Starting phenix.real_space_refine
on Mon Jul 28 12:04:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ny3_8980/07_2025/6ny3_8980.cif"
  }
  resolution = 3.7
  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=   0.004 sd=   0.110
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     164      5.49       5
     S      21      5.16       5
     C    5880      2.51       5
     N    1863      2.21       5
     O    2286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 10214
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 614
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "D"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 485
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    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: 5055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5055
          Classifications: {'peptide': 678}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121}
          Link IDs: {'PTRANS': 22, 'TRANS': 655}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 356
          Unresolved non-hydrogen angles: 468
          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: 2
          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: "B"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2344
          Classifications: {'RNA': 110}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45}
          Link IDs: {'rna2p': 10, 'rna3p': 99}
          Chain breaks: 2
  Time building chain proxies: 6.60, per 1000 atoms: 0.65
  Number of scatterers: 10214
  At special positions: 0
  Unit cell: (97.2, 139.5, 123.3, 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      21     16.00
     P     164     15.00
     O    2286      8.00
     N    1863      7.00
     C    5880      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS Y 826 " - pdb=" SG  CYS Y 928 " distance=2.02

  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 7 sheets defined
      44.5% alpha, 7.7% beta
      63 base pairs and 99 stacking pairs defined.
    Time for finding SS restraints: 4.25
  Creating SS restraints...
    Processing helix  chain 'Y' and resid 4 through 13
      removed outlier: 3.566A  pdb=" N   ILE Y   8 " --> pdb=" O   ARG Y   4 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG Y   9 " --> pdb=" O   ILE Y   5 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS Y  10 " --> pdb=" O   ASN Y   6 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 37 through 42
    Processing helix  chain 'Y' and resid 60 through 88
      removed outlier: 3.641A  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 222 through 260
      removed outlier: 4.440A  pdb=" N   ASP Y 245 " --> pdb=" O   SER Y 241 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 262 through 271
      removed outlier: 4.476A  pdb=" N   ALA Y 268 " --> pdb=" O   LEU Y 264 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 287 through 308
    Processing helix  chain 'Y' and resid 343 through 357
      removed outlier: 3.953A  pdb=" N   LYS Y 357 " --> pdb=" O   LEU Y 353 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 361 through 366
      removed outlier: 3.917A  pdb=" N   TRP Y 365 " --> pdb=" O   GLY Y 361 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 371 through 380
    Processing helix  chain 'Y' and resid 404 through 417
    Processing helix  chain 'Y' and resid 423 through 429
      removed outlier: 4.306A  pdb=" N   ASP Y 427 " --> pdb=" O   GLY Y 423 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 433 through 448
      removed outlier: 3.575A  pdb=" N   LEU Y 440 " --> pdb=" O   LYS Y 436 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS Y 443 " --> pdb=" O   GLY Y 439 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU Y 445 " --> pdb=" O   THR Y 441 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ARG Y 446 " --> pdb=" O   SER Y 442 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 458 through 473
    Processing helix  chain 'Y' and resid 475 through 480
    Processing helix  chain 'Y' and resid 481 through 501
      removed outlier: 4.371A  pdb=" N   TYR Y 485 " --> pdb=" O   GLU Y 481 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ALA Y 486 " --> pdb=" O   LYS Y 482 " (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: 3.884A  pdb=" N   ARG Y 728 " --> pdb=" O   VAL Y 724 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 738 through 762
      removed outlier: 3.904A  pdb=" N   ASN Y 742 " --> pdb=" O   SER Y 738 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   HIS Y 762 " --> pdb=" O   HIS Y 758 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 783 through 787
    Processing helix  chain 'Y' and resid 790 through 802
      removed outlier: 4.049A  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 904
    Processing helix  chain 'Y' and resid 906 through 914
      removed outlier: 3.747A  pdb=" N   UNK Y 910 " --> pdb=" O   UNK Y 906 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 945 through 950
    Processing helix  chain 'Y' and resid 965 through 978
      removed outlier: 3.534A  pdb=" N   ARG Y 976 " --> pdb=" O   ALA Y 972 " (cutoff:3.500A)
    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: 3.605A  pdb=" N   ASN Y 626 " --> pdb=" O   THR Y 651 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   GLU Y 653 " --> pdb=" O   LEU Y 624 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU Y 624 " --> pdb=" O   GLU Y 653 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG Y 510 " --> pdb=" O   GLU Y 631 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 3.605A  pdb=" N   ASN Y 626 " --> pdb=" O   THR Y 651 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   GLU Y 653 " --> pdb=" O   LEU Y 624 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   LEU Y 624 " --> pdb=" O   GLU Y 653 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 33 through 34
      removed outlier: 3.695A  pdb=" N   ARG Y  33 " --> pdb=" O   ALA Y 600 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 518 through 519
      removed outlier: 4.031A  pdb=" N   SER Y 518 " --> pdb=" O   GLN Y 527 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 557 through 558
      removed outlier: 4.036A  pdb=" N   ARG Y 557 " --> pdb=" O   THR Y 586 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 669 through 670
      removed outlier: 6.363A  pdb=" N   ILE Y 669 " --> pdb=" O   VAL Y 767 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ALA Y 769 " --> pdb=" O   ILE Y 669 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   LEU Y 766 " --> pdb=" O   SER Y 812 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   THR Y 814 " --> pdb=" O   LEU Y 766 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   PHE Y 768 " --> pdb=" O   THR Y 814 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    250 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      153 hydrogen bonds
      288 hydrogen bond angles
      0 basepair planarities
      63 basepair parallelities
      99 stacking parallelities
  Total time for adding SS restraints: 5.18

  Time building geometry restraints manager: 3.37 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: 1454
        1.32 -     1.44: 3695
        1.44 -     1.57: 5236
        1.57 -     1.69: 323
        1.69 -     1.81: 34
  Bond restraints: 10742
  Sorted by residual:
  bond pdb=" CA  HIS Y 199 "
       pdb=" CB  HIS Y 199 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.69e-02 3.50e+03 6.27e+00
  bond pdb=" CA  LEU Y 615 "
       pdb=" CB  LEU Y 615 "
    ideal  model  delta    sigma   weight residual
    1.531  1.449  0.082 3.28e-02 9.30e+02 6.18e+00
  bond pdb=" CG  LEU Y 585 "
       pdb=" CD1 LEU Y 585 "
    ideal  model  delta    sigma   weight residual
    1.521  1.441  0.080 3.30e-02 9.18e+02 5.95e+00
  bond pdb=" C   SER Y 197 "
       pdb=" N   ILE Y 198 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 1.36e-02 5.41e+03 5.40e+00
  bond pdb=" C   ASN Y 501 "
       pdb=" N   PRO Y 502 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.020 8.40e-03 1.42e+04 5.39e+00
  ... (remaining 10737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 14984
        3.27 -     6.55: 273
        6.55 -     9.82: 30
        9.82 -    13.09: 4
       13.09 -    16.37: 1
  Bond angle restraints: 15292
  Sorted by residual:
  angle pdb=" N   GLY Y 572 "
        pdb=" CA  GLY Y 572 "
        pdb=" C   GLY Y 572 "
      ideal   model   delta    sigma   weight residual
     113.18  129.55  -16.37 2.37e+00 1.78e-01 4.77e+01
  angle pdb=" CA  TRP Y 534 "
        pdb=" CB  TRP Y 534 "
        pdb=" CG  TRP Y 534 "
      ideal   model   delta    sigma   weight residual
     113.60  125.99  -12.39 1.90e+00 2.77e-01 4.25e+01
  angle pdb=" N   SER Y 197 "
        pdb=" CA  SER Y 197 "
        pdb=" C   SER Y 197 "
      ideal   model   delta    sigma   weight residual
     114.64  104.98    9.66 1.52e+00 4.33e-01 4.04e+01
  angle pdb=" C   ILE Y 198 "
        pdb=" N   HIS Y 199 "
        pdb=" CA  HIS Y 199 "
      ideal   model   delta    sigma   weight residual
     121.54  131.42   -9.88 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" N   THR Y 954 "
        pdb=" CA  THR Y 954 "
        pdb=" C   THR Y 954 "
      ideal   model   delta    sigma   weight residual
     114.62  109.13    5.49 1.14e+00 7.69e-01 2.32e+01
  ... (remaining 15287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.22: 5796
       34.22 -    68.44: 555
       68.44 -   102.65: 46
      102.65 -   136.87: 1
      136.87 -   171.09: 4
  Dihedral angle restraints: 6402
    sinusoidal: 3745
      harmonic: 2657
  Sorted by residual:
  dihedral pdb=" CA  ILE Y 198 "
           pdb=" C   ILE Y 198 "
           pdb=" N   HIS Y 199 "
           pdb=" CA  HIS Y 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.16  -41.84     0      5.00e+00 4.00e-02 7.00e+01
  dihedral pdb=" O4'   U B  17 "
           pdb=" C1'   U B  17 "
           pdb=" N1    U B  17 "
           pdb=" C2    U B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   64.29  167.71     1      1.70e+01 3.46e-03 6.57e+01
  dihedral pdb=" CA  GLY Y 367 "
           pdb=" C   GLY Y 367 "
           pdb=" N   VAL Y 368 "
           pdb=" CA  VAL Y 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.98  -34.02     0      5.00e+00 4.00e-02 4.63e+01
  ... (remaining 6399 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1507
       0.068 -    0.137: 250
       0.137 -    0.205: 48
       0.205 -    0.273: 6
       0.273 -    0.341: 5
  Chirality restraints: 1816
  Sorted by residual:
  chirality pdb=" CB  ILE Y 677 "
            pdb=" CA  ILE Y 677 "
            pdb=" CG1 ILE Y 677 "
            pdb=" CG2 ILE Y 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.91e+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   -2.17   -0.31 2.00e-01 2.50e+01 2.41e+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   -2.17   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1813 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP Y 534 "   -0.025 2.00e-02 2.50e+03   1.97e-02 9.70e+00
        pdb=" CG  TRP Y 534 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP Y 534 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP Y 534 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP Y 534 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP Y 534 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP Y 534 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP Y 534 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP Y 534 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP Y 534 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  56 "   -0.039 2.00e-02 2.50e+03   1.85e-02 9.41e+00
        pdb=" N9    A B  56 "    0.045 2.00e-02 2.50e+03
        pdb=" C8    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A B  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A B  56 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A B  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1    A B  56 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A B  56 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    A B  56 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN Y 501 "    0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO Y 502 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 502 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 502 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2340
        2.78 -     3.31: 8487
        3.31 -     3.84: 18053
        3.84 -     4.37: 19591
        4.37 -     4.90: 30769
  Nonbonded interactions: 79240
  Sorted by model distance:
  nonbonded pdb=" OH  TYR Y 196 "
            pdb=" O   SER Y 221 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O4    U B  65 "
            pdb=" O6    G B  87 "
     model   vdw
     2.295 2.432
  nonbonded pdb=" OG1 THR Y 603 "
            pdb=" OP2   A B  18 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   SER Y 204 "
            pdb=" OG  SER Y 204 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   SER Y 661 "
            pdb=" OG  SER Y 661 "
     model   vdw
     2.334 3.040
  ... (remaining 79235 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:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     31.600
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
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      :  0.009   0.082  10744  Z= 0.410
  Angle     :  1.131  16.367  15297  Z= 0.624
  Chirality :  0.056   0.341   1816
  Planarity :  0.007   0.071   1363
  Dihedral  : 22.552 171.087   4672
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 16.88 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 11.51 %
    Favored  : 88.16 %
  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: -5.86 (0.20), residues: 782
  helix: -3.34 (0.18), residues: 349
  sheet: -4.27 (0.40), residues: 92
  loop : -4.33 (0.24), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP Y 534 
 HIS   0.019   0.004   HIS Y 250 
 PHE   0.039   0.004   PHE Y 609 
 TYR   0.022   0.003   TYR Y 732 
 ARG   0.003   0.000   ARG Y 787 

Details of bonding type rmsd
  link_TRANS           : bond        0.00138 (    1)
  link_TRANS           : angle       0.78483 (    3)
  hydrogen bonds       : bond        0.15717 (  400)
  hydrogen bonds       : angle       6.77320 ( 1020)
  SS BOND              : bond        0.00789 (    1)
  SS BOND              : angle       2.50922 (    2)
  covalent geometry    : bond        0.00909 (10742)
  covalent geometry    : angle       1.13080 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.814 
Fit side-chains
REVERT: Y  498 LEU cc_start: 0.8628 (mt) cc_final: 0.8302 (mt)
REVERT: Y  950 ASN cc_start: 0.8438 (p0) cc_final: 0.8233 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.3010
  time to fit residues: 34.9578
Evaluate side-chains
  64 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 84 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
Y  60 ASN
Y  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114816 restraints weight = 13753.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117756 restraints weight = 7983.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119694 restraints weight = 5736.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10744  Z= 0.136
  Angle     :  0.684   9.383  15297  Z= 0.360
  Chirality :  0.038   0.212   1816
  Planarity :  0.005   0.048   1363
  Dihedral  : 23.307 179.500   3232
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 14.96 %
    Favored  : 84.78 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.62 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -3.91 (0.26), residues: 782
  helix: -1.17 (0.27), residues: 334
  sheet: -3.84 (0.45), residues: 92
  loop : -3.71 (0.27), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP Y 534 
 HIS   0.006   0.001   HIS Y 250 
 PHE   0.022   0.002   PHE Y 503 
 TYR   0.009   0.001   TYR Y 528 
 ARG   0.006   0.000   ARG Y 475 

Details of bonding type rmsd
  link_TRANS           : bond        0.00069 (    1)
  link_TRANS           : angle       0.74599 (    3)
  hydrogen bonds       : bond        0.05279 (  400)
  hydrogen bonds       : angle       4.31867 ( 1020)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       1.08367 (    2)
  covalent geometry    : bond        0.00279 (10742)
  covalent geometry    : angle       0.68407 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.905 
Fit side-chains
REVERT: Y  219 TYR cc_start: 0.8534 (m-10) cc_final: 0.8293 (m-10)
REVERT: Y  316 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8075 (mmt90)
REVERT: Y  585 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8026 (pp)
REVERT: Y  639 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5669 (pt)
  outliers start: 18
  outliers final: 5
  residues processed: 91
  average time/residue: 0.2449
  time to fit residues: 31.3300
Evaluate side-chains
  73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue  585 LEU
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.153030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.115367 restraints weight = 13982.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.118325 restraints weight = 8077.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.120239 restraints weight = 5773.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10744  Z= 0.137
  Angle     :  0.645   8.889  15297  Z= 0.338
  Chirality :  0.036   0.212   1816
  Planarity :  0.004   0.046   1363
  Dihedral  : 23.156 179.524   3232
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.09 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.91 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -3.06 (0.29), residues: 782
  helix: -0.28 (0.29), residues: 336
  sheet: -3.15 (0.54), residues: 84
  loop : -3.57 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP Y 534 
 HIS   0.005   0.001   HIS Y 250 
 PHE   0.021   0.002   PHE Y 775 
 TYR   0.011   0.001   TYR Y 528 
 ARG   0.003   0.000   ARG Y 475 

Details of bonding type rmsd
  link_TRANS           : bond        0.00064 (    1)
  link_TRANS           : angle       0.94591 (    3)
  hydrogen bonds       : bond        0.04893 (  400)
  hydrogen bonds       : angle       3.88033 ( 1020)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.85658 (    2)
  covalent geometry    : bond        0.00287 (10742)
  covalent geometry    : angle       0.64520 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.777 
Fit side-chains
REVERT: Y  219 TYR cc_start: 0.8494 (m-10) cc_final: 0.8239 (m-10)
REVERT: Y  316 ARG cc_start: 0.8692 (tpp80) cc_final: 0.8263 (mmt90)
REVERT: Y  337 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8094 (mtp85)
REVERT: Y  530 ASN cc_start: 0.8969 (m-40) cc_final: 0.8730 (m-40)
REVERT: Y  639 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5652 (pt)
REVERT: Y  735 LYS cc_start: 0.8959 (ttpt) cc_final: 0.8710 (ttpp)
  outliers start: 20
  outliers final: 11
  residues processed: 89
  average time/residue: 0.2129
  time to fit residues: 27.6477
Evaluate side-chains
  82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  341 VAL
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0270
   chunk 17 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 88 optimal weight:   30.0000
   chunk 76 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0470
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.158058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120782 restraints weight = 13853.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123830 restraints weight = 8009.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125829 restraints weight = 5701.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10744  Z= 0.118
  Angle     :  0.604   8.189  15297  Z= 0.316
  Chirality :  0.035   0.212   1816
  Planarity :  0.004   0.045   1363
  Dihedral  : 23.054 179.485   3232
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.07 %
    Favored  : 85.93 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.23 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -2.58 (0.30), residues: 782
  helix:  0.17 (0.29), residues: 344
  sheet: -3.17 (0.53), residues: 91
  loop : -3.36 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP Y 534 
 HIS   0.003   0.001   HIS Y 285 
 PHE   0.024   0.001   PHE Y 775 
 TYR   0.011   0.001   TYR Y 196 
 ARG   0.002   0.000   ARG Y 777 

Details of bonding type rmsd
  link_TRANS           : bond        0.00057 (    1)
  link_TRANS           : angle       0.99061 (    3)
  hydrogen bonds       : bond        0.04254 (  400)
  hydrogen bonds       : angle       3.64914 ( 1020)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.72663 (    2)
  covalent geometry    : bond        0.00242 (10742)
  covalent geometry    : angle       0.60434 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 1.847 
Fit side-chains
REVERT: Y  219 TYR cc_start: 0.8291 (m-10) cc_final: 0.8022 (m-10)
REVERT: Y  233 MET cc_start: 0.8374 (mmp) cc_final: 0.8025 (mmp)
REVERT: Y  639 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5745 (pt)
REVERT: Y  735 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8643 (ttpp)
  outliers start: 21
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2812
  time to fit residues: 39.9225
Evaluate side-chains
  80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  341 VAL
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 72 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   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 = 0.3816 r_free = 0.3816 target = 0.156714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.119231 restraints weight = 13706.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.122245 restraints weight = 7949.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.124251 restraints weight = 5669.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10744  Z= 0.125
  Angle     :  0.607   7.831  15297  Z= 0.317
  Chirality :  0.035   0.209   1816
  Planarity :  0.004   0.043   1363
  Dihedral  : 22.996 179.462   3232
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.83 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 20.39 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -2.24 (0.30), residues: 782
  helix:  0.46 (0.29), residues: 344
  sheet: -3.03 (0.60), residues: 68
  loop : -3.22 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP Y 534 
 HIS   0.014   0.002   HIS Y 933 
 PHE   0.030   0.001   PHE Y 775 
 TYR   0.009   0.001   TYR Y 196 
 ARG   0.004   0.000   ARG Y 316 

Details of bonding type rmsd
  link_TRANS           : bond        0.00022 (    1)
  link_TRANS           : angle       1.07835 (    3)
  hydrogen bonds       : bond        0.04431 (  400)
  hydrogen bonds       : angle       3.56361 ( 1020)
  SS BOND              : bond        0.00220 (    1)
  SS BOND              : angle       0.37405 (    2)
  covalent geometry    : bond        0.00262 (10742)
  covalent geometry    : angle       0.60719 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.913 
Fit side-chains
REVERT: Y   48 LYS cc_start: 0.8995 (tptt) cc_final: 0.8750 (tptt)
REVERT: Y  219 TYR cc_start: 0.8335 (m-10) cc_final: 0.8038 (m-10)
REVERT: Y  639 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5748 (pt)
REVERT: Y  784 MET cc_start: 0.7949 (mmm) cc_final: 0.7623 (mtp)
REVERT: Y  785 THR cc_start: 0.8874 (m) cc_final: 0.8667 (m)
REVERT: Y  794 ASP cc_start: 0.8745 (t0) cc_final: 0.8399 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 89
  average time/residue: 0.2426
  time to fit residues: 31.4415
Evaluate side-chains
  82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.153099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114608 restraints weight = 13990.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117564 restraints weight = 8220.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.119455 restraints weight = 5925.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10744  Z= 0.158
  Angle     :  0.642   9.048  15297  Z= 0.334
  Chirality :  0.037   0.213   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 22.984 178.118   3232
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.71 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.37 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -2.23 (0.30), residues: 782
  helix:  0.50 (0.29), residues: 344
  sheet: -3.25 (0.56), residues: 76
  loop : -3.18 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP Y 534 
 HIS   0.009   0.002   HIS Y 933 
 PHE   0.021   0.002   PHE Y 775 
 TYR   0.012   0.001   TYR Y 575 
 ARG   0.002   0.000   ARG Y 604 

Details of bonding type rmsd
  link_TRANS           : bond        0.00038 (    1)
  link_TRANS           : angle       1.01051 (    3)
  hydrogen bonds       : bond        0.04996 (  400)
  hydrogen bonds       : angle       3.60391 ( 1020)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       0.20117 (    2)
  covalent geometry    : bond        0.00343 (10742)
  covalent geometry    : angle       0.64198 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.906 
Fit side-chains
REVERT: Y   35 MET cc_start: 0.8382 (mtp) cc_final: 0.8100 (mtm)
REVERT: Y   48 LYS cc_start: 0.9032 (tptt) cc_final: 0.8791 (mmtt)
REVERT: Y  219 TYR cc_start: 0.8498 (m-10) cc_final: 0.8188 (m-10)
REVERT: Y  639 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5655 (pt)
REVERT: Y  794 ASP cc_start: 0.8718 (t0) cc_final: 0.8374 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 82
  average time/residue: 0.1955
  time to fit residues: 24.6244
Evaluate side-chains
  80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  247 ILE
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0980
   chunk 3 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.156839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.118544 restraints weight = 14133.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121609 restraints weight = 8223.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.123529 restraints weight = 5885.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10744  Z= 0.122
  Angle     :  0.602   7.935  15297  Z= 0.314
  Chirality :  0.035   0.212   1816
  Planarity :  0.004   0.044   1363
  Dihedral  : 22.949 177.454   3232
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.96 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.20 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -2.01 (0.31), residues: 782
  helix:  0.71 (0.29), residues: 344
  sheet: -3.20 (0.58), residues: 75
  loop : -3.07 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP Y 534 
 HIS   0.008   0.001   HIS Y 933 
 PHE   0.037   0.002   PHE Y 775 
 TYR   0.015   0.001   TYR Y 528 
 ARG   0.002   0.000   ARG Y 706 

Details of bonding type rmsd
  link_TRANS           : bond        0.00023 (    1)
  link_TRANS           : angle       1.01203 (    3)
  hydrogen bonds       : bond        0.04442 (  400)
  hydrogen bonds       : angle       3.52190 ( 1020)
  SS BOND              : bond        0.00760 (    1)
  SS BOND              : angle       2.79348 (    2)
  covalent geometry    : bond        0.00256 (10742)
  covalent geometry    : angle       0.60067 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: Y   35 MET cc_start: 0.8253 (mtp) cc_final: 0.7978 (mtm)
REVERT: Y  409 ASP cc_start: 0.8620 (m-30) cc_final: 0.8226 (m-30)
REVERT: Y  639 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5735 (pt)
REVERT: Y  794 ASP cc_start: 0.8773 (t0) cc_final: 0.8419 (t0)
  outliers start: 20
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1868
  time to fit residues: 24.0684
Evaluate side-chains
  84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue   58 SER
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0870
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0770
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 85 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.160303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.122633 restraints weight = 13927.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125743 restraints weight = 8017.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127822 restraints weight = 5698.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10744  Z= 0.112
  Angle     :  0.585   8.186  15297  Z= 0.305
  Chirality :  0.034   0.208   1816
  Planarity :  0.004   0.048   1363
  Dihedral  : 22.892 179.226   3232
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.32 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.04 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.31), residues: 782
  helix:  0.98 (0.30), residues: 344
  sheet: -2.95 (0.56), residues: 85
  loop : -3.04 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP Y 534 
 HIS   0.006   0.001   HIS Y 933 
 PHE   0.029   0.001   PHE Y 775 
 TYR   0.011   0.001   TYR Y 528 
 ARG   0.005   0.000   ARG Y 787 

Details of bonding type rmsd
  link_TRANS           : bond        0.00048 (    1)
  link_TRANS           : angle       1.09508 (    3)
  hydrogen bonds       : bond        0.04158 (  400)
  hydrogen bonds       : angle       3.43355 ( 1020)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       1.99507 (    2)
  covalent geometry    : bond        0.00229 (10742)
  covalent geometry    : angle       0.58482 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: Y   35 MET cc_start: 0.8232 (mtp) cc_final: 0.7833 (mtm)
REVERT: Y  233 MET cc_start: 0.8388 (mmp) cc_final: 0.7995 (mmp)
REVERT: Y  381 ASN cc_start: 0.8800 (t0) cc_final: 0.8344 (t0)
REVERT: Y  409 ASP cc_start: 0.8557 (m-30) cc_final: 0.8105 (m-30)
REVERT: Y  488 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: Y  639 ILE cc_start: 0.6056 (OUTLIER) cc_final: 0.5768 (pt)
REVERT: Y  765 VAL cc_start: 0.7290 (OUTLIER) cc_final: 0.7006 (p)
REVERT: Y  794 ASP cc_start: 0.8790 (t0) cc_final: 0.8426 (t0)
REVERT: Y  920 GLN cc_start: 0.6592 (tp-100) cc_final: 0.6073 (tp-100)
  outliers start: 22
  outliers final: 18
  residues processed: 87
  average time/residue: 0.4109
  time to fit residues: 54.7181
Evaluate side-chains
  85 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 1.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  517 PHE
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  594 LEU
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  932 VAL
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 88 optimal weight:   30.0000
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 64 optimal weight:    0.2980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.0762

-------------------------------------------------------------------------------
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 = 0.156327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117648 restraints weight = 14073.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120675 restraints weight = 8254.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.122553 restraints weight = 5930.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10744  Z= 0.142
  Angle     :  0.621   8.707  15297  Z= 0.322
  Chirality :  0.036   0.211   1816
  Planarity :  0.004   0.042   1363
  Dihedral  : 22.876 177.390   3232
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.09 %
    Favored  : 84.78 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.34 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.31), residues: 782
  helix:  0.94 (0.30), residues: 345
  sheet: -2.62 (0.60), residues: 78
  loop : -3.06 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP Y 534 
 HIS   0.005   0.001   HIS Y 933 
 PHE   0.034   0.002   PHE Y 775 
 TYR   0.015   0.001   TYR Y 528 
 ARG   0.003   0.000   ARG Y 706 

Details of bonding type rmsd
  link_TRANS           : bond        0.00019 (    1)
  link_TRANS           : angle       0.98638 (    3)
  hydrogen bonds       : bond        0.04700 (  400)
  hydrogen bonds       : angle       3.53014 ( 1020)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.68574 (    2)
  covalent geometry    : bond        0.00306 (10742)
  covalent geometry    : angle       0.62101 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: Y   35 MET cc_start: 0.8394 (mtp) cc_final: 0.8023 (mtm)
REVERT: Y  381 ASN cc_start: 0.8830 (t0) cc_final: 0.8363 (t0)
REVERT: Y  639 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5749 (pt)
REVERT: Y  794 ASP cc_start: 0.8754 (t0) cc_final: 0.8402 (t0)
REVERT: Y  920 GLN cc_start: 0.6623 (tp-100) cc_final: 0.6128 (tp-100)
  outliers start: 18
  outliers final: 15
  residues processed: 76
  average time/residue: 0.2007
  time to fit residues: 22.9873
Evaluate side-chains
  79 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.156958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118301 restraints weight = 14057.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121297 restraints weight = 8260.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.123294 restraints weight = 5948.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10744  Z= 0.132
  Angle     :  0.617   8.475  15297  Z= 0.320
  Chirality :  0.035   0.212   1816
  Planarity :  0.004   0.043   1363
  Dihedral  : 22.870 176.951   3232
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.58 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.67 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.31), residues: 782
  helix:  0.96 (0.30), residues: 346
  sheet: -2.95 (0.57), residues: 83
  loop : -2.99 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP Y 534 
 HIS   0.005   0.001   HIS Y 933 
 PHE   0.032   0.002   PHE Y 775 
 TYR   0.015   0.001   TYR Y 528 
 ARG   0.003   0.000   ARG Y 706 

Details of bonding type rmsd
  link_TRANS           : bond        0.00002 (    1)
  link_TRANS           : angle       0.92101 (    3)
  hydrogen bonds       : bond        0.04565 (  400)
  hydrogen bonds       : angle       3.51597 ( 1020)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       1.60642 (    2)
  covalent geometry    : bond        0.00281 (10742)
  covalent geometry    : angle       0.61692 (15292)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: Y   35 MET cc_start: 0.8330 (mtp) cc_final: 0.7966 (mtm)
REVERT: Y  233 MET cc_start: 0.8443 (mmp) cc_final: 0.8122 (mmp)
REVERT: Y  381 ASN cc_start: 0.8827 (t0) cc_final: 0.8368 (t0)
REVERT: Y  409 ASP cc_start: 0.8630 (m-30) cc_final: 0.8206 (m-30)
REVERT: Y  639 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5738 (pt)
REVERT: Y  794 ASP cc_start: 0.8785 (t0) cc_final: 0.8420 (t0)
REVERT: Y  920 GLN cc_start: 0.6601 (tp-100) cc_final: 0.6108 (tp-100)
  outliers start: 18
  outliers final: 16
  residues processed: 76
  average time/residue: 0.2075
  time to fit residues: 23.9539
Evaluate side-chains
  82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   21 VAL
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   52 VAL
Chi-restraints excluded: chain Y residue  199 HIS
Chi-restraints excluded: chain Y residue  273 LEU
Chi-restraints excluded: chain Y residue  368 VAL
Chi-restraints excluded: chain Y residue  418 TYR
Chi-restraints excluded: chain Y residue  512 VAL
Chi-restraints excluded: chain Y residue  524 HIS
Chi-restraints excluded: chain Y residue  630 ILE
Chi-restraints excluded: chain Y residue  634 ILE
Chi-restraints excluded: chain Y residue  639 ILE
Chi-restraints excluded: chain Y residue  669 ILE
Chi-restraints excluded: chain Y residue  684 THR
Chi-restraints excluded: chain Y residue  765 VAL
Chi-restraints excluded: chain Y residue  782 THR
Chi-restraints excluded: chain Y residue  949 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 73 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.155637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116890 restraints weight = 13979.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.119861 restraints weight = 8280.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121805 restraints weight = 5996.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10744  Z= 0.153
  Angle     :  0.631   8.538  15297  Z= 0.326
  Chirality :  0.036   0.214   1816
  Planarity :  0.004   0.042   1363
  Dihedral  : 22.861 176.811   3232
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.83 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.67 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.31), residues: 782
  helix:  0.84 (0.29), residues: 351
  sheet: -2.61 (0.61), residues: 78
  loop : -3.00 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP Y 534 
 HIS   0.005   0.001   HIS Y 933 
 PHE   0.038   0.002   PHE Y 775 
 TYR   0.015   0.001   TYR Y 528 
 ARG   0.002   0.000   ARG Y 604 

Details of bonding type rmsd
  link_TRANS           : bond        0.00028 (    1)
  link_TRANS           : angle       0.93918 (    3)
  hydrogen bonds       : bond        0.04810 (  400)
  hydrogen bonds       : angle       3.52543 ( 1020)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       1.49562 (    2)
  covalent geometry    : bond        0.00335 (10742)
  covalent geometry    : angle       0.63056 (15292)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3765.97 seconds
wall clock time: 69 minutes 10.45 seconds (4150.45 seconds total)