Starting phenix.real_space_refine
on Tue Mar 11 14:30:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q74_18203/03_2025/8q74_18203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q74_18203/03_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_18203/03_2025/8q74_18203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q74_18203/03_2025/8q74_18203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q74_18203/03_2025/8q74_18203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q74_18203/03_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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5943
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 5942
          Classifications: {'peptide': 783}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CU': 1}
          Classifications: {'undetermined': 1}

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

  Time building chain proxies: 3.50, per 1000 atoms: 0.59
  Number of scatterers: 5943
  At special positions: 0
  Unit cell: (80.408, 86.3328, 141.349, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cu      1     28.99
     S      34     16.00
     O    1108      8.00
     N     988      7.00
     C    3812      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 739.5 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: 0.64
  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: 1.44

  Time building geometry restraints manager: 1.48 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:             1.420
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     15.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.140
-------------------------------------------------------------------------------
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  : 0.688 
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: 0.1499
  time to fit residues: 16.6589
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  : 0.653 
-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.102745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.064483 restraints weight = 24172.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.066352 restraints weight = 10512.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.067391 restraints weight = 6845.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TRP cc_start: 0.8175 (m100) cc_final: 0.7966 (m-10)
REVERT: A  315 MET cc_start: 0.9106 (ppp) cc_final: 0.8829 (tmm)
REVERT: A  319 MET cc_start: 0.8395 (mpp) cc_final: 0.8120 (mpp)
REVERT: A  601 LEU cc_start: 0.9178 (mm) cc_final: 0.8862 (mm)
REVERT: A  689 TYR cc_start: 0.8950 (p90) cc_final: 0.8604 (p90)
REVERT: A  799 MET cc_start: 0.8999 (ppp) cc_final: 0.8427 (ppp)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1268
  time to fit residues: 11.5349
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  : 0.608 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.102045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061828 restraints weight = 23953.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.063654 restraints weight = 10630.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.064540 restraints weight = 6942.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6057  Z= 0.229
  Angle     :  0.780   8.633   8226  Z= 0.404
  Chirality :  0.046   0.229    974
  Planarity :  0.006   0.062   1041
  Dihedral  :  6.284  35.866    826
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 14.34 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.41 %
    Favored  : 83.67 %
  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: -1.58 (0.31), residues: 781
  helix:  1.05 (0.27), residues: 389
  sheet: -2.22 (0.85), residues: 21
  loop : -3.54 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.021   0.002   PHE A 331 
 TYR   0.013   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
  65 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8463 (mpp) cc_final: 0.8176 (mpp)
REVERT: A  331 PHE cc_start: 0.8780 (m-80) cc_final: 0.8373 (m-80)
REVERT: A  689 TYR cc_start: 0.9068 (p90) cc_final: 0.8649 (p90)
REVERT: A  799 MET cc_start: 0.8932 (ppp) cc_final: 0.8498 (ppp)
  outliers start: 19
  outliers final: 12
  residues processed: 62
  average time/residue: 0.1238
  time to fit residues: 11.6559
Evaluate side-chains
  56 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  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:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 41 optimal weight:    0.2980
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:   40.0000
   chunk 3 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.102926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.063565 restraints weight = 24459.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.065488 restraints weight = 10501.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.066540 restraints weight = 6738.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2647

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= 0.195
  Angle     :  0.752  11.669   8226  Z= 0.383
  Chirality :  0.046   0.185    974
  Planarity :  0.005   0.061   1041
  Dihedral  :  6.123  37.727    826
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 13.32 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.18 %
    Favored  : 83.36 %
  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: -1.39 (0.31), residues: 781
  helix:  1.30 (0.27), residues: 395
  sheet: -1.98 (0.86), residues: 21
  loop : -3.65 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.011   0.002   PHE A 659 
 TYR   0.022   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

*********************** 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
  66 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9290 (tmm) cc_final: 0.9019 (tmm)
REVERT: A  319 MET cc_start: 0.8389 (mpp) cc_final: 0.8135 (mpp)
REVERT: A  331 PHE cc_start: 0.8776 (m-80) cc_final: 0.8409 (m-80)
REVERT: A  689 TYR cc_start: 0.9046 (p90) cc_final: 0.8566 (p90)
REVERT: A  799 MET cc_start: 0.8944 (ppp) cc_final: 0.8686 (tmm)
  outliers start: 16
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1403
  time to fit residues: 13.0837
Evaluate side-chains
  48 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 53 optimal weight:   20.0000
   chunk 68 optimal weight:    8.9990
   chunk 63 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 837 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.102712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.063780 restraints weight = 24128.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.065722 restraints weight = 10431.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.066727 restraints weight = 6763.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2978

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= 0.191
  Angle     :  0.749  10.697   8226  Z= 0.377
  Chirality :  0.045   0.162    974
  Planarity :  0.005   0.058   1041
  Dihedral  :  5.941  38.436    826
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  : 12.80 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.72 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.31), residues: 781
  helix:  1.46 (0.27), residues: 392
  sheet: -2.05 (0.90), residues: 31
  loop : -3.68 (0.29), residues: 358

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

*********************** 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
  66 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8433 (mpp) cc_final: 0.8160 (mpp)
REVERT: A  331 PHE cc_start: 0.8808 (m-80) cc_final: 0.8500 (m-80)
REVERT: A  689 TYR cc_start: 0.9131 (p90) cc_final: 0.8653 (p90)
REVERT: A  705 MET cc_start: 0.8586 (ppp) cc_final: 0.8249 (ppp)
REVERT: A  799 MET cc_start: 0.8913 (ppp) cc_final: 0.8610 (tmm)
REVERT: A  845 MET cc_start: 0.8410 (ppp) cc_final: 0.7929 (ptm)
  outliers start: 22
  outliers final: 14
  residues processed: 60
  average time/residue: 0.1527
  time to fit residues: 13.0186
Evaluate side-chains
  58 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  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  657 LYS
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  704 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0470
   chunk 57 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.9484

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.102919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.063220 restraints weight = 24295.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.065124 restraints weight = 10520.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.066016 restraints weight = 6829.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6057  Z= 0.197
  Angle     :  0.736  10.639   8226  Z= 0.370
  Chirality :  0.044   0.144    974
  Planarity :  0.005   0.057   1041
  Dihedral  :  5.833  38.929    826
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.68 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.64 %
    Favored  : 80.59 %
  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: -1.20 (0.31), residues: 781
  helix:  1.55 (0.27), residues: 391
  sheet: -1.99 (0.90), residues: 31
  loop : -3.64 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 558 
 HIS   0.012   0.001   HIS A 473 
 PHE   0.010   0.001   PHE A 710 
 TYR   0.019   0.001   TYR A 689 
 ARG   0.003   0.000   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
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9270 (tmm) cc_final: 0.8942 (tmm)
REVERT: A  319 MET cc_start: 0.8425 (mpp) cc_final: 0.8156 (mpp)
REVERT: A  331 PHE cc_start: 0.8880 (m-80) cc_final: 0.8598 (m-80)
REVERT: A  689 TYR cc_start: 0.9200 (p90) cc_final: 0.8735 (p90)
REVERT: A  705 MET cc_start: 0.8688 (ppp) cc_final: 0.8439 (ppp)
REVERT: A  799 MET cc_start: 0.8922 (ppp) cc_final: 0.8623 (tmm)
  outliers start: 18
  outliers final: 12
  residues processed: 60
  average time/residue: 0.1611
  time to fit residues: 13.6174
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  : 0.664 
-------------------------------------------------------------------------------
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  371 VAL
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  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:   30.0000
   chunk 31 optimal weight:   30.0000
   chunk 54 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:   30.0000
   chunk 55 optimal weight:    0.0070
   chunk 74 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.7604

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.101284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.061537 restraints weight = 24584.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.063393 restraints weight = 10892.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.064317 restraints weight = 7154.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6057  Z= 0.240
  Angle     :  0.739  11.648   8226  Z= 0.377
  Chirality :  0.045   0.142    974
  Planarity :  0.005   0.057   1041
  Dihedral  :  5.802  39.227    826
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.55 %
    Favored  : 86.56 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.49 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.31), residues: 781
  helix:  1.43 (0.27), residues: 393
  sheet: -2.59 (0.73), residues: 41
  loop : -3.65 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.012   0.001   HIS A 473 
 PHE   0.012   0.001   PHE A 395 
 TYR   0.018   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
  64 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 MET cc_start: 0.8487 (mpp) cc_final: 0.8201 (mpp)
REVERT: A  331 PHE cc_start: 0.8898 (m-80) cc_final: 0.8563 (m-80)
REVERT: A  689 TYR cc_start: 0.9221 (p90) cc_final: 0.8799 (p90)
REVERT: A  705 MET cc_start: 0.8612 (ppp) cc_final: 0.8407 (ppp)
REVERT: A  799 MET cc_start: 0.8961 (ppp) cc_final: 0.8652 (tmm)
REVERT: A  845 MET cc_start: 0.8350 (ptm) cc_final: 0.8125 (ptp)
  outliers start: 21
  outliers final: 17
  residues processed: 61
  average time/residue: 0.1496
  time to fit residues: 13.0365
Evaluate side-chains
  59 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  605 THR
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  949 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:   30.0000
   chunk 14 optimal weight:    0.0040
   chunk 44 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:   30.0000
   chunk 49 optimal weight:    0.0670
   chunk 43 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 31 optimal weight:   30.0000
   overall best weight:    0.5932

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.103073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.063469 restraints weight = 24614.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.065394 restraints weight = 10560.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.066242 restraints weight = 6864.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6057  Z= 0.194
  Angle     :  0.757  13.361   8226  Z= 0.380
  Chirality :  0.046   0.396    974
  Planarity :  0.005   0.066   1041
  Dihedral  :  5.827  39.574    826
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 11.91 %
    Favored  : 87.20 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.34 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.31), residues: 781
  helix:  1.44 (0.27), residues: 393
  sheet: -2.53 (0.72), residues: 41
  loop : -3.68 (0.29), residues: 347

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 710 
 TYR   0.019   0.001   TYR A 689 
 ARG   0.001   0.000   ARG A 785 

*********************** 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
  60 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9789 (mmtm) cc_final: 0.9309 (tppt)
REVERT: A  315 MET cc_start: 0.9296 (tmm) cc_final: 0.8984 (tmm)
REVERT: A  319 MET cc_start: 0.8410 (mpp) cc_final: 0.8143 (mpp)
REVERT: A  331 PHE cc_start: 0.8905 (m-80) cc_final: 0.8585 (m-80)
REVERT: A  579 MET cc_start: 0.9208 (pmm) cc_final: 0.9008 (pmm)
REVERT: A  689 TYR cc_start: 0.9244 (p90) cc_final: 0.8813 (p90)
REVERT: A  799 MET cc_start: 0.8982 (ppp) cc_final: 0.8680 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 57
  average time/residue: 0.1472
  time to fit residues: 12.1483
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  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  478 MET
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  899 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  946 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 24 optimal weight:   40.0000
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0470
   chunk 53 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.8086

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.101147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.061955 restraints weight = 24655.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.063716 restraints weight = 10881.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.064603 restraints weight = 7074.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6057  Z= 0.264
  Angle     :  0.817  18.611   8226  Z= 0.407
  Chirality :  0.047   0.348    974
  Planarity :  0.005   0.069   1041
  Dihedral  :  5.787  38.936    826
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 12.04 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.26 %
    Favored  : 78.74 %
  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: -2.43 (0.82), residues: 23
  loop : -3.58 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 558 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.012   0.001   PHE A 395 
 TYR   0.018   0.001   TYR A 689 
 ARG   0.003   0.000   ARG A 322 

*********************** 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
  54 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 MET cc_start: 0.9302 (tmm) cc_final: 0.8994 (tmm)
REVERT: A  319 MET cc_start: 0.8505 (mpp) cc_final: 0.8210 (mpp)
REVERT: A  331 PHE cc_start: 0.8939 (m-80) cc_final: 0.8632 (m-80)
REVERT: A  689 TYR cc_start: 0.9250 (p90) cc_final: 0.8825 (p90)
REVERT: A  799 MET cc_start: 0.8989 (ppp) cc_final: 0.8693 (tmm)
  outliers start: 13
  outliers final: 11
  residues processed: 53
  average time/residue: 0.1231
  time to fit residues: 10.0940
Evaluate side-chains
  52 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
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  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  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:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 52 optimal weight:   30.0000
   chunk 70 optimal weight:    0.0020
   chunk 73 optimal weight:    0.3980
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.5188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.103562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.064067 restraints weight = 24918.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.066047 restraints weight = 10718.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.067020 restraints weight = 6867.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6057  Z= 0.207
  Angle     :  0.814  18.074   8226  Z= 0.403
  Chirality :  0.046   0.298    974
  Planarity :  0.005   0.074   1041
  Dihedral  :  5.741  39.666    826
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 11.78 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.88 %
    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: -1.36 (0.31), residues: 781
  helix:  1.35 (0.27), residues: 393
  sheet: -2.33 (0.72), residues: 31
  loop : -3.62 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 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   0.004   0.000   ARG A 269 

********************** 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
  57 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 LYS cc_start: 0.9800 (mmtm) cc_final: 0.9284 (tppt)
REVERT: A  315 MET cc_start: 0.9297 (tmm) cc_final: 0.9010 (tmm)
REVERT: A  319 MET cc_start: 0.8403 (mpp) cc_final: 0.8133 (mpp)
REVERT: A  331 PHE cc_start: 0.8913 (m-80) cc_final: 0.8529 (m-80)
REVERT: A  689 TYR cc_start: 0.9235 (p90) cc_final: 0.8795 (p90)
REVERT: A  799 MET cc_start: 0.9012 (ppp) cc_final: 0.8722 (tmm)
REVERT: A  845 MET cc_start: 0.8264 (ppp) cc_final: 0.7844 (ptm)
  outliers start: 11
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1441
  time to fit residues: 11.3409
Evaluate side-chains
  57 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  605 THR
Chi-restraints excluded: chain A residue  667 LEU
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 70 optimal weight:    0.6980
   chunk 61 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0870
   chunk 36 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 32 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    0.2980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.104654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.065296 restraints weight = 25472.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.067342 restraints weight = 10693.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.068410 restraints weight = 6769.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6057  Z= 0.201
  Angle     :  0.789  16.810   8226  Z= 0.391
  Chirality :  0.045   0.299    974
  Planarity :  0.005   0.078   1041
  Dihedral  :  5.539  39.648    826
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 11.52 %
    Favored  : 87.58 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.72 %
    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: -1.19 (0.31), residues: 781
  helix:  1.46 (0.27), residues: 394
  sheet: -2.08 (0.83), residues: 23
  loop : -3.51 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 335 
 HIS   0.011   0.001   HIS A 473 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.018   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: 2844.77 seconds
wall clock time: 49 minutes 48.36 seconds (2988.36 seconds total)