367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.061078 restraints weight = 23450.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062856 restraints weight = 10767.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.063653 restraints weight = 7275.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6057  Z= 0.203
  Angle     :  0.750  10.655   8226  Z= 0.384
  Chirality :  0.047   0.405    974
  Planarity :  0.005   0.065   1041
  Dihedral  :  5.953  39.112    826
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.04 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.41 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.31), residues: 781
  helix:  1.29 (0.26), residues: 394
  sheet: -2.62 (0.84), residues: 33
  loop : -3.72 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.010   0.001   PHE A 303 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.001   0.000   ARG A 269 

*********************** 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
  63 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9320 (tmm) cc_final: 0.9086 (tmm)
REVERT: A  331 PHE cc_start: 0.8860 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  689 TYR cc_start: 0.9200 (p90) cc_final: 0.8767 (p90)
REVERT: A  705 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8576 (ppp)
REVERT: A  799 MET cc_start: 0.8948 (ppp) cc_final: 0.8690 (tmm)
REVERT: A  845 MET cc_start: 0.8088 (ptm) cc_final: 0.7787 (ptt)
  outliers start: 17
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1431
  time to fit residues: 12.4430
Evaluate side-chains
  56 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
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 58 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   chunk 66 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.102819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.062566 restraints weight = 24453.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.064475 restraints weight = 10610.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.065481 restraints weight = 6932.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6057  Z= 0.205
  Angle     :  0.767  12.727   8226  Z= 0.392
  Chirality :  0.046   0.328    974
  Planarity :  0.005   0.074   1041
  Dihedral  :  5.829  38.860    826
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 13.06 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.72 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.30), residues: 781
  helix:  1.32 (0.27), residues: 394
  sheet: -2.72 (0.69), residues: 31
  loop : -3.70 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.019   0.001   TYR A 689 
 ARG   0.001   0.000   ARG A 347 

*********************** 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
  59 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9276 (tmm) cc_final: 0.9021 (tmm)
REVERT: A  319 MET cc_start: 0.7977 (mtp) cc_final: 0.7546 (ttm)
REVERT: A  331 PHE cc_start: 0.8876 (m-80) cc_final: 0.8531 (m-80)
REVERT: A  689 TYR cc_start: 0.9228 (p90) cc_final: 0.8787 (p90)
REVERT: A  705 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8477 (ppp)
REVERT: A  799 MET cc_start: 0.8988 (ppp) cc_final: 0.8717 (tmm)
  outliers start: 13
  outliers final: 11
  residues processed: 55
  average time/residue: 0.1473
  time to fit residues: 11.9684
Evaluate side-chains
  58 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0570
   chunk 71 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.9302

-------------------------------------------------------------------------------
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 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.102747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062702 restraints weight = 24481.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.064668 restraints weight = 10584.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.065660 restraints weight = 6812.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6057  Z= 0.209
  Angle     :  0.764  13.686   8226  Z= 0.388
  Chirality :  0.046   0.273    974
  Planarity :  0.005   0.079   1041
  Dihedral  :  5.773  39.269    826
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.68 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.57 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.31), residues: 781
  helix:  1.32 (0.27), residues: 394
  sheet: -2.34 (0.82), residues: 23
  loop : -3.59 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.017   0.001   TYR A 689 
 ARG   0.002   0.000   ARG A 322 

********************** 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
  62 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9282 (tmm) cc_final: 0.9061 (tmm)
REVERT: A  331 PHE cc_start: 0.8885 (m-80) cc_final: 0.8498 (m-80)
REVERT: A  689 TYR cc_start: 0.9242 (p90) cc_final: 0.8810 (p90)
REVERT: A  705 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8488 (ppp)
REVERT: A  799 MET cc_start: 0.9007 (ppp) cc_final: 0.8729 (tmm)
  outliers start: 16
  outliers final: 13
  residues processed: 58
  average time/residue: 0.1435
  time to fit residues: 12.3130
Evaluate side-chains
  59 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  478 MET
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  705 MET
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  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 70 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0040
   chunk 68 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.103835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.063998 restraints weight = 25278.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.065862 restraints weight = 10707.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.066930 restraints weight = 6935.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6057  Z= 0.202
  Angle     :  0.770  11.645   8226  Z= 0.392
  Chirality :  0.045   0.271    974
  Planarity :  0.006   0.081   1041
  Dihedral  :  5.660  39.338    826
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.55 %
    Favored  : 86.56 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.88 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.31), residues: 781
  helix:  1.36 (0.27), residues: 393
  sheet: -2.40 (0.70), residues: 31
  loop : -3.59 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 935 
 HIS   0.011   0.002   HIS A 473 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.017   0.001   TYR A 689 
 ARG   0.004   0.000   ARG A 269 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2833.26 seconds
wall clock time: 51 minutes 19.95 seconds (3079.95 seconds total)