Starting phenix.real_space_refine
on Sat Dec  9 07:57:17 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/12_2023/6gjz_0012_updated.pdb"
  }
  resolution = 4.06
  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=   0.001 sd=   0.009
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      31      5.49       5
     S      35      5.16       5
     C    3744      2.51       5
     N    1063      2.21       5
     O    1227      1.98       5
     H    4402      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  806": "NH1" <-> "NH2"
    Residue "A TYR  939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  942": "NH1" <-> "NH2"
  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: 10503
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 682, 9874
          Classifications: {'peptide': 682}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 661}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "X"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 308
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 13}
    Chain: "Y"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 289
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' ZN': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8332  SG  CYS A 907      77.322  30.711  39.800  1.00183.18           S
  ATOM   8379  SG  CYS A 910      81.069  29.924  39.936  1.00185.36           S
  ATOM   9041  SG  CYS A 962      79.747  30.998  43.514  1.00195.13           S
  ATOM   9060  SG  CYS A 964      79.539  33.780  41.219  1.00187.69           S

  Time building chain proxies: 5.59, per 1000 atoms: 0.53
  Number of scatterers: 10503
  At special positions: 0
  Unit cell: (100.58, 86.67, 69.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     P      31     15.00
     O    1227      8.00
     N    1063      7.00
     C    3744      6.00
     H    4402      1.00
    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: 9.19
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "
      Number of angles added : 6


  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1304

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 6 sheets defined
      45.0% alpha, 8.8% beta
      14 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 5.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 311 through 321
      removed outlier: 3.744A  pdb=" N   GLU A 315 " --> pdb=" O   PRO A 311 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 316 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
    Processing helix  chain 'A' and resid 336 through 353
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 379 through 382
      No H-bonds generated for 'chain 'A' and resid 379 through 382'
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 3.594A  pdb=" N   VAL A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS A 406 " --> pdb=" O   PRO A 402 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 406'
    Processing helix  chain 'A' and resid 416 through 427
    Processing helix  chain 'A' and resid 435 through 437
      No H-bonds generated for 'chain 'A' and resid 435 through 437'
    Processing helix  chain 'A' and resid 446 through 448
      No H-bonds generated for 'chain 'A' and resid 446 through 448'
    Processing helix  chain 'A' and resid 457 through 473
    Processing helix  chain 'A' and resid 500 through 514
    Processing helix  chain 'A' and resid 526 through 532
    Processing helix  chain 'A' and resid 551 through 566
      removed outlier: 4.050A  pdb=" N   ILE A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 593
    Processing helix  chain 'A' and resid 599 through 615
      removed outlier: 3.657A  pdb=" N   LYS A 607 " --> pdb=" O   GLU A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 642
    Processing helix  chain 'A' and resid 671 through 691
      removed outlier: 3.724A  pdb=" N   ASP A 682 " --> pdb=" O   ASN A 678 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASN A 683 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   LYS A 685 " --> pdb=" O   PHE A 681 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   MET A 686 " --> pdb=" O   ASP A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 696
      No H-bonds generated for 'chain 'A' and resid 694 through 696'
    Processing helix  chain 'A' and resid 699 through 715
    Processing helix  chain 'A' and resid 729 through 740
    Processing helix  chain 'A' and resid 742 through 747
    Processing helix  chain 'A' and resid 768 through 780
    Processing helix  chain 'A' and resid 813 through 820
    Processing helix  chain 'A' and resid 841 through 862
      removed outlier: 3.765A  pdb=" N   TYR A 855 " --> pdb=" O   GLU A 851 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 883
    Processing helix  chain 'A' and resid 886 through 889
      No H-bonds generated for 'chain 'A' and resid 886 through 889'
    Processing helix  chain 'A' and resid 933 through 938
      removed outlier: 3.619A  pdb=" N   LEU A 938 " --> pdb=" O   GLU A 934 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 326 through 329
      removed outlier: 3.704A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 537 through 542
      removed outlier: 3.507A  pdb=" N   THR A 834 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 721 through 724
    Processing sheet with id=  D, first strand: chain 'A' and resid 903 through 907
    Processing sheet with id=  E, first strand: chain 'A' and resid 920 through 923
    Processing sheet with id=  F, first strand: chain 'A' and resid 940 through 942
      removed outlier: 3.688A  pdb=" N   GLU A 959 " --> pdb=" O   ARG A 942 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    681 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 3.99

  Time building geometry restraints manager: 9.14 seconds

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

  Histogram of bond lengths:
        0.83 -     1.02: 4391
        1.02 -     1.22: 17
        1.22 -     1.42: 2595
        1.42 -     1.62: 3597
        1.62 -     1.82: 58
  Bond restraints: 10658
  Sorted by residual:
  bond pdb=" O3A ANP A1102 "
       pdb=" PB  ANP A1102 "
    ideal  model  delta    sigma   weight residual
    1.700  1.552  0.148 2.00e-02 2.50e+03 5.48e+01
  bond pdb=" N3B ANP A1102 "
       pdb=" PG  ANP A1102 "
    ideal  model  delta    sigma   weight residual
    1.795  1.685  0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" O5' ANP A1102 "
       pdb=" PA  ANP A1102 "
    ideal  model  delta    sigma   weight residual
    1.655  1.577  0.078 2.00e-02 2.50e+03 1.52e+01
  bond pdb=" CD  ARG A 824 "
       pdb=" NE  ARG A 824 "
    ideal  model  delta    sigma   weight residual
    1.458  1.410  0.048 1.40e-02 5.10e+03 1.16e+01
  bond pdb=" C   SER A 995 "
       pdb=" O   SER A 995 "
    ideal  model  delta    sigma   weight residual
    1.233  1.219  0.014 4.80e-03 4.34e+04 7.96e+00
  ... (remaining 10653 not shown)

  Histogram of bond angle deviations from ideal:
       61.11 -    77.41: 14
       77.41 -    93.71: 0
       93.71 -   110.01: 7892
      110.01 -   126.31: 10559
      126.31 -   142.62: 157
  Bond angle restraints: 18622
  Sorted by residual:
  angle pdb=" C   LYS A 884 "
        pdb=" N   LYS A 885 "
        pdb=" H   LYS A 885 "
      ideal   model   delta    sigma   weight residual
     124.88   69.70   55.18 3.00e+00 1.11e-01 3.38e+02
  angle pdb=" C   MET A 886 "
        pdb=" N   LYS A 887 "
        pdb=" H   LYS A 887 "
      ideal   model   delta    sigma   weight residual
     124.96   70.80   54.16 3.00e+00 1.11e-01 3.26e+02
  angle pdb=" C   LYS A 451 "
        pdb=" N   GLU A 452 "
        pdb=" H   GLU A 452 "
      ideal   model   delta    sigma   weight residual
     124.38   70.51   53.87 3.00e+00 1.11e-01 3.22e+02
  angle pdb=" CA  LYS A 887 "
        pdb=" N   LYS A 887 "
        pdb=" H   LYS A 887 "
      ideal   model   delta    sigma   weight residual
     114.66   61.11   53.55 3.00e+00 1.11e-01 3.19e+02
  angle pdb=" CA  LYS A 885 "
        pdb=" N   LYS A 885 "
        pdb=" H   LYS A 885 "
      ideal   model   delta    sigma   weight residual
     114.58   61.37   53.21 3.00e+00 1.11e-01 3.15e+02
  ... (remaining 18617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4985
       17.46 -    34.91: 187
       34.91 -    52.37: 48
       52.37 -    69.83: 30
       69.83 -    87.28: 24
  Dihedral angle restraints: 5274
    sinusoidal: 3008
      harmonic: 2266
  Sorted by residual:
  dihedral pdb=" CA  VAL A 454 "
           pdb=" C   VAL A 454 "
           pdb=" N   TYR A 455 "
           pdb=" CA  TYR A 455 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   92.72   87.28     0      5.00e+00 4.00e-02 3.05e+02
  dihedral pdb=" CA  GLU A 548 "
           pdb=" C   GLU A 548 "
           pdb=" N   ASN A 549 "
           pdb=" CA  ASN A 549 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.68  -36.32     0      5.00e+00 4.00e-02 5.28e+01
  dihedral pdb=" CA  PRO A 550 "
           pdb=" C   PRO A 550 "
           pdb=" N   PHE A 551 "
           pdb=" CA  PHE A 551 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.10  -34.90     0      5.00e+00 4.00e-02 4.87e+01
  ... (remaining 5271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 716
       0.053 -    0.107: 224
       0.107 -    0.160: 40
       0.160 -    0.213: 5
       0.213 -    0.266: 2
  Chirality restraints: 987
  Sorted by residual:
  chirality pdb=" C3' ANP A1102 "
            pdb=" C2' ANP A1102 "
            pdb=" C4' ANP A1102 "
            pdb=" O3' ANP A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.62    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  ILE A 984 "
            pdb=" CA  ILE A 984 "
            pdb=" CG1 ILE A 984 "
            pdb=" CG2 ILE A 984 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  VAL A 316 "
            pdb=" CA  VAL A 316 "
            pdb=" CG1 VAL A 316 "
            pdb=" CG2 VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.53e-01
  ... (remaining 984 not shown)

  Planarity restraints: 1564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 455 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   TYR A 455 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   TYR A 455 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ASN A 456 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 457 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.46e+00
        pdb=" N   ILE A 458 "    0.044 2.00e-02 2.50e+03
        pdb=" CA  ILE A 458 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   ILE A 458 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 344 "   -0.011 2.00e-02 2.50e+03   2.22e-02 4.91e+00
        pdb=" C   THR A 344 "    0.038 2.00e-02 2.50e+03
        pdb=" O   THR A 344 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A 345 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1561 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 357
        2.18 -     2.78: 19138
        2.78 -     3.39: 25297
        3.39 -     3.99: 34197
        3.99 -     4.60: 54267
  Nonbonded interactions: 133256
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 498 "
            pdb=" HA  LYS A 498 "
     model   vdw
     1.571 1.816
  nonbonded pdb=" H   VAL A 888 "
            pdb=" HA  VAL A 888 "
     model   vdw
     1.604 1.816
  nonbonded pdb=" H   GLY A 795 "
            pdb=" HA3 GLY A 795 "
     model   vdw
     1.631 1.816
  nonbonded pdb=" H   LYS A 887 "
            pdb=" HA  LYS A 887 "
     model   vdw
     1.633 1.816
  nonbonded pdb=" O   LEU A 529 "
            pdb=" H   ILE A 533 "
     model   vdw
     1.644 1.850
  ... (remaining 133251 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:             0.570
  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:             0.170
  Extract box with map and model:          2.980
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     45.050
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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      :  0.011   0.148   6256  Z= 0.748
  Angle     :  1.109  20.305   8553  Z= 0.619
  Chirality :  0.052   0.266    987
  Planarity :  0.006   0.049    979
  Dihedral  : 14.155  87.282   2605
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.83 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -4.09 (0.27), residues: 674
  helix: -1.53 (0.24), residues: 327
  sheet: -3.18 (0.47), residues: 85
  loop : -4.07 (0.30), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.003   TRP A1003 
   HIS   0.012   0.003   HIS A 506 
   PHE   0.016   0.002   PHE A 517 
   TYR   0.024   0.003   TYR A 408 
   ARG   0.015   0.001   ARG A 619 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  179 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.3913
  time to fit residues: 88.6565
Evaluate side-chains
  105 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.890 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1164
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 ASN
A 513 ASN
A 531 HIS
A 563 GLN
A 577 GLN
A 678 ASN
A 759 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6256  Z= 0.170
  Angle     :  0.730  21.284   8553  Z= 0.401
  Chirality :  0.038   0.157    987
  Planarity :  0.004   0.048    979
  Dihedral  : 15.737  85.978   1180
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 21.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.50 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.82 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: 674
  helix:  0.09 (0.27), residues: 324
  sheet: -2.63 (0.51), residues: 91
  loop : -3.74 (0.31), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.003   0.001   TRP A 968 
   HIS   0.007   0.001   HIS A 871 
   PHE   0.007   0.001   PHE A 551 
   TYR   0.015   0.001   TYR A 342 
   ARG   0.003   0.000   ARG A 820 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  126 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.3336
  time to fit residues: 55.4288
Evaluate side-chains
  93 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.890 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1175
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
A 759 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6256  Z= 0.208
  Angle     :  0.731  20.980   8553  Z= 0.403
  Chirality :  0.038   0.171    987
  Planarity :  0.003   0.038    979
  Dihedral  : 15.194  89.766   1180
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 23.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.94 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -1.63 (0.32), residues: 674
  helix:  1.10 (0.29), residues: 317
  sheet: -2.46 (0.49), residues: 93
  loop : -3.41 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 737 
   HIS   0.006   0.001   HIS A 506 
   PHE   0.011   0.001   PHE A 401 
   TYR   0.012   0.001   TYR A 342 
   ARG   0.002   0.000   ARG A 619 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.3527
  time to fit residues: 48.2688
Evaluate side-chains
  77 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.931 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1641
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6256  Z= 0.175
  Angle     :  0.694  21.114   8553  Z= 0.382
  Chirality :  0.037   0.154    987
  Planarity :  0.003   0.031    979
  Dihedral  : 15.074 101.977   1180
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 21.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -1.13 (0.32), residues: 674
  helix:  1.61 (0.29), residues: 319
  sheet: -2.33 (0.47), residues: 97
  loop : -3.31 (0.32), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 737 
   HIS   0.010   0.002   HIS A 927 
   PHE   0.010   0.001   PHE A 401 
   TYR   0.014   0.001   TYR A 455 
   ARG   0.005   0.000   ARG A1009 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3572
  time to fit residues: 45.7731
Evaluate side-chains
  77 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2812
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   overall best weight:    5.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 577 GLN
A 678 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   6256  Z= 0.375
  Angle     :  0.823  20.798   8553  Z= 0.454
  Chirality :  0.039   0.163    987
  Planarity :  0.004   0.067    979
  Dihedral  : 15.382 115.172   1180
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 30.71
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 12.31 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -1.60 (0.31), residues: 674
  helix:  1.07 (0.27), residues: 314
  sheet: -2.24 (0.50), residues: 94
  loop : -3.36 (0.32), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP A 737 
   HIS   0.010   0.002   HIS A 928 
   PHE   0.017   0.002   PHE A 401 
   TYR   0.014   0.002   TYR A 408 
   ARG   0.005   0.001   ARG A 606 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.3037
  time to fit residues: 35.5622
Evaluate side-chains
  70 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.897 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0980
   chunk 7 optimal weight:    0.0470
   chunk 38 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    1.6082

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.5684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6256  Z= 0.139
  Angle     :  0.689  21.119   8553  Z= 0.379
  Chirality :  0.037   0.156    987
  Planarity :  0.003   0.042    979
  Dihedral  : 14.953 113.970   1180
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 24.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.93 (0.33), residues: 674
  helix:  1.64 (0.29), residues: 320
  sheet: -1.93 (0.53), residues: 89
  loop : -3.15 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 737 
   HIS   0.008   0.001   HIS A 928 
   PHE   0.008   0.001   PHE A 401 
   TYR   0.013   0.001   TYR A 455 
   ARG   0.003   0.000   ARG A 310 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.3534
  time to fit residues: 42.4100
Evaluate side-chains
  75 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.054 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1969
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.6117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6256  Z= 0.274
  Angle     :  0.742  20.933   8553  Z= 0.409
  Chirality :  0.037   0.151    987
  Planarity :  0.003   0.033    979
  Dihedral  : 15.223 118.124   1180
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 30.13
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.28 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.32), residues: 674
  helix:  1.38 (0.28), residues: 320
  sheet: -2.03 (0.51), residues: 94
  loop : -3.24 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 737 
   HIS   0.008   0.002   HIS A 928 
   PHE   0.016   0.001   PHE A 401 
   TYR   0.011   0.002   TYR A 342 
   ARG   0.004   0.000   ARG A 843 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.3181
  time to fit residues: 35.9997
Evaluate side-chains
  67 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1720
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 42 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0270
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 62 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.6236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6256  Z= 0.122
  Angle     :  0.676  21.213   8553  Z= 0.369
  Chirality :  0.036   0.150    987
  Planarity :  0.003   0.036    979
  Dihedral  : 14.890 118.545   1180
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 23.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.56 (0.33), residues: 674
  helix:  2.01 (0.29), residues: 321
  sheet: -1.80 (0.54), residues: 89
  loop : -3.05 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 582 
   HIS   0.007   0.001   HIS A 871 
   PHE   0.007   0.001   PHE A 724 
   TYR   0.016   0.001   TYR A 455 
   ARG   0.003   0.000   ARG A 942 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.3128
  time to fit residues: 36.8943
Evaluate side-chains
  70 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.363 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2155
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.6359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6256  Z= 0.173
  Angle     :  0.690  21.059   8553  Z= 0.379
  Chirality :  0.036   0.145    987
  Planarity :  0.003   0.035    979
  Dihedral  : 14.953 119.564   1180
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 26.63
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.64 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.59 (0.33), residues: 674
  helix:  1.91 (0.29), residues: 326
  sheet: -1.91 (0.51), residues: 94
  loop : -3.02 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 385 
   HIS   0.006   0.001   HIS A 871 
   PHE   0.012   0.001   PHE A 724 
   TYR   0.013   0.001   TYR A 455 
   ARG   0.002   0.000   ARG A 843 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2847
  time to fit residues: 33.1800
Evaluate side-chains
  67 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.863 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0902
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.6505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6256  Z= 0.145
  Angle     :  0.685  21.138   8553  Z= 0.376
  Chirality :  0.037   0.149    987
  Planarity :  0.003   0.035    979
  Dihedral  : 14.935 120.511   1180
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 25.30
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.64 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.49 (0.33), residues: 674
  helix:  1.96 (0.29), residues: 326
  sheet: -1.57 (0.55), residues: 84
  loop : -3.04 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 968 
   HIS   0.005   0.001   HIS A 928 
   PHE   0.011   0.001   PHE A 724 
   TYR   0.014   0.001   TYR A 455 
   ARG   0.002   0.000   ARG A 843 

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

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

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1348 Ramachandran restraints generated.
    674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2785
  time to fit residues: 32.7814
Evaluate side-chains
  70 residues out of total 612 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0984
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 372 GLN
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 HIS
** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.067911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.054449 restraints weight = 65232.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057175 restraints weight = 27755.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.058881 restraints weight = 16013.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.6622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6256  Z= 0.152
  Angle     :  0.687  21.121   8553  Z= 0.376
  Chirality :  0.036   0.142    987
  Planarity :  0.003   0.035    979
  Dihedral  : 15.014 121.269   1180
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 26.13
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.09 %
    Favored  : 89.76 %
  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 : 0.15 %

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: -0.44 (0.33), residues: 674
  helix:  2.01 (0.29), residues: 325
  sheet: -1.58 (0.55), residues: 84
  loop : -2.98 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 968 
   HIS   0.005   0.001   HIS A 531 
   PHE   0.009   0.001   PHE A 401 
   TYR   0.012   0.001   TYR A 455 
   ARG   0.002   0.000   ARG A 843 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2676.38 seconds
wall clock time: 48 minutes 35.01 seconds (2915.01 seconds total)