Starting phenix.real_space_refine
on Wed Mar  4 02:57:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ny1_8994/03_2026/6ny1_8994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ny1_8994/03_2026/6ny1_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_8994/03_2026/6ny1_8994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ny1_8994/03_2026/6ny1_8994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ny1_8994/03_2026/6ny1_8994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ny1_8994/03_2026/6ny1_8994.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'UNK:plan-1': 57, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1}
          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: {'UNK:plan-1': 64, 'GLU:plan': 3, '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: 2.43, per 1000 atoms: 0.25
  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: 0.75
  Conformation dependent library (CDL) restraints added in 395.0 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: 1.22
  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: 2.46

  Time building geometry restraints manager: 0.98 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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.680
  Find NCS groups from input model:        0.040
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.630
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG Y 753 
 TYR   0.020   0.003   TYR Y 418 
 PHE   0.033   0.003   PHE Y 609 
 TRP   0.025   0.003   TRP Y 534 
 HIS   0.009   0.002   HIS Y 250 

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

*********************** 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  : 0.315 
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: 0.9352 (tt)
REVERT: Y   67 MET cc_start: 0.8116 (ttp) cc_final: 0.7738 (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: 0.9234 (tmm) cc_final: 0.8880 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 94
  average time/residue: 0.1152
  time to fit residues: 14.8037
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   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 = 0.3740 r_free = 0.3740 target = 0.098626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.073561 restraints weight = 32562.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.076097 restraints weight = 15933.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077742 restraints weight = 10091.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.078779 restraints weight = 7599.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.079429 restraints weight = 6405.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10413  Z= 0.171
  Angle     :  0.742   8.046  14808  Z= 0.400
  Chirality :  0.042   0.286   1762
  Planarity :  0.005   0.059   1334
  Dihedral  : 25.208 176.547   3107
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.06 %
    Favored  : 82.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.28), residues: 768
  helix: -0.73 (0.26), residues: 337
  sheet: -3.40 (0.53), residues: 78
  loop : -3.80 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 749 
 TYR   0.013   0.002   TYR Y 196 
 PHE   0.031   0.002   PHE Y 736 
 TRP   0.024   0.002   TRP Y 534 
 HIS   0.003   0.001   HIS Y 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10412)
  covalent geometry    : angle       0.74252 (14805)
  hydrogen bonds       : bond        0.06257 (  404)
  hydrogen bonds       : angle       5.00295 ( 1059)
  link_TRANS           : bond        0.00227 (    1)
  link_TRANS           : angle       0.22276 (    3)

*********************** 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
  95 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8806 (mtm) cc_final: 0.8488 (mtp)
REVERT: Y  490 GLN cc_start: 0.9416 (tt0) cc_final: 0.9043 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7553 (m-80) cc_final: 0.7052 (m-80)
REVERT: Y  574 LEU cc_start: 0.9223 (tp) cc_final: 0.8946 (tp)
REVERT: Y  747 MET cc_start: 0.9209 (tmm) cc_final: 0.8843 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0890
  time to fit residues: 11.9601
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  : 0.207 
-------------------------------------------------------------------------------
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 16 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   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 = 0.3726 r_free = 0.3726 target = 0.098035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.073281 restraints weight = 32617.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.075771 restraints weight = 16169.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.077425 restraints weight = 10299.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.078474 restraints weight = 7716.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.079120 restraints weight = 6471.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10413  Z= 0.190
  Angle     :  0.734   7.608  14808  Z= 0.394
  Chirality :  0.042   0.262   1762
  Planarity :  0.005   0.055   1334
  Dihedral  : 25.076 171.095   3107
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.45 %
    Favored  : 82.42 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  6.35 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.29), residues: 768
  helix:  0.12 (0.28), residues: 333
  sheet: -3.42 (0.52), residues: 81
  loop : -3.75 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Y 628 
 TYR   0.014   0.002   TYR Y  83 
 PHE   0.017   0.002   PHE Y 609 
 TRP   0.016   0.002   TRP Y 534 
 HIS   0.005   0.001   HIS Y 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10412)
  covalent geometry    : angle       0.73455 (14805)
  hydrogen bonds       : bond        0.06165 (  404)
  hydrogen bonds       : angle       4.84233 ( 1059)
  link_TRANS           : bond        0.00182 (    1)
  link_TRANS           : angle       0.38084 (    3)

*********************** 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
  98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8780 (mtm) cc_final: 0.8460 (mtp)
REVERT: Y  326 LYS cc_start: 0.8935 (tmmt) cc_final: 0.8709 (ptmm)
REVERT: Y  371 GLU cc_start: 0.8763 (mp0) cc_final: 0.8552 (mp0)
REVERT: Y  490 GLN cc_start: 0.9379 (tt0) cc_final: 0.9113 (tp-100)
REVERT: Y  747 MET cc_start: 0.9159 (tmm) cc_final: 0.8775 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0939
  time to fit residues: 13.0839
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  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0770
   chunk 1 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 88 optimal weight:    7.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    1.0340

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.102050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.078115 restraints weight = 32199.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.080732 restraints weight = 15579.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.082439 restraints weight = 9691.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.083532 restraints weight = 7178.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.084229 restraints weight = 5966.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10413  Z= 0.136
  Angle     :  0.673   7.678  14808  Z= 0.359
  Chirality :  0.040   0.257   1762
  Planarity :  0.004   0.047   1334
  Dihedral  : 24.807 171.846   3107
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.89 %
    Favored  : 84.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.30), residues: 768
  helix:  0.52 (0.28), residues: 332
  sheet: -3.03 (0.56), residues: 76
  loop : -3.66 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Y 299 
 TYR   0.014   0.001   TYR Y 196 
 PHE   0.013   0.001   PHE Y 609 
 TRP   0.018   0.001   TRP Y 344 
 HIS   0.012   0.002   HIS Y 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10412)
  covalent geometry    : angle       0.67302 (14805)
  hydrogen bonds       : bond        0.05490 (  404)
  hydrogen bonds       : angle       4.50391 ( 1059)
  link_TRANS           : bond        0.00072 (    1)
  link_TRANS           : angle       0.19704 (    3)

*********************** 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
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8164 (ttp) cc_final: 0.7863 (ttm)
REVERT: Y   75 MET cc_start: 0.8801 (mtm) cc_final: 0.8480 (mtp)
REVERT: Y  240 LEU cc_start: 0.9021 (tp) cc_final: 0.8635 (tp)
REVERT: Y  462 THR cc_start: 0.9432 (p) cc_final: 0.9176 (p)
REVERT: Y  490 GLN cc_start: 0.9372 (tt0) cc_final: 0.9097 (tp-100)
REVERT: Y  747 MET cc_start: 0.8509 (tmm) cc_final: 0.7713 (mmp)
REVERT: Y  964 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7701 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1055
  time to fit residues: 15.8481
Evaluate side-chains
  71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0970
   chunk 60 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:   30.0000
   chunk 78 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.103903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.078999 restraints weight = 31964.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.081766 restraints weight = 15686.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.083603 restraints weight = 9807.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.084792 restraints weight = 7220.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085394 restraints weight = 5939.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3151

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= 0.128
  Angle     :  0.651   8.018  14808  Z= 0.345
  Chirality :  0.039   0.244   1762
  Planarity :  0.004   0.043   1334
  Dihedral  : 24.581 174.044   3107
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.89 %
    Favored  : 84.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.30), residues: 768
  helix:  0.69 (0.28), residues: 330
  sheet: -3.01 (0.56), residues: 78
  loop : -3.54 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 299 
 TYR   0.019   0.001   TYR Y 293 
 PHE   0.016   0.001   PHE Y 609 
 TRP   0.015   0.001   TRP Y 344 
 HIS   0.009   0.001   HIS Y 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10412)
  covalent geometry    : angle       0.65140 (14805)
  hydrogen bonds       : bond        0.05240 (  404)
  hydrogen bonds       : angle       4.33731 ( 1059)
  link_TRANS           : bond        0.00053 (    1)
  link_TRANS           : angle       0.30693 (    3)

*********************** 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  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   27 MET cc_start: 0.6645 (mmt) cc_final: 0.6305 (mmt)
REVERT: Y   75 MET cc_start: 0.8804 (mtm) cc_final: 0.8507 (mtp)
REVERT: Y  233 MET cc_start: 0.8672 (mmp) cc_final: 0.8173 (mmp)
REVERT: Y  240 LEU cc_start: 0.8931 (tp) cc_final: 0.8487 (tp)
REVERT: Y  280 LEU cc_start: 0.8731 (mt) cc_final: 0.8520 (mt)
REVERT: Y  462 THR cc_start: 0.9433 (p) cc_final: 0.9147 (p)
REVERT: Y  490 GLN cc_start: 0.9408 (tt0) cc_final: 0.9117 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7512 (m-80) cc_final: 0.7278 (m-80)
REVERT: Y  719 GLN cc_start: 0.9379 (mm110) cc_final: 0.9054 (mm110)
REVERT: Y  747 MET cc_start: 0.8571 (tmm) cc_final: 0.7746 (mmp)
REVERT: Y  971 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7600 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0908
  time to fit residues: 13.2304
Evaluate side-chains
  78 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 61 optimal weight:    7.9990
   chunk 84 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    3.7388

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.097483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.072510 restraints weight = 32724.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.074966 restraints weight = 16343.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.076587 restraints weight = 10465.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077647 restraints weight = 7898.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.078143 restraints weight = 6637.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2874

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= 0.241
  Angle     :  0.767   8.020  14808  Z= 0.403
  Chirality :  0.043   0.258   1762
  Planarity :  0.005   0.049   1334
  Dihedral  : 24.653 165.145   3107
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.49 %
    Favored  : 81.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.30), residues: 768
  helix:  0.52 (0.28), residues: 329
  sheet: -3.19 (0.54), residues: 79
  loop : -3.57 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Y 944 
 TYR   0.022   0.002   TYR Y  83 
 PHE   0.017   0.002   PHE Y 609 
 TRP   0.020   0.002   TRP Y 795 
 HIS   0.008   0.002   HIS Y 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (10412)
  covalent geometry    : angle       0.76704 (14805)
  hydrogen bonds       : bond        0.06391 (  404)
  hydrogen bonds       : angle       4.72407 ( 1059)
  link_TRANS           : bond        0.00230 (    1)
  link_TRANS           : angle       0.53671 (    3)

*********************** 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
  100 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   27 MET cc_start: 0.6919 (mmt) cc_final: 0.6696 (mmt)
REVERT: Y   67 MET cc_start: 0.8445 (ptp) cc_final: 0.8234 (ptp)
REVERT: Y   75 MET cc_start: 0.8769 (mtm) cc_final: 0.8461 (mtp)
REVERT: Y  462 THR cc_start: 0.9431 (p) cc_final: 0.9163 (p)
REVERT: Y  490 GLN cc_start: 0.9423 (tt0) cc_final: 0.9014 (tp-100)
REVERT: Y  499 ARG cc_start: 0.8566 (tpt90) cc_final: 0.8329 (tpt90)
REVERT: Y  719 GLN cc_start: 0.9383 (mm110) cc_final: 0.9033 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0962
  time to fit residues: 13.6037
Evaluate side-chains
  65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:   20.0000
   chunk 69 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   chunk 31 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.098821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.073920 restraints weight = 32292.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076406 restraints weight = 16202.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.078035 restraints weight = 10375.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.079083 restraints weight = 7853.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.079615 restraints weight = 6606.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10413  Z= 0.183
  Angle     :  0.710   8.554  14808  Z= 0.373
  Chirality :  0.041   0.254   1762
  Planarity :  0.004   0.045   1334
  Dihedral  : 24.562 166.733   3107
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.06 %
    Favored  : 82.94 %
  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 : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.30), residues: 768
  helix:  0.69 (0.28), residues: 324
  sheet: -3.22 (0.53), residues: 81
  loop : -3.52 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Y 917 
 TYR   0.017   0.002   TYR Y 382 
 PHE   0.019   0.002   PHE Y 609 
 TRP   0.014   0.001   TRP Y 795 
 HIS   0.008   0.002   HIS Y 916 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (10412)
  covalent geometry    : angle       0.71008 (14805)
  hydrogen bonds       : bond        0.05861 (  404)
  hydrogen bonds       : angle       4.61116 ( 1059)
  link_TRANS           : bond        0.00168 (    1)
  link_TRANS           : angle       0.36754 (    3)

*********************** 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
  96 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8787 (mtm) cc_final: 0.8491 (mtp)
REVERT: Y  417 LYS cc_start: 0.7445 (tttt) cc_final: 0.7082 (ttpt)
REVERT: Y  490 GLN cc_start: 0.9413 (tt0) cc_final: 0.9027 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9371 (mm110) cc_final: 0.9147 (mm110)
REVERT: Y  749 ARG cc_start: 0.8892 (ptp-170) cc_final: 0.8579 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0844
  time to fit residues: 11.9801
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 59 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 10 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.102976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.077996 restraints weight = 31941.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.080715 restraints weight = 15760.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.082519 restraints weight = 9927.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.083680 restraints weight = 7348.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.084434 restraints weight = 6100.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10413  Z= 0.133
  Angle     :  0.668   9.850  14808  Z= 0.351
  Chirality :  0.039   0.243   1762
  Planarity :  0.004   0.038   1334
  Dihedral  : 24.412 172.263   3107
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.80 %
    Favored  : 83.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.30), residues: 768
  helix:  0.88 (0.28), residues: 332
  sheet: -3.08 (0.54), residues: 81
  loop : -3.43 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 299 
 TYR   0.013   0.001   TYR Y 974 
 PHE   0.018   0.001   PHE Y 609 
 TRP   0.016   0.001   TRP Y 344 
 HIS   0.007   0.001   HIS Y 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10412)
  covalent geometry    : angle       0.66837 (14805)
  hydrogen bonds       : bond        0.05235 (  404)
  hydrogen bonds       : angle       4.36818 ( 1059)
  link_TRANS           : bond        0.00065 (    1)
  link_TRANS           : angle       0.27532 (    3)

*********************** 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
  109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8357 (ptp) cc_final: 0.8063 (ptp)
REVERT: Y   75 MET cc_start: 0.8835 (mtm) cc_final: 0.8528 (mtp)
REVERT: Y   95 MET cc_start: 0.8042 (mtm) cc_final: 0.7793 (mtt)
REVERT: Y   98 PHE cc_start: 0.8818 (m-80) cc_final: 0.8170 (m-80)
REVERT: Y  462 THR cc_start: 0.9410 (p) cc_final: 0.9042 (p)
REVERT: Y  490 GLN cc_start: 0.9430 (tt0) cc_final: 0.9062 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9367 (mm110) cc_final: 0.9143 (mm110)
REVERT: Y  747 MET cc_start: 0.8427 (tmm) cc_final: 0.7755 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0855
  time to fit residues: 13.4464
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  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 13 optimal weight:   30.0000
   chunk 9 optimal weight:    0.0470
   chunk 72 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.9884

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.101447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076481 restraints weight = 32317.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.079124 restraints weight = 15990.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.080896 restraints weight = 10105.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.082023 restraints weight = 7514.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.082601 restraints weight = 6247.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10413  Z= 0.161
  Angle     :  0.690   8.293  14808  Z= 0.361
  Chirality :  0.040   0.247   1762
  Planarity :  0.004   0.040   1334
  Dihedral  : 24.376 167.957   3107
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.49 %
    Favored  : 84.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.30), residues: 768
  helix:  0.86 (0.28), residues: 332
  sheet: -3.06 (0.55), residues: 81
  loop : -3.39 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Y 628 
 TYR   0.013   0.002   TYR Y 974 
 PHE   0.017   0.002   PHE Y 609 
 TRP   0.014   0.001   TRP Y 795 
 HIS   0.010   0.002   HIS Y 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10412)
  covalent geometry    : angle       0.69024 (14805)
  hydrogen bonds       : bond        0.05346 (  404)
  hydrogen bonds       : angle       4.42306 ( 1059)
  link_TRANS           : bond        0.00118 (    1)
  link_TRANS           : angle       0.44215 (    3)

*********************** 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
  99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8421 (ptp) cc_final: 0.8145 (ptp)
REVERT: Y   75 MET cc_start: 0.8848 (mtm) cc_final: 0.8562 (mtp)
REVERT: Y   95 MET cc_start: 0.8168 (mtm) cc_final: 0.7940 (mtt)
REVERT: Y   98 PHE cc_start: 0.8798 (m-80) cc_final: 0.8362 (m-80)
REVERT: Y  462 THR cc_start: 0.9417 (p) cc_final: 0.9083 (p)
REVERT: Y  490 GLN cc_start: 0.9453 (tt0) cc_final: 0.9076 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9409 (mm110) cc_final: 0.9145 (mm110)
REVERT: Y  747 MET cc_start: 0.8552 (tmm) cc_final: 0.7758 (mmp)
REVERT: Y  749 ARG cc_start: 0.8891 (ptp-170) cc_final: 0.8633 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0866
  time to fit residues: 12.5648
Evaluate side-chains
  69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0980
   chunk 19 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0370
   chunk 35 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.2196

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.108206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.083608 restraints weight = 31668.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.086463 restraints weight = 15715.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.088358 restraints weight = 9820.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.089600 restraints weight = 7217.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.090361 restraints weight = 5936.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10413  Z= 0.125
  Angle     :  0.651   8.774  14808  Z= 0.339
  Chirality :  0.039   0.232   1762
  Planarity :  0.004   0.035   1334
  Dihedral  : 24.227 175.365   3107
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.49 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.31), residues: 768
  helix:  1.08 (0.28), residues: 333
  sheet: -2.76 (0.58), residues: 78
  loop : -3.34 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Y 628 
 TYR   0.015   0.001   TYR Y 974 
 PHE   0.016   0.001   PHE Y 609 
 TRP   0.021   0.001   TRP Y 344 
 HIS   0.005   0.001   HIS Y 758 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10412)
  covalent geometry    : angle       0.65079 (14805)
  hydrogen bonds       : bond        0.05141 (  404)
  hydrogen bonds       : angle       4.20809 ( 1059)
  link_TRANS           : bond        0.00011 (    1)
  link_TRANS           : angle       0.19856 (    3)

********************** 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
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8319 (ptp) cc_final: 0.7714 (ppp)
REVERT: Y   95 MET cc_start: 0.7915 (mtm) cc_final: 0.7672 (mtm)
REVERT: Y   98 PHE cc_start: 0.8635 (m-80) cc_final: 0.8170 (m-80)
REVERT: Y  411 LEU cc_start: 0.8971 (mm) cc_final: 0.8256 (tp)
REVERT: Y  462 THR cc_start: 0.9391 (p) cc_final: 0.8972 (p)
REVERT: Y  490 GLN cc_start: 0.9431 (tt0) cc_final: 0.9091 (tp-100)
REVERT: Y  719 GLN cc_start: 0.9385 (mm110) cc_final: 0.9149 (mm110)
REVERT: Y  747 MET cc_start: 0.8207 (tmm) cc_final: 0.7698 (mmm)
REVERT: Y  749 ARG cc_start: 0.8801 (ptp-170) cc_final: 0.8533 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0887
  time to fit residues: 13.2807
Evaluate side-chains
  73 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   chunk 70 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.105237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.080237 restraints weight = 32353.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.083013 restraints weight = 16139.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.084827 restraints weight = 10156.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086035 restraints weight = 7563.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.086629 restraints weight = 6264.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10413  Z= 0.140
  Angle     :  0.664   8.657  14808  Z= 0.348
  Chirality :  0.040   0.237   1762
  Planarity :  0.004   0.040   1334
  Dihedral  : 24.199 169.547   3107
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.36 %
    Favored  : 84.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.31), residues: 768
  helix:  1.17 (0.28), residues: 333
  sheet: -2.49 (0.61), residues: 74
  loop : -3.33 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 654 
 TYR   0.022   0.002   TYR Y 293 
 PHE   0.017   0.001   PHE Y 195 
 TRP   0.015   0.001   TRP Y 534 
 HIS   0.007   0.001   HIS Y 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10412)
  covalent geometry    : angle       0.66417 (14805)
  hydrogen bonds       : bond        0.05004 (  404)
  hydrogen bonds       : angle       4.25714 ( 1059)
  link_TRANS           : bond        0.00073 (    1)
  link_TRANS           : angle       0.47354 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.79 seconds
wall clock time: 30 minutes 50.42 seconds (1850.42 seconds total)