Starting phenix.real_space_refine
on Mon Jul 28 11:59:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ny1_8994/07_2025/6ny1_8994.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     154      5.49       5
     S      20      5.16       5
     C    5724      2.51       5
     N    1805      2.21       5
     O    2208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9911
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "Y"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 829
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "Y"
      Number of atoms: 4955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 667, 4955
          Classifications: {'peptide': 667}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121}
          Link IDs: {'PTRANS': 22, 'TRANS': 644}
          Unresolved chain links: 1
          Chain breaks: 5
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 359
          Unresolved non-hydrogen angles: 470
          Unresolved non-hydrogen dihedrals: 249
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 57, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 237
    Chain: "Y"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 887
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'UNK:plan-1': 64, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 346
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "B"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2300
          Classifications: {'RNA': 108}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 14, 'rna3p': 93}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 594
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
  Time building chain proxies: 6.29, per 1000 atoms: 0.63
  Number of scatterers: 9911
  At special positions: 0
  Unit cell: (99, 138.6, 120.6, 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)
     S      20     16.00
     P     154     15.00
     O    2208      8.00
     N    1805      7.00
     C    5724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " UNK Y 104 " - " SER Y 103 "
  Time building additional restraints: 2.30
  Conformation dependent library (CDL) restraints added in 954.1 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 5 sheets defined
      47.1% alpha, 7.5% beta
      54 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 4.31
  Creating SS restraints...
    Processing helix  chain 'Y' and resid 4 through 15
      removed outlier: 3.541A  pdb=" N   ASP Y  15 " --> pdb=" O   LYS Y  11 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 37 through 44
    Processing helix  chain 'Y' and resid 59 through 88
      removed outlier: 4.457A  pdb=" N   ASN Y  63 " --> pdb=" O   ASN Y  59 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN Y  64 " --> pdb=" O   ASN Y  60 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 90 through 98
    Processing helix  chain 'Y' and resid 194 through 198
    Processing helix  chain 'Y' and resid 222 through 260
      removed outlier: 3.755A  pdb=" N   ASP Y 245 " --> pdb=" O   SER Y 241 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 262 through 267
    Processing helix  chain 'Y' and resid 287 through 309
      removed outlier: 3.593A  pdb=" N   ASP Y 291 " --> pdb=" O   LYS Y 287 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 342 through 357
    Processing helix  chain 'Y' and resid 361 through 366
      removed outlier: 3.804A  pdb=" N   TRP Y 365 " --> pdb=" O   GLY Y 361 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER Y 366 " --> pdb=" O   ARG Y 362 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 361 through 366'
    Processing helix  chain 'Y' and resid 370 through 380
    Processing helix  chain 'Y' and resid 403 through 418
    Processing helix  chain 'Y' and resid 424 through 449
      removed outlier: 3.569A  pdb=" N   ARG Y 432 " --> pdb=" O   GLU Y 428 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS Y 436 " --> pdb=" O   ARG Y 432 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU Y 445 " --> pdb=" O   THR Y 441 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 456 through 473
      removed outlier: 3.746A  pdb=" N   VAL Y 460 " --> pdb=" O   GLN Y 456 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU Y 461 " --> pdb=" O   SER Y 457 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 474 through 476
      No H-bonds generated for 'chain 'Y' and resid 474 through 476'
    Processing helix  chain 'Y' and resid 483 through 501
      removed outlier: 3.840A  pdb=" N   CYS Y 487 " --> pdb=" O   GLU Y 483 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 502 through 504
      No H-bonds generated for 'chain 'Y' and resid 502 through 504'
    Processing helix  chain 'Y' and resid 602 through 610
    Processing helix  chain 'Y' and resid 711 through 728
      removed outlier: 3.541A  pdb=" N   ARG Y 727 " --> pdb=" O   GLU Y 723 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG Y 728 " --> pdb=" O   VAL Y 724 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 737 through 761
      removed outlier: 4.173A  pdb=" N   ARG Y 741 " --> pdb=" O   ALA Y 737 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 790 through 802
      removed outlier: 3.769A  pdb=" N   TYR Y 802 " --> pdb=" O   ALA Y 798 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 886 through 892
    Processing helix  chain 'Y' and resid 897 through 903
    Processing helix  chain 'Y' and resid 906 through 914
      removed outlier: 4.825A  pdb=" N   UNK Y 910 " --> pdb=" O   UNK Y 906 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 935 through 938
    Processing helix  chain 'Y' and resid 939 through 951
      removed outlier: 3.764A  pdb=" N   LEU Y 947 " --> pdb=" O   ALA Y 943 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN Y 950 " --> pdb=" O   TRP Y 946 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 965 through 978
    Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19
    Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 530 through 532
      removed outlier: 3.554A  pdb=" N   LEU Y 547 " --> pdb=" O   LEU Y 531 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 680 through 682
      removed outlier: 3.840A  pdb=" N   ALA Y 682 " --> pdb=" O   GLY Y 670 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ILE Y 669 " --> pdb=" O   VAL Y 767 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    807 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      134 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 4.76

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1448
        1.32 -     1.44: 3542
        1.44 -     1.57: 5087
        1.57 -     1.69: 303
        1.69 -     1.81: 32
  Bond restraints: 10412
  Sorted by residual:
  bond pdb=" C   ASP Y 685 "
       pdb=" N   PRO Y 686 "
    ideal  model  delta    sigma   weight residual
    1.330  1.377 -0.047 1.25e-02 6.40e+03 1.39e+01
  bond pdb=" CA  ASN Y 501 "
       pdb=" C   ASN Y 501 "
    ideal  model  delta    sigma   weight residual
    1.521  1.543 -0.021 1.17e-02 7.31e+03 3.27e+00
  bond pdb=" CB  PHE Y 544 "
       pdb=" CG  PHE Y 544 "
    ideal  model  delta    sigma   weight residual
    1.502  1.460  0.042 2.30e-02 1.89e+03 3.26e+00
  bond pdb=" N   PHE Y 736 "
       pdb=" CA  PHE Y 736 "
    ideal  model  delta    sigma   weight residual
    1.462  1.484 -0.023 1.31e-02 5.83e+03 3.02e+00
  bond pdb=" C   TYR Y 196 "
       pdb=" N   SER Y 197 "
    ideal  model  delta    sigma   weight residual
    1.334  1.304  0.030 1.79e-02 3.12e+03 2.74e+00
  ... (remaining 10407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 14558
        3.55 -     7.10: 223
        7.10 -    10.65: 19
       10.65 -    14.20: 4
       14.20 -    17.75: 1
  Bond angle restraints: 14805
  Sorted by residual:
  angle pdb=" N   PHE Y 736 "
        pdb=" CA  PHE Y 736 "
        pdb=" C   PHE Y 736 "
      ideal   model   delta    sigma   weight residual
     110.91  124.49  -13.58 1.17e+00 7.31e-01 1.35e+02
  angle pdb=" C   LYS Y 735 "
        pdb=" N   PHE Y 736 "
        pdb=" CA  PHE Y 736 "
      ideal   model   delta    sigma   weight residual
     122.93  132.33   -9.40 1.51e+00 4.39e-01 3.88e+01
  angle pdb=" C   PHE Y 609 "
        pdb=" N   ILE Y 610 "
        pdb=" CA  ILE Y 610 "
      ideal   model   delta    sigma   weight residual
     123.16  117.10    6.06 1.06e+00 8.90e-01 3.26e+01
  angle pdb=" C   LEU Y 574 "
        pdb=" N   TYR Y 575 "
        pdb=" CA  TYR Y 575 "
      ideal   model   delta    sigma   weight residual
     121.54  132.44  -10.90 1.91e+00 2.74e-01 3.26e+01
  angle pdb=" CA  LEU Y 574 "
        pdb=" CB  LEU Y 574 "
        pdb=" CG  LEU Y 574 "
      ideal   model   delta    sigma   weight residual
     116.30   98.55   17.75 3.50e+00 8.16e-02 2.57e+01
  ... (remaining 14800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 5628
       35.46 -    70.92: 534
       70.92 -   106.39: 54
      106.39 -   141.85: 2
      141.85 -   177.31: 7
  Dihedral angle restraints: 6225
    sinusoidal: 3602
      harmonic: 2623
  Sorted by residual:
  dihedral pdb=" CA  LYS Y 735 "
           pdb=" C   LYS Y 735 "
           pdb=" N   PHE Y 736 "
           pdb=" CA  PHE Y 736 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -47.13 -132.87     0      5.00e+00 4.00e-02 7.06e+02
  dihedral pdb=" CA  VAL Y 368 "
           pdb=" C   VAL Y 368 "
           pdb=" N   THR Y 369 "
           pdb=" CA  THR Y 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  124.13   55.87     0      5.00e+00 4.00e-02 1.25e+02
  dihedral pdb=" C4'   C B  40 "
           pdb=" C3'   C B  40 "
           pdb=" C2'   C B  40 "
           pdb=" C1'   C B  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   36.19  -71.19     1      8.00e+00 1.56e-02 1.02e+02
  ... (remaining 6222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1498
       0.076 -    0.152: 227
       0.152 -    0.228: 30
       0.228 -    0.303: 5
       0.303 -    0.379: 2
  Chirality restraints: 1762
  Sorted by residual:
  chirality pdb=" C3'   C B 111 "
            pdb=" C4'   C B 111 "
            pdb=" O3'   C B 111 "
            pdb=" C2'   C B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.37   -0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" C3'   G B  30 "
            pdb=" C4'   G B  30 "
            pdb=" O3'   G B  30 "
            pdb=" C2'   G B  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" C3'   G B  44 "
            pdb=" C4'   G B  44 "
            pdb=" O3'   G B  44 "
            pdb=" C2'   G B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.18   -0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 1759 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 105 "    0.038 2.00e-02 2.50e+03   1.95e-02 8.53e+00
        pdb=" N1    C B 105 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2    C B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C B 105 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3    C B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C B 105 "    0.019 2.00e-02 2.50e+03
        pdb=" C5    C B 105 "   -0.020 2.00e-02 2.50e+03
        pdb=" C6    C B 105 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  52 "   -0.028 2.00e-02 2.50e+03   1.67e-02 8.39e+00
        pdb=" N9    G B  52 "    0.012 2.00e-02 2.50e+03
        pdb=" C8    G B  52 "    0.012 2.00e-02 2.50e+03
        pdb=" N7    G B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    G B  52 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    G B  52 "    0.020 2.00e-02 2.50e+03
        pdb=" O6    G B  52 "   -0.027 2.00e-02 2.50e+03
        pdb=" N1    G B  52 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2    G B  52 "    0.022 2.00e-02 2.50e+03
        pdb=" N2    G B  52 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  52 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  52 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY Y  25 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.08e+00
        pdb=" N   PRO Y  26 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  26 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  26 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 381
        2.66 -     3.22: 8575
        3.22 -     3.78: 17833
        3.78 -     4.34: 20284
        4.34 -     4.90: 29980
  Nonbonded interactions: 77053
  Sorted by model distance:
  nonbonded pdb=" O2'   C B  40 "
            pdb=" OP1   U B  41 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" OD1 ASP Y 513 "
            pdb=" OG  SER Y 515 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR Y  29 "
            pdb=" O2    U B 103 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ALA Y 816 "
            pdb=" OG1 THR Y 819 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR Y 382 "
            pdb=" O   SER Y 470 "
     model   vdw
     2.300 3.040
  ... (remaining 77048 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.440
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
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      :  0.007   0.051  10413  Z= 0.351
  Angle     :  1.114  17.747  14808  Z= 0.597
  Chirality :  0.058   0.379   1762
  Planarity :  0.008   0.071   1334
  Dihedral  : 23.729 177.312   4518
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 18.62 %
    Favored  : 80.99 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 12.71 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -4.83 (0.24), residues: 768
  helix: -2.46 (0.21), residues: 326
  sheet: -3.32 (0.56), residues: 73
  loop : -3.95 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP Y 534 
 HIS   0.009   0.002   HIS Y 250 
 PHE   0.033   0.003   PHE Y 609 
 TYR   0.020   0.003   TYR Y 418 
 ARG   0.007   0.001   ARG Y 753 

Details of bonding type rmsd
  link_TRANS           : bond        0.00388 (    1)
  link_TRANS           : angle       1.14797 (    3)
  hydrogen bonds       : bond        0.14230 (  404)
  hydrogen bonds       : angle       6.92977 ( 1059)
  covalent geometry    : bond        0.00719 (10412)
  covalent geometry    : angle       1.11429 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y    8 ILE cc_start: 0.9688 (mm) cc_final: 0.9351 (tt)
REVERT: Y   67 MET cc_start: 0.8116 (ttp) cc_final: 0.7737 (tpp)
REVERT: Y   75 MET cc_start: 0.8495 (mtm) cc_final: 0.8245 (mtp)
REVERT: Y  490 GLN cc_start: 0.9402 (tt0) cc_final: 0.9026 (tp-100)
REVERT: Y  747 MET cc_start: 0.9235 (tmm) cc_final: 0.8893 (tmm)
REVERT: Y  749 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8660 (ttm170)
  outliers start: 2
  outliers final: 1
  residues processed: 94
  average time/residue: 0.2609
  time to fit residues: 33.5297
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.098715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.073551 restraints weight = 32206.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.076089 restraints weight = 15953.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.077717 restraints weight = 10117.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10413  Z= 0.171
  Angle     :  0.741   8.065  14808  Z= 0.400
  Chirality :  0.043   0.286   1762
  Planarity :  0.005   0.058   1334
  Dihedral  : 25.201 176.679   3107
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.19 %
    Favored  : 82.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -3.52 (0.28), residues: 768
  helix: -0.71 (0.26), residues: 335
  sheet: -3.39 (0.53), residues: 78
  loop : -3.81 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP Y 534 
 HIS   0.003   0.001   HIS Y 199 
 PHE   0.027   0.002   PHE Y 736 
 TYR   0.013   0.002   TYR Y 196 
 ARG   0.003   0.000   ARG Y 753 

Details of bonding type rmsd
  link_TRANS           : bond        0.00207 (    1)
  link_TRANS           : angle       0.16742 (    3)
  hydrogen bonds       : bond        0.06268 (  404)
  hydrogen bonds       : angle       4.99083 ( 1059)
  covalent geometry    : bond        0.00345 (10412)
  covalent geometry    : angle       0.74148 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8795 (mtm) cc_final: 0.8472 (mtp)
REVERT: Y  490 GLN cc_start: 0.9416 (tt0) cc_final: 0.9048 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7571 (m-80) cc_final: 0.7110 (m-80)
REVERT: Y  574 LEU cc_start: 0.9221 (tp) cc_final: 0.8951 (tp)
REVERT: Y  747 MET cc_start: 0.9261 (tmm) cc_final: 0.8909 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2416
  time to fit residues: 31.5133
Evaluate side-chains
  67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:   30.0000
   chunk 66 optimal weight:    0.0370
   chunk 29 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 69 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 87 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   overall best weight:    3.3462

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.096691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.071713 restraints weight = 33162.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.074185 restraints weight = 16364.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075822 restraints weight = 10411.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  10413  Z= 0.225
  Angle     :  0.777   8.441  14808  Z= 0.413
  Chirality :  0.043   0.265   1762
  Planarity :  0.005   0.056   1334
  Dihedral  : 25.142 170.719   3107
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.88 %
    Favored  : 80.99 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.19 %
    Favored  : 92.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -2.92 (0.29), residues: 768
  helix:  0.09 (0.28), residues: 331
  sheet: -3.43 (0.52), residues: 81
  loop : -3.70 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP Y 534 
 HIS   0.008   0.002   HIS Y 443 
 PHE   0.017   0.002   PHE Y 609 
 TYR   0.018   0.002   TYR Y  83 
 ARG   0.005   0.001   ARG Y 299 

Details of bonding type rmsd
  link_TRANS           : bond        0.00221 (    1)
  link_TRANS           : angle       0.42805 (    3)
  hydrogen bonds       : bond        0.06497 (  404)
  hydrogen bonds       : angle       4.95899 ( 1059)
  covalent geometry    : bond        0.00460 (10412)
  covalent geometry    : angle       0.77719 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8800 (mtm) cc_final: 0.8489 (mtp)
REVERT: Y  326 LYS cc_start: 0.8878 (tmmt) cc_final: 0.8605 (ptmm)
REVERT: Y  490 GLN cc_start: 0.9421 (tt0) cc_final: 0.9058 (tp-100)
REVERT: Y  747 MET cc_start: 0.9284 (tmm) cc_final: 0.8932 (tmm)
REVERT: Y  749 ARG cc_start: 0.9044 (ttm170) cc_final: 0.8836 (ttm170)
  outliers start: 2
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2239
  time to fit residues: 29.0529
Evaluate side-chains
  61 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:   30.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.099562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.074723 restraints weight = 31480.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.077291 restraints weight = 15156.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.079000 restraints weight = 9474.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10413  Z= 0.157
  Angle     :  0.701   8.029  14808  Z= 0.373
  Chirality :  0.041   0.262   1762
  Planarity :  0.004   0.049   1334
  Dihedral  : 24.912 168.201   3107
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.32 %
    Favored  : 82.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -2.66 (0.30), residues: 768
  helix:  0.47 (0.29), residues: 331
  sheet: -3.38 (0.52), residues: 81
  loop : -3.72 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP Y 534 
 HIS   0.004   0.001   HIS Y 250 
 PHE   0.016   0.002   PHE Y 609 
 TYR   0.011   0.001   TYR Y 974 
 ARG   0.005   0.000   ARG Y 299 

Details of bonding type rmsd
  link_TRANS           : bond        0.00122 (    1)
  link_TRANS           : angle       0.30265 (    3)
  hydrogen bonds       : bond        0.05735 (  404)
  hydrogen bonds       : angle       4.60791 ( 1059)
  covalent geometry    : bond        0.00318 (10412)
  covalent geometry    : angle       0.70087 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8834 (mtm) cc_final: 0.8533 (mtp)
REVERT: Y  240 LEU cc_start: 0.9048 (tp) cc_final: 0.8624 (tp)
REVERT: Y  462 THR cc_start: 0.9455 (p) cc_final: 0.9194 (p)
REVERT: Y  490 GLN cc_start: 0.9427 (tt0) cc_final: 0.9092 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7676 (m-80) cc_final: 0.7432 (m-80)
REVERT: Y  964 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7621 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2120
  time to fit residues: 30.5745
Evaluate side-chains
  68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.099082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.074098 restraints weight = 32208.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.076587 restraints weight = 15972.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.078240 restraints weight = 10201.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10413  Z= 0.177
  Angle     :  0.709   7.508  14808  Z= 0.376
  Chirality :  0.041   0.253   1762
  Planarity :  0.004   0.047   1334
  Dihedral  : 24.833 167.757   3107
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.36 %
    Favored  : 81.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.64 (0.30), residues: 768
  helix:  0.38 (0.28), residues: 337
  sheet: -3.27 (0.54), residues: 79
  loop : -3.68 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 534 
 HIS   0.010   0.002   HIS Y 250 
 PHE   0.018   0.002   PHE Y 609 
 TYR   0.013   0.002   TYR Y  83 
 ARG   0.004   0.000   ARG Y 734 

Details of bonding type rmsd
  link_TRANS           : bond        0.00142 (    1)
  link_TRANS           : angle       0.40186 (    3)
  hydrogen bonds       : bond        0.05750 (  404)
  hydrogen bonds       : angle       4.65372 ( 1059)
  covalent geometry    : bond        0.00368 (10412)
  covalent geometry    : angle       0.70870 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   27 MET cc_start: 0.6780 (mmt) cc_final: 0.6468 (mmt)
REVERT: Y   67 MET cc_start: 0.8133 (ttp) cc_final: 0.7848 (ttm)
REVERT: Y   75 MET cc_start: 0.8825 (mtm) cc_final: 0.8489 (mtp)
REVERT: Y  462 THR cc_start: 0.9452 (p) cc_final: 0.9185 (p)
REVERT: Y  490 GLN cc_start: 0.9415 (tt0) cc_final: 0.9043 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9383 (mm110) cc_final: 0.9058 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2311
  time to fit residues: 33.3816
Evaluate side-chains
  64 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.098750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.073848 restraints weight = 32287.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076310 restraints weight = 16265.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.077947 restraints weight = 10429.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10413  Z= 0.185
  Angle     :  0.717   8.163  14808  Z= 0.379
  Chirality :  0.041   0.253   1762
  Planarity :  0.004   0.051   1334
  Dihedral  : 24.746 167.786   3107
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.97 %
    Favored  : 82.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.49 (0.30), residues: 768
  helix:  0.68 (0.29), residues: 322
  sheet: -3.26 (0.54), residues: 79
  loop : -3.61 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y 534 
 HIS   0.011   0.002   HIS Y 199 
 PHE   0.019   0.002   PHE Y 609 
 TYR   0.016   0.002   TYR Y 536 
 ARG   0.004   0.000   ARG Y 299 

Details of bonding type rmsd
  link_TRANS           : bond        0.00164 (    1)
  link_TRANS           : angle       0.43179 (    3)
  hydrogen bonds       : bond        0.05779 (  404)
  hydrogen bonds       : angle       4.63493 ( 1059)
  covalent geometry    : bond        0.00382 (10412)
  covalent geometry    : angle       0.71726 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   27 MET cc_start: 0.6750 (mmt) cc_final: 0.6508 (mmt)
REVERT: Y   67 MET cc_start: 0.8085 (ttp) cc_final: 0.7797 (ttm)
REVERT: Y   75 MET cc_start: 0.8792 (mtm) cc_final: 0.8453 (mtp)
REVERT: Y   91 HIS cc_start: 0.7923 (m90) cc_final: 0.7654 (m90)
REVERT: Y  462 THR cc_start: 0.9437 (p) cc_final: 0.9211 (p)
REVERT: Y  490 GLN cc_start: 0.9406 (tt0) cc_final: 0.9054 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9371 (mm110) cc_final: 0.9119 (mm110)
REVERT: Y  749 ARG cc_start: 0.8760 (ptp-170) cc_final: 0.8494 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2280
  time to fit residues: 31.0935
Evaluate side-chains
  62 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0870
   chunk 60 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0010
   chunk 53 optimal weight:    9.9990
   chunk 29 optimal weight:    0.1980
   chunk 32 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0020
   chunk 34 optimal weight:    0.0020
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.0580

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.107491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082662 restraints weight = 31588.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.085500 restraints weight = 15373.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.087400 restraints weight = 9514.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10413  Z= 0.129
  Angle     :  0.654   8.193  14808  Z= 0.342
  Chirality :  0.038   0.235   1762
  Planarity :  0.004   0.043   1334
  Dihedral  : 24.344 178.724   3107
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.17 (0.30), residues: 768
  helix:  0.94 (0.28), residues: 329
  sheet: -2.96 (0.56), residues: 78
  loop : -3.55 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP Y 344 
 HIS   0.012   0.002   HIS Y 443 
 PHE   0.018   0.001   PHE Y 609 
 TYR   0.014   0.001   TYR Y 974 
 ARG   0.011   0.001   ARG Y 917 

Details of bonding type rmsd
  link_TRANS           : bond        0.00013 (    1)
  link_TRANS           : angle       0.13659 (    3)
  hydrogen bonds       : bond        0.05357 (  404)
  hydrogen bonds       : angle       4.35595 ( 1059)
  covalent geometry    : bond        0.00252 (10412)
  covalent geometry    : angle       0.65443 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8170 (ttp) cc_final: 0.7798 (ttm)
REVERT: Y   75 MET cc_start: 0.8761 (mtm) cc_final: 0.8481 (mtp)
REVERT: Y  462 THR cc_start: 0.9385 (p) cc_final: 0.9057 (p)
REVERT: Y  490 GLN cc_start: 0.9440 (tt0) cc_final: 0.9127 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9391 (mm110) cc_final: 0.9018 (mm110)
REVERT: Y  747 MET cc_start: 0.8352 (tmm) cc_final: 0.7761 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2269
  time to fit residues: 35.2289
Evaluate side-chains
  77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 86 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0270
   chunk 84 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.4842

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.103953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.079240 restraints weight = 31866.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.081920 restraints weight = 15787.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.083718 restraints weight = 9962.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10413  Z= 0.142
  Angle     :  0.663   9.181  14808  Z= 0.346
  Chirality :  0.039   0.241   1762
  Planarity :  0.004   0.043   1334
  Dihedral  : 24.240 170.626   3107
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.10 %
    Favored  : 84.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.04 (0.31), residues: 768
  helix:  1.06 (0.29), residues: 330
  sheet: -2.90 (0.57), residues: 78
  loop : -3.51 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP Y 534 
 HIS   0.003   0.001   HIS Y 916 
 PHE   0.014   0.001   PHE Y 609 
 TYR   0.014   0.001   TYR Y 974 
 ARG   0.011   0.000   ARG Y 734 

Details of bonding type rmsd
  link_TRANS           : bond        0.00081 (    1)
  link_TRANS           : angle       0.45799 (    3)
  hydrogen bonds       : bond        0.05092 (  404)
  hydrogen bonds       : angle       4.34760 ( 1059)
  covalent geometry    : bond        0.00291 (10412)
  covalent geometry    : angle       0.66281 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8240 (ttp) cc_final: 0.7879 (ttm)
REVERT: Y   75 MET cc_start: 0.8832 (mtm) cc_final: 0.8546 (mtp)
REVERT: Y  490 GLN cc_start: 0.9402 (tt0) cc_final: 0.9097 (tp-100)
REVERT: Y  574 LEU cc_start: 0.9028 (tp) cc_final: 0.8801 (tp)
REVERT: Y  719 GLN cc_start: 0.9407 (mm110) cc_final: 0.9151 (mm110)
REVERT: Y  747 MET cc_start: 0.8465 (tmm) cc_final: 0.7716 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2625
  time to fit residues: 37.2414
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 68 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.098587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.073412 restraints weight = 32615.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075912 restraints weight = 16327.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077555 restraints weight = 10471.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10413  Z= 0.222
  Angle     :  0.752   8.343  14808  Z= 0.391
  Chirality :  0.042   0.252   1762
  Planarity :  0.005   0.047   1334
  Dihedral  : 24.433 165.253   3107
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.84 %
    Favored  : 82.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.32 (0.30), residues: 768
  helix:  0.79 (0.28), residues: 334
  sheet: -3.21 (0.53), residues: 81
  loop : -3.62 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP Y 795 
 HIS   0.007   0.001   HIS Y 250 
 PHE   0.017   0.002   PHE Y 609 
 TYR   0.015   0.002   TYR Y 536 
 ARG   0.005   0.001   ARG Y 628 

Details of bonding type rmsd
  link_TRANS           : bond        0.00195 (    1)
  link_TRANS           : angle       0.53921 (    3)
  hydrogen bonds       : bond        0.06154 (  404)
  hydrogen bonds       : angle       4.70942 ( 1059)
  covalent geometry    : bond        0.00459 (10412)
  covalent geometry    : angle       0.75221 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y    8 ILE cc_start: 0.9550 (mm) cc_final: 0.9339 (tt)
REVERT: Y   67 MET cc_start: 0.8230 (ttp) cc_final: 0.7967 (ttm)
REVERT: Y   75 MET cc_start: 0.8798 (mtm) cc_final: 0.8500 (mtp)
REVERT: Y   95 MET cc_start: 0.8482 (mpp) cc_final: 0.8235 (mpp)
REVERT: Y  385 ASN cc_start: 0.7882 (p0) cc_final: 0.7555 (p0)
REVERT: Y  462 THR cc_start: 0.9338 (p) cc_final: 0.9051 (p)
REVERT: Y  490 GLN cc_start: 0.9446 (tt0) cc_final: 0.9044 (tp-100)
REVERT: Y  574 LEU cc_start: 0.9197 (tp) cc_final: 0.8975 (tp)
REVERT: Y  719 GLN cc_start: 0.9450 (mm110) cc_final: 0.9179 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2667
  time to fit residues: 36.6965
Evaluate side-chains
  66 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.101082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076086 restraints weight = 31889.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.078657 restraints weight = 16023.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.080370 restraints weight = 10216.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10413  Z= 0.157
  Angle     :  0.696   8.560  14808  Z= 0.364
  Chirality :  0.040   0.246   1762
  Planarity :  0.004   0.042   1334
  Dihedral  : 24.396 168.778   3107
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.02 %
    Favored  : 83.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.17 (0.30), residues: 768
  helix:  0.89 (0.28), residues: 335
  sheet: -3.04 (0.55), residues: 81
  loop : -3.55 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP Y 795 
 HIS   0.003   0.001   HIS Y 250 
 PHE   0.022   0.002   PHE Y 609 
 TYR   0.014   0.002   TYR Y 974 
 ARG   0.005   0.000   ARG Y 628 

Details of bonding type rmsd
  link_TRANS           : bond        0.00117 (    1)
  link_TRANS           : angle       0.36233 (    3)
  hydrogen bonds       : bond        0.05498 (  404)
  hydrogen bonds       : angle       4.50581 ( 1059)
  covalent geometry    : bond        0.00325 (10412)
  covalent geometry    : angle       0.69619 (14805)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8124 (ttp) cc_final: 0.7860 (ttm)
REVERT: Y   75 MET cc_start: 0.8793 (mtm) cc_final: 0.8490 (mtp)
REVERT: Y  385 ASN cc_start: 0.7811 (p0) cc_final: 0.7448 (p0)
REVERT: Y  462 THR cc_start: 0.9416 (p) cc_final: 0.9060 (p)
REVERT: Y  490 GLN cc_start: 0.9411 (tt0) cc_final: 0.9025 (tp-100)
REVERT: Y  499 ARG cc_start: 0.8587 (tpt90) cc_final: 0.8382 (tpt90)
REVERT: Y  574 LEU cc_start: 0.9120 (tp) cc_final: 0.8893 (tp)
REVERT: Y  719 GLN cc_start: 0.9425 (mm110) cc_final: 0.9159 (mm110)
REVERT: Y  747 MET cc_start: 0.8530 (tmm) cc_final: 0.7679 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1995
  time to fit residues: 27.6149
Evaluate side-chains
  66 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
Y  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.101758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.076812 restraints weight = 31669.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.079414 restraints weight = 15721.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.081144 restraints weight = 9968.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10413  Z= 0.152
  Angle     :  0.683   8.749  14808  Z= 0.357
  Chirality :  0.040   0.244   1762
  Planarity :  0.004   0.043   1334
  Dihedral  : 24.368 169.258   3107
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.09 (0.30), residues: 768
  helix:  0.96 (0.28), residues: 334
  sheet: -2.97 (0.56), residues: 81
  loop : -3.51 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 795 
 HIS   0.004   0.001   HIS Y 250 
 PHE   0.019   0.002   PHE Y 609 
 TYR   0.020   0.001   TYR Y  83 
 ARG   0.004   0.000   ARG Y 628 

Details of bonding type rmsd
  link_TRANS           : bond        0.00105 (    1)
  link_TRANS           : angle       0.42011 (    3)
  hydrogen bonds       : bond        0.05354 (  404)
  hydrogen bonds       : angle       4.46722 ( 1059)
  covalent geometry    : bond        0.00316 (10412)
  covalent geometry    : angle       0.68340 (14805)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4057.81 seconds
wall clock time: 74 minutes 13.43 seconds (4453.43 seconds total)