Starting phenix.real_space_refine
on Sat Dec  9 04:13:23 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_8994.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_8994.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_8994.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_8994.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/12_2023/6ny1_8994.pdb"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     154      5.49       5
     S      20      5.16       5
     C    5724      2.51       5
     N    1805      2.21       5
     O    2208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "Y GLU   44": "OE1" <-> "OE2"
    Residue "Y TYR  196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  288": "OE1" <-> "OE2"
    Residue "Y PHE  328": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  378": "OE1" <-> "OE2"
    Residue "Y ARG  475": "NH1" <-> "NH2"
    Residue "Y TYR  485": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  488": "OE1" <-> "OE2"
    Residue "Y ASP  513": "OD1" <-> "OD2"
    Residue "Y TYR  545": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y ASP  591": "OD1" <-> "OD2"
    Residue "Y PHE  601": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y TYR  789": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE  923": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y TYR  974": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 9911
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "Y"
      Number of atoms: 6671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 904, 6671
          Classifications: {'peptide': 904}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 193}
          Link IDs: {'PTRANS': 29, 'TRANS': 874}
          Unresolved chain links: 1
          Chain breaks: 9
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 512
          Unresolved non-hydrogen angles: 693
          Unresolved non-hydrogen dihedrals: 332
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 121, 'ASP:plan': 16, 'GLU:plan': 26, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 316
    Chain: "D"
      Number of atoms: 346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 346
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "B"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2300
          Classifications: {'RNA': 108}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 14, 'rna3p': 93}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 594
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
  Time building chain proxies: 6.16, per 1000 atoms: 0.62
  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  - 3.50
        Amino acid           : False - 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
  Time building additional restraints: 5.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 3.70
  Creating SS restraints...
    Processing helix  chain 'Y' and resid 4 through 15
      removed outlier: 3.541A  pdb=" N   ASP Y  15 " --> pdb=" O   LYS Y  11 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 37 through 44
    Processing helix  chain 'Y' and resid 59 through 88
      removed outlier: 4.457A  pdb=" N   ASN Y  63 " --> pdb=" O   ASN Y  59 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN Y  64 " --> pdb=" O   ASN Y  60 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 90 through 98
    Processing helix  chain 'Y' and resid 194 through 198
    Processing helix  chain 'Y' and resid 222 through 260
      removed outlier: 3.755A  pdb=" N   ASP Y 245 " --> pdb=" O   SER Y 241 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 262 through 267
    Processing helix  chain 'Y' and resid 287 through 309
      removed outlier: 3.593A  pdb=" N   ASP Y 291 " --> pdb=" O   LYS Y 287 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 342 through 357
    Processing helix  chain 'Y' and resid 361 through 366
      removed outlier: 3.804A  pdb=" N   TRP Y 365 " --> pdb=" O   GLY Y 361 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER Y 366 " --> pdb=" O   ARG Y 362 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 361 through 366'
    Processing helix  chain 'Y' and resid 370 through 380
    Processing helix  chain 'Y' and resid 403 through 418
    Processing helix  chain 'Y' and resid 424 through 449
      removed outlier: 3.569A  pdb=" N   ARG Y 432 " --> pdb=" O   GLU Y 428 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS Y 436 " --> pdb=" O   ARG Y 432 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU Y 445 " --> pdb=" O   THR Y 441 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 456 through 473
      removed outlier: 3.746A  pdb=" N   VAL Y 460 " --> pdb=" O   GLN Y 456 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU Y 461 " --> pdb=" O   SER Y 457 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 474 through 476
      No H-bonds generated for 'chain 'Y' and resid 474 through 476'
    Processing helix  chain 'Y' and resid 483 through 501
      removed outlier: 3.840A  pdb=" N   CYS Y 487 " --> pdb=" O   GLU Y 483 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 502 through 504
      No H-bonds generated for 'chain 'Y' and resid 502 through 504'
    Processing helix  chain 'Y' and resid 602 through 610
    Processing helix  chain 'Y' and resid 711 through 728
      removed outlier: 3.541A  pdb=" N   ARG Y 727 " --> pdb=" O   GLU Y 723 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG Y 728 " --> pdb=" O   VAL Y 724 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 737 through 761
      removed outlier: 4.173A  pdb=" N   ARG Y 741 " --> pdb=" O   ALA Y 737 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 790 through 802
      removed outlier: 3.769A  pdb=" N   TYR Y 802 " --> pdb=" O   ALA Y 798 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 886 through 892
    Processing helix  chain 'Y' and resid 897 through 903
    Processing helix  chain 'Y' and resid 906 through 914
      removed outlier: 4.825A  pdb=" N   UNK Y 910 " --> pdb=" O   UNK Y 906 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 935 through 938
    Processing helix  chain 'Y' and resid 939 through 951
      removed outlier: 3.764A  pdb=" N   LEU Y 947 " --> pdb=" O   ALA Y 943 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN Y 950 " --> pdb=" O   TRP Y 946 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 965 through 978
    Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19
    Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 530 through 532
      removed outlier: 3.554A  pdb=" N   LEU Y 547 " --> pdb=" O   LEU Y 531 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 680 through 682
      removed outlier: 3.840A  pdb=" N   ALA Y 682 " --> pdb=" O   GLY Y 670 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ILE Y 669 " --> pdb=" O   VAL Y 767 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    807 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      134 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 4.66

  Time building geometry restraints manager: 5.61 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: 3543
        1.44 -     1.57: 5087
        1.57 -     1.69: 303
        1.69 -     1.81: 32
  Bond restraints: 10413
  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 10408 not shown)

  Histogram of bond angle deviations from ideal:
       96.73 -   104.35: 673
      104.35 -   111.98: 5348
      111.98 -   119.60: 3806
      119.60 -   127.23: 4583
      127.23 -   134.86: 398
  Bond angle restraints: 14808
  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 14803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 5574
       35.46 -    70.92: 482
       70.92 -   106.39: 54
      106.39 -   141.85: 2
      141.85 -   177.31: 7
  Dihedral angle restraints: 6119
    sinusoidal: 3496
      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 6116 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 2.440
  nonbonded pdb=" OD1 ASP Y 513 "
            pdb=" OG  SER Y 515 "
     model   vdw
     2.231 2.440
  nonbonded pdb=" OG1 THR Y  29 "
            pdb=" O2    U B 103 "
     model   vdw
     2.243 2.440
  nonbonded pdb=" O   ALA Y 816 "
            pdb=" OG1 THR Y 819 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" OH  TYR Y 382 "
            pdb=" O   SER Y 470 "
     model   vdw
     2.300 2.440
  ... (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
========== 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.040
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     34.660
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.960
-------------------------------------------------------------------------------
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= 0.453
  Angle     :  1.114  17.747  14808  Z= 0.597
  Chirality :  0.058   0.379   1762
  Planarity :  0.008   0.071   1335
  Dihedral  : 23.288 177.312   4415
  Min Nonbonded Distance : 2.099

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.84 (0.24), residues: 768
  helix: -2.46 (0.21), residues: 326
  sheet: -3.42 (0.51), residues: 83
  loop : -3.92 (0.27), residues: 359

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

*********************** 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 fitting.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 94
  average time/residue: 0.2641
  time to fit residues: 33.7028
Evaluate side-chains
  62 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.827 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0864
  time to fit residues: 1.1468
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:   30.0000
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0040
   chunk 80 optimal weight:   50.0000
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
Y  16 ASN
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 283 GLN
Y 398 ASN
Y 636 ASN
** Y 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 930 HIS
Y 937 GLN
Y 950 ASN
** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10413  Z= 0.205
  Angle     :  0.715   7.881  14808  Z= 0.385
  Chirality :  0.041   0.259   1762
  Planarity :  0.005   0.057   1335
  Dihedral  : 24.633 173.192   3004
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 16.93 %
    Favored  : 82.81 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  5.35 %
    Favored  : 94.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.28), residues: 768
  helix: -0.65 (0.26), residues: 335
  sheet: -3.34 (0.50), residues: 86
  loop : -3.75 (0.29), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP Y 534 
   HIS   0.002   0.001   HIS Y 199 
   PHE   0.033   0.002   PHE Y 736 
   TYR   0.014   0.002   TYR Y 196 
   ARG   0.003   0.000   ARG Y   4 

*********************** 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
  99 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.2336
  time to fit residues: 32.6549
Evaluate side-chains
  66 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.882 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0902
  time to fit residues: 1.2380
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0370
   chunk 77 optimal weight:   20.0000
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 93 optimal weight:    9.9990
   chunk 101 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   overall best weight:    4.0066

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 374 ASN
Y 381 ASN
Y 715 GLN
** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10413  Z= 0.323
  Angle     :  0.795   8.824  14808  Z= 0.420
  Chirality :  0.044   0.275   1762
  Planarity :  0.005   0.056   1335
  Dihedral  : 24.658 178.597   3004
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 19.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 19.27 %
    Favored  : 80.60 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  8.03 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.29), residues: 768
  helix:  0.05 (0.28), residues: 332
  sheet: -3.32 (0.50), residues: 85
  loop : -3.80 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP Y 534 
   HIS   0.009   0.002   HIS Y 443 
   PHE   0.018   0.002   PHE Y 544 
   TYR   0.020   0.002   TYR Y  83 
   ARG   0.004   0.000   ARG Y 299 

*********************** 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
  88 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 88
  average time/residue: 0.2233
  time to fit residues: 28.5702
Evaluate side-chains
  59 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.919 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0904
  time to fit residues: 1.2263
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0170
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 94 optimal weight:    9.9990
   chunk 99 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.0024

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 374 ASN
Y 726 GLN
Y 758 HIS
Y 762 HIS
** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10413  Z= 0.172
  Angle     :  0.675   7.417  14808  Z= 0.359
  Chirality :  0.040   0.273   1762
  Planarity :  0.004   0.047   1335
  Dihedral  : 24.366 175.595   3004
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.41 %
    Favored  : 83.46 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.17 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.30), residues: 768
  helix:  0.57 (0.29), residues: 324
  sheet: -3.36 (0.49), residues: 86
  loop : -3.57 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP Y 344 
   HIS   0.003   0.001   HIS Y 199 
   PHE   0.026   0.002   PHE Y 609 
   TYR   0.012   0.001   TYR Y 196 
   ARG   0.005   0.000   ARG Y 299 

*********************** 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
  105 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2263
  time to fit residues: 33.5866
Evaluate side-chains
  69 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.922 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1685
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:   50.0000
   chunk 56 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 374 ASN
** Y 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10413  Z= 0.267
  Angle     :  0.727   7.974  14808  Z= 0.385
  Chirality :  0.041   0.271   1762
  Planarity :  0.005   0.049   1335
  Dihedral  : 24.395 171.877   3004
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 19.27 %
    Favored  : 80.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (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: -2.71 (0.30), residues: 768
  helix:  0.38 (0.29), residues: 333
  sheet: -3.55 (0.47), residues: 89
  loop : -3.66 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP Y 534 
   HIS   0.007   0.002   HIS Y 933 
   PHE   0.018   0.002   PHE Y 609 
   TYR   0.028   0.002   TYR Y 196 
   ARG   0.004   0.000   ARG Y 944 

*********************** 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
  96 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2090
  time to fit residues: 29.0290
Evaluate side-chains
  61 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.954 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   chunk 82 optimal weight:   50.0000
   chunk 46 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
Y  85 GLN
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 719 GLN
Y 933 HIS
** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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      :  0.004   0.035  10413  Z= 0.251
  Angle     :  0.724   8.166  14808  Z= 0.384
  Chirality :  0.042   0.264   1762
  Planarity :  0.004   0.048   1335
  Dihedral  : 24.394 171.839   3004
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.10 %
    Favored  : 81.77 %
  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 (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: -2.60 (0.30), residues: 768
  helix:  0.51 (0.29), residues: 328
  sheet: -3.46 (0.47), residues: 89
  loop : -3.59 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP Y 534 
   HIS   0.008   0.002   HIS Y 199 
   PHE   0.018   0.002   PHE Y 609 
   TYR   0.012   0.001   TYR Y 974 
   ARG   0.004   0.000   ARG Y 944 

*********************** 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
  92 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2373
  time to fit residues: 31.9227
Evaluate side-chains
  60 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.905 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1054
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 56 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0970
   chunk 83 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0980
   chunk 99 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.6982

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

Flipped N/Q/H residues before XYZ refinement:
Y 190 GLN
** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 971 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10413  Z= 0.191
  Angle     :  0.674   8.117  14808  Z= 0.355
  Chirality :  0.039   0.230   1762
  Planarity :  0.004   0.044   1335
  Dihedral  : 24.251 171.275   3004
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.93 %
    Favored  : 82.94 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.18 %
    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 (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: -2.39 (0.30), residues: 768
  helix:  0.74 (0.29), residues: 321
  sheet: -3.23 (0.49), residues: 86
  loop : -3.50 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP Y 534 
   HIS   0.004   0.001   HIS Y 199 
   PHE   0.016   0.002   PHE Y 609 
   TYR   0.012   0.001   TYR Y 974 
   ARG   0.007   0.000   ARG Y 917 

*********************** 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
  99 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2151
  time to fit residues: 30.4844
Evaluate side-chains
  65 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.949 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0040
   chunk 63 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 49 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:   40.0000
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    2.0998

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 758 HIS
Y 971 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10413  Z= 0.213
  Angle     :  0.697   9.505  14808  Z= 0.368
  Chirality :  0.040   0.233   1762
  Planarity :  0.004   0.045   1335
  Dihedral  : 24.185 171.682   3004
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.97 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.17 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (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: -2.40 (0.30), residues: 768
  helix:  0.65 (0.28), residues: 329
  sheet: -3.14 (0.51), residues: 86
  loop : -3.53 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP Y 534 
   HIS   0.004   0.001   HIS Y 930 
   PHE   0.016   0.002   PHE Y 609 
   TYR   0.015   0.002   TYR Y  83 
   ARG   0.003   0.000   ARG Y 944 

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

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1914
  time to fit residues: 27.3877
Evaluate side-chains
  66 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9986
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 95 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0000
   chunk 87 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0870
   chunk 97 optimal weight:   20.0000
   overall best weight:    1.8168

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 250 HIS
** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 971 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3396

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= 0.198
  Angle     :  0.679   8.869  14808  Z= 0.357
  Chirality :  0.039   0.232   1762
  Planarity :  0.004   0.044   1335
  Dihedral  : 24.065 171.521   3004
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.32 %
    Favored  : 82.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.30), residues: 768
  helix:  0.72 (0.28), residues: 340
  sheet: -2.65 (0.58), residues: 74
  loop : -3.63 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP Y 795 
   HIS   0.004   0.001   HIS Y 250 
   PHE   0.016   0.002   PHE Y 609 
   TYR   0.017   0.001   TYR Y 382 
   ARG   0.004   0.000   ARG Y 299 

*********************** 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
  97 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.2066
  time to fit residues: 29.4611
Evaluate side-chains
  68 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.916 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0639
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:   30.0000
   chunk 102 optimal weight:    6.9990
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   30.0000
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 87 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10413  Z= 0.291
  Angle     :  0.759   8.176  14808  Z= 0.397
  Chirality :  0.042   0.243   1762
  Planarity :  0.004   0.048   1335
  Dihedral  : 24.120 172.483   3004
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 20.44
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 19.14 %
    Favored  : 80.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.30), residues: 768
  helix:  0.58 (0.28), residues: 339
  sheet: -3.23 (0.50), residues: 89
  loop : -3.69 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.002   TRP Y 795 
   HIS   0.007   0.002   HIS Y 250 
   PHE   0.024   0.002   PHE Y 484 
   TYR   0.031   0.002   TYR Y 196 
   ARG   0.005   0.001   ARG Y 944 

********************** 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
  91 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2044
  time to fit residues: 27.5572
Evaluate side-chains
  60 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0408
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    0.0010
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:   30.0000
   chunk 22 optimal weight:    2.9990
   chunk 81 optimal weight:   30.0000
   chunk 34 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 10 optimal weight:    0.2980
   chunk 15 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.0588

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

Flipped N/Q/H residues before XYZ refinement:
Y 250 HIS
** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.103205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.078178 restraints weight = 31996.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.080866 restraints weight = 16139.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.082661 restraints weight = 10283.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3693

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= 0.168
  Angle     :  0.661   9.508  14808  Z= 0.346
  Chirality :  0.038   0.227   1762
  Planarity :  0.004   0.039   1335
  Dihedral  : 23.950 172.270   3004
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.15 %
    Favored  : 83.72 %
  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 (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: -2.07 (0.31), residues: 768
  helix:  0.87 (0.28), residues: 337
  sheet: -2.57 (0.59), residues: 76
  loop : -3.52 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP Y 344 
   HIS   0.003   0.001   HIS Y 930 
   PHE   0.024   0.002   PHE Y 484 
   TYR   0.022   0.001   TYR Y 196 
   ARG   0.004   0.000   ARG Y 299 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1820.54 seconds
wall clock time: 34 minutes 11.77 seconds (2051.77 seconds total)