Starting phenix.real_space_refine
on Thu Jan 18 23:25:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2i_30958/01_2024/7e2i_30958.pdb"
  }
  resolution = 4.07
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1208 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      67      5.16       5
     C    5595      2.51       5
     N    1354      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "G GLU  136": "OE1" <-> "OE2"
    Residue "G GLU  142": "OE1" <-> "OE2"
    Residue "G ARG  153": "NH1" <-> "NH2"
    Residue "G GLU  167": "OE1" <-> "OE2"
    Residue "D ARG  302": "NH1" <-> "NH2"
    Residue "D ARG  364": "NH1" <-> "NH2"
    Residue "D ARG  373": "NH1" <-> "NH2"
    Residue "D GLU  488": "OE1" <-> "OE2"
    Residue "D ARG  631": "NH1" <-> "NH2"
    Residue "D ARG  661": "NH1" <-> "NH2"
    Residue "D ARG  703": "NH1" <-> "NH2"
    Residue "D GLU  751": "OE1" <-> "OE2"
    Residue "D ARG  892": "NH1" <-> "NH2"
    Residue "D GLU  946": "OE1" <-> "OE2"
    Residue "D PHE  996": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG 1061": "NH1" <-> "NH2"
    Residue "D ARG 1078": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 8569
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 1209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1209
          Classifications: {'peptide': 151}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 7058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 907, 7058
          Classifications: {'peptide': 907}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 37, 'TRANS': 869}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 92
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 301
          Unusual residues: {'NAG': 4, 'Y01': 7}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.04, per 1000 atoms: 0.59
  Number of scatterers: 8569
  At special positions: 0
  Unit cell: (109.172, 115.856, 115.856, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      67     16.00
     O    1552      8.00
     N    1354      7.00
     C    5595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG D1608 " - " ASN D 476 "
      " NAG D1610 " - " ASN D 917 "
      " NAG D1611 " - " ASN D 836 "
  Time building additional restraints: 3.57
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN G 501 "
        pdb="ZN    ZN G 501 " - pdb=" NE2 HIS G 140 "
        pdb="ZN    ZN G 501 " - pdb=" ND1 HIS G 182 "


  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 5 sheets defined
      55.0% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'G' and resid 71 through 74
    Processing helix  chain 'G' and resid 100 through 117
      removed outlier: 3.604A  pdb=" N   LYS G 105 " --> pdb=" O   ARG G 101 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 138 through 143
      removed outlier: 3.754A  pdb=" N   GLU G 142 " --> pdb=" O   SER G 138 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 155 through 168
      removed outlier: 3.592A  pdb=" N   GLY G 159 " --> pdb=" O   ARG G 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG G 163 " --> pdb=" O   GLY G 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 186
      removed outlier: 4.083A  pdb=" N   ALA D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 182 through 186'
    Processing helix  chain 'D' and resid 189 through 210
    Processing helix  chain 'D' and resid 230 through 243
    Processing helix  chain 'D' and resid 315 through 330
    Processing helix  chain 'D' and resid 353 through 363
    Processing helix  chain 'D' and resid 372 through 388
      removed outlier: 3.505A  pdb=" N   SER D 376 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS D 388 " --> pdb=" O   THR D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 430
    Processing helix  chain 'D' and resid 463 through 472
      removed outlier: 4.479A  pdb=" N   ILE D 467 " --> pdb=" O   SER D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 492 through 503
      removed outlier: 4.366A  pdb=" N   GLN D 497 " --> pdb=" O   HIS D 493 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ASP D 498 " --> pdb=" O   SER D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 522
      removed outlier: 3.518A  pdb=" N   ALA D 508 " --> pdb=" O   THR D 504 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 524 through 548
    Processing helix  chain 'D' and resid 558 through 587
      removed outlier: 3.834A  pdb=" N   LEU D 563 " --> pdb=" O   ASN D 559 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE D 564 " --> pdb=" O   LEU D 560 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE D 565 " --> pdb=" O   THR D 561 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL D 576 " --> pdb=" O   ASN D 572 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU D 577 " --> pdb=" O   ASN D 573 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP D 587 " --> pdb=" O   TYR D 583 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 623
      removed outlier: 5.132A  pdb=" N   LEU D 606 " --> pdb=" O   GLN D 602 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER D 607 " --> pdb=" O   HIS D 603 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   THR D 615 " --> pdb=" O   THR D 611 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 627 through 659
      removed outlier: 4.537A  pdb=" N   PHE D 633 " --> pdb=" O   ALA D 629 " (cutoff:3.500A)
      Proline residue:  D 653  - end of helix
    Processing helix  chain 'D' and resid 688 through 718
      removed outlier: 5.084A  pdb=" N   LEU D 710 " --> pdb=" O   PHE D 706 " (cutoff:3.500A)
      Proline residue:  D 711  - end of helix
    Processing helix  chain 'D' and resid 719 through 738
    Processing helix  chain 'D' and resid 748 through 752
      removed outlier: 3.676A  pdb=" N   PHE D 752 " --> pdb=" O   LEU D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 759 through 765
      removed outlier: 4.261A  pdb=" N   ASP D 765 " --> pdb=" O   PHE D 761 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 768 through 771
    Processing helix  chain 'D' and resid 772 through 779
    Processing helix  chain 'D' and resid 820 through 835
    Processing helix  chain 'D' and resid 851 through 860
      removed outlier: 4.006A  pdb=" N   THR D 855 " --> pdb=" O   CYS D 851 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 883 through 902
      removed outlier: 4.347A  pdb=" N   LYS D 891 " --> pdb=" O   GLU D 887 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG D 892 " --> pdb=" O   LEU D 888 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 936 through 953
      removed outlier: 3.965A  pdb=" N   MET D 940 " --> pdb=" O   ALA D 936 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER D 953 " --> pdb=" O   SER D 949 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 971 through 1004
    Processing helix  chain 'D' and resid 1005 through 1030
    Processing helix  chain 'D' and resid 1036 through 1059
      removed outlier: 4.479A  pdb=" N   VAL D1040 " --> pdb=" O   VAL D1036 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR D1041 " --> pdb=" O   LEU D1037 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE D1042 " --> pdb=" O   GLU D1038 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER D1043 " --> pdb=" O   SER D1039 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL D1046 " --> pdb=" O   ILE D1042 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY D1047 " --> pdb=" O   SER D1043 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D1051 " --> pdb=" O   GLY D1047 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE D1052 " --> pdb=" O   LEU D1048 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D1053 " --> pdb=" O   SER D1049 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   HIS D1055 " --> pdb=" O   ASN D1051 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1068 through 1098
      removed outlier: 3.520A  pdb=" N   VAL D1072 " --> pdb=" O   ARG D1068 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE D1073 " --> pdb=" O   GLU D1069 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   SER D1081 " --> pdb=" O   SER D1077 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ALA D1082 " --> pdb=" O   ARG D1078 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR D1090 " --> pdb=" O   ALA D1086 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1102 through 1133
      removed outlier: 3.792A  pdb=" N   THR D1106 " --> pdb=" O   VAL D1102 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS D1131 " --> pdb=" O   PHE D1127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 76 through 78
    Processing sheet with id=AA2, first strand: chain 'G' and resid 85 through 86
      removed outlier: 7.775A  pdb=" N   ILE G  85 " --> pdb=" O   VAL G 124 " (cutoff:3.500A)
      removed outlier: 8.935A  pdb=" N   GLU G 126 " --> pdb=" O   ILE G  85 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ASP G 147 " --> pdb=" O   THR G 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 451 through 459
      removed outlier: 4.668A  pdb=" N   SER D 301 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ARG D 302 " --> pdb=" O   ILE D 487 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ILE D 487 " --> pdb=" O   ARG D 302 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL D 304 " --> pdb=" O   THR D 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 788 through 789
    Processing sheet with id=AA5, first strand: chain 'D' and resid 913 through 914
      removed outlier: 6.290A  pdb=" N   ARG D 913 " --> pdb=" O   ARG D 921 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1356
        1.32 -     1.44: 2434
        1.44 -     1.57: 4908
        1.57 -     1.69: 0
        1.69 -     1.81: 103
  Bond restraints: 8801
  Sorted by residual:
  bond pdb=" CB  TRP D 966 "
       pdb=" CG  TRP D 966 "
    ideal  model  delta    sigma   weight residual
    1.498  1.414  0.084 3.10e-02 1.04e+03 7.31e+00
  bond pdb=" C   MET D 785 "
       pdb=" N   PRO D 786 "
    ideal  model  delta    sigma   weight residual
    1.333  1.307  0.026 1.20e-02 6.94e+03 4.85e+00
  bond pdb=" C   SER D 758 "
       pdb=" N   HIS D 759 "
    ideal  model  delta    sigma   weight residual
    1.331  1.287  0.044 2.07e-02 2.33e+03 4.57e+00
  bond pdb=" CG  ASN D 476 "
       pdb=" ND2 ASN D 476 "
    ideal  model  delta    sigma   weight residual
    1.328  1.369 -0.041 2.10e-02 2.27e+03 3.90e+00
  bond pdb=" C   LEU D 749 "
       pdb=" N   SER D 750 "
    ideal  model  delta    sigma   weight residual
    1.331  1.301  0.031 1.62e-02 3.81e+03 3.57e+00
  ... (remaining 8796 not shown)

  Histogram of bond angle deviations from ideal:
       97.75 -   105.01: 186
      105.01 -   112.26: 4595
      112.26 -   119.51: 2798
      119.51 -   126.76: 4289
      126.76 -   134.01: 137
  Bond angle restraints: 12005
  Sorted by residual:
  angle pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
        pdb=" C   PHE D 255 "
      ideal   model   delta    sigma   weight residual
     108.19  116.33   -8.14 1.29e+00 6.01e-01 3.98e+01
  angle pdb=" N   PRO D 254 "
        pdb=" CA  PRO D 254 "
        pdb=" C   PRO D 254 "
      ideal   model   delta    sigma   weight residual
     112.47  120.58   -8.11 2.06e+00 2.36e-01 1.55e+01
  angle pdb=" C   PRO D 254 "
        pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
      ideal   model   delta    sigma   weight residual
     122.08  115.53    6.55 1.84e+00 2.95e-01 1.27e+01
  angle pdb=" C   LEU D 749 "
        pdb=" N   SER D 750 "
        pdb=" CA  SER D 750 "
      ideal   model   delta    sigma   weight residual
     122.31  115.38    6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" C   PHE D 554 "
        pdb=" N   PHE D 555 "
        pdb=" CA  PHE D 555 "
      ideal   model   delta    sigma   weight residual
     121.80  113.75    8.05 2.44e+00 1.68e-01 1.09e+01
  ... (remaining 12000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 4962
       16.97 -    33.95: 491
       33.95 -    50.92: 77
       50.92 -    67.90: 23
       67.90 -    84.87: 5
  Dihedral angle restraints: 5558
    sinusoidal: 2452
      harmonic: 3106
  Sorted by residual:
  dihedral pdb=" CA  SER D 290 "
           pdb=" C   SER D 290 "
           pdb=" N   PHE D 291 "
           pdb=" CA  PHE D 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.86  -24.14     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  TYR D 253 "
           pdb=" C   TYR D 253 "
           pdb=" N   PRO D 254 "
           pdb=" CA  PRO D 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  PHE D1127 "
           pdb=" C   PHE D1127 "
           pdb=" N   GLN D1128 "
           pdb=" CA  GLN D1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 5555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1367
       0.132 -    0.264: 14
       0.264 -    0.396: 0
       0.396 -    0.529: 1
       0.529 -    0.661: 1
  Chirality restraints: 1383
  Sorted by residual:
  chirality pdb=" C1  NAG D1610 "
            pdb=" ND2 ASN D 917 "
            pdb=" C2  NAG D1610 "
            pdb=" O5  NAG D1610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" C1  NAG D1611 "
            pdb=" ND2 ASN D 836 "
            pdb=" C2  NAG D1611 "
            pdb=" O5  NAG D1611 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  PRO D 254 "
            pdb=" N   PRO D 254 "
            pdb=" C   PRO D 254 "
            pdb=" CB  PRO D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1380 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 883 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.61e+00
        pdb=" C   GLN D 883 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLN D 883 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU D 884 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 456 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO D 457 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 457 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 457 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 291 "    0.004 2.00e-02 2.50e+03   1.26e-02 2.79e+00
        pdb=" CG  PHE D 291 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 291 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 291 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 291 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 291 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 291 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 166
        2.63 -     3.19: 9307
        3.19 -     3.76: 13529
        3.76 -     4.33: 17745
        4.33 -     4.90: 26852
  Nonbonded interactions: 67599
  Sorted by model distance:
  nonbonded pdb=" O   PRO D 350 "
            pdb=" ND2 ASN D 356 "
     model   vdw
     2.056 2.520
  nonbonded pdb=" OD1 ASP G 147 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.074 2.230
  nonbonded pdb=" OE1 GLU G 176 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.094 2.230
  nonbonded pdb=" O   ALA D1059 "
            pdb=" OG  SER D1075 "
     model   vdw
     2.105 2.440
  nonbonded pdb=" O   GLU G  53 "
            pdb=" OG  SER G  59 "
     model   vdw
     2.106 2.440
  ... (remaining 67594 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=0.00 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          1.500
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     27.810
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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      :  0.006   0.084   8801  Z= 0.401
  Angle     :  0.820   8.141  12005  Z= 0.439
  Chirality :  0.051   0.661   1383
  Planarity :  0.005   0.047   1465
  Dihedral  : 13.723  84.873   3546
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.66 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.21), residues: 1046
  helix: -2.23 (0.18), residues: 534
  sheet: -3.19 (0.67), residues: 52
  loop : -3.60 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D1120 
 HIS   0.005   0.001   HIS D 778 
 PHE   0.024   0.002   PHE D 967 
 TYR   0.017   0.002   TYR D1060 
 ARG   0.012   0.001   ARG D 329 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.899 
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: G   81 ASN cc_start: 0.8670 (t0) cc_final: 0.8455 (t0)
REVERT: G   98 MET cc_start: 0.8708 (ptm) cc_final: 0.8233 (ptp)
REVERT: G  102 CYS cc_start: 0.9143 (t) cc_final: 0.8353 (t)
REVERT: G  141 TYR cc_start: 0.8299 (m-10) cc_final: 0.7834 (m-10)
REVERT: G  154 ASP cc_start: 0.8478 (m-30) cc_final: 0.8256 (m-30)
REVERT: G  175 TYR cc_start: 0.7553 (t80) cc_final: 0.6516 (t80)
REVERT: G  186 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8247 (ttmt)
REVERT: G  188 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: D  343 THR cc_start: 0.7712 (t) cc_final: 0.7454 (m)
REVERT: D  460 LYS cc_start: 0.9241 (pttm) cc_final: 0.8865 (pttm)
REVERT: D  502 MET cc_start: 0.8768 (tmm) cc_final: 0.8526 (tmm)
REVERT: D  530 MET cc_start: 0.8998 (tpp) cc_final: 0.8459 (tpp)
REVERT: D  595 GLU cc_start: 0.8961 (mp0) cc_final: 0.8512 (mp0)
REVERT: D  641 ILE cc_start: 0.9617 (tp) cc_final: 0.9379 (tp)
REVERT: D  753 GLN cc_start: 0.8912 (pt0) cc_final: 0.8634 (pt0)
REVERT: D  796 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8031 (tm-30)
REVERT: D  896 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: D  926 GLU cc_start: 0.8271 (pm20) cc_final: 0.8006 (pm20)
REVERT: D 1011 TYR cc_start: 0.9243 (m-80) cc_final: 0.8795 (m-80)
REVERT: D 1097 MET cc_start: 0.9178 (ttm) cc_final: 0.8868 (tmm)
REVERT: D 1126 PHE cc_start: 0.8840 (t80) cc_final: 0.8417 (t80)
REVERT: D 1128 GLN cc_start: 0.9315 (mp10) cc_final: 0.9031 (mp10)
REVERT: D 1129 CYS cc_start: 0.9471 (t) cc_final: 0.8999 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1918
  time to fit residues: 69.0960
Evaluate side-chains
  202 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
D 252 ASN
** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 622 ASN
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 964 ASN
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1035 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8801  Z= 0.216
  Angle     :  0.678   9.428  12005  Z= 0.347
  Chirality :  0.042   0.248   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  7.442  54.242   1710
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.30 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.25), residues: 1046
  helix: -0.52 (0.21), residues: 536
  sheet: -3.29 (0.63), residues: 58
  loop : -3.04 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D1120 
 HIS   0.004   0.001   HIS D 692 
 PHE   0.023   0.002   PHE D 291 
 TYR   0.013   0.001   TYR G  80 
 ARG   0.004   0.000   ARG D 899 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.944 
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: G   98 MET cc_start: 0.8433 (ptm) cc_final: 0.8217 (ptp)
REVERT: G  106 LEU cc_start: 0.9481 (tt) cc_final: 0.9193 (pp)
REVERT: G  141 TYR cc_start: 0.8250 (m-10) cc_final: 0.7908 (m-10)
REVERT: G  154 ASP cc_start: 0.8412 (m-30) cc_final: 0.8204 (m-30)
REVERT: G  184 SER cc_start: 0.8629 (p) cc_final: 0.8004 (p)
REVERT: G  186 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8357 (ttmt)
REVERT: G  188 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8293 (mm-30)
REVERT: D  373 ARG cc_start: 0.9273 (mmt-90) cc_final: 0.8746 (mmp80)
REVERT: D  453 MET cc_start: 0.8934 (tmm) cc_final: 0.7868 (tmm)
REVERT: D  454 LEU cc_start: 0.8443 (tp) cc_final: 0.7817 (tp)
REVERT: D  460 LYS cc_start: 0.9190 (pttp) cc_final: 0.8948 (pttm)
REVERT: D  502 MET cc_start: 0.8467 (tmm) cc_final: 0.8065 (tpp)
REVERT: D  530 MET cc_start: 0.9116 (tpp) cc_final: 0.8407 (tpp)
REVERT: D  554 PHE cc_start: 0.8528 (t80) cc_final: 0.8210 (t80)
REVERT: D  575 PHE cc_start: 0.8871 (m-10) cc_final: 0.8031 (m-80)
REVERT: D  595 GLU cc_start: 0.8918 (mp0) cc_final: 0.8354 (mp0)
REVERT: D  796 GLU cc_start: 0.8988 (mt-10) cc_final: 0.7675 (tm-30)
REVERT: D  996 PHE cc_start: 0.8796 (t80) cc_final: 0.8587 (t80)
REVERT: D 1011 TYR cc_start: 0.8988 (m-80) cc_final: 0.8643 (m-80)
REVERT: D 1085 MET cc_start: 0.8888 (tpp) cc_final: 0.8508 (tpp)
REVERT: D 1126 PHE cc_start: 0.8813 (t80) cc_final: 0.8394 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1882
  time to fit residues: 66.3078
Evaluate side-chains
  207 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 29 optimal weight:   20.0000
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0050
   chunk 32 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    2.4000

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1107 GLN
D1128 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8801  Z= 0.234
  Angle     :  0.678   9.363  12005  Z= 0.345
  Chirality :  0.042   0.235   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  7.201  53.970   1710
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.26), residues: 1046
  helix:  0.17 (0.22), residues: 533
  sheet: -3.49 (0.61), residues: 57
  loop : -2.83 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D1120 
 HIS   0.002   0.001   HIS D 778 
 PHE   0.029   0.002   PHE D 292 
 TYR   0.013   0.001   TYR D 468 
 ARG   0.004   0.000   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.907 
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: G   80 TYR cc_start: 0.9170 (m-10) cc_final: 0.8754 (m-80)
REVERT: G  141 TYR cc_start: 0.8303 (m-10) cc_final: 0.7801 (m-80)
REVERT: G  157 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7975 (tptt)
REVERT: G  175 TYR cc_start: 0.7166 (t80) cc_final: 0.6918 (t80)
REVERT: G  186 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8377 (ttmt)
REVERT: G  188 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8350 (mm-30)
REVERT: D  453 MET cc_start: 0.9063 (tmm) cc_final: 0.7999 (tmm)
REVERT: D  454 LEU cc_start: 0.8610 (tp) cc_final: 0.7958 (tp)
REVERT: D  460 LYS cc_start: 0.9094 (pttp) cc_final: 0.8844 (pttm)
REVERT: D  467 ILE cc_start: 0.9192 (mp) cc_final: 0.8929 (mp)
REVERT: D  502 MET cc_start: 0.8406 (tmm) cc_final: 0.8010 (tpp)
REVERT: D  530 MET cc_start: 0.9118 (tpp) cc_final: 0.8369 (tpp)
REVERT: D  575 PHE cc_start: 0.8849 (m-10) cc_final: 0.8036 (m-80)
REVERT: D  595 GLU cc_start: 0.8927 (mp0) cc_final: 0.8314 (mp0)
REVERT: D  753 GLN cc_start: 0.8756 (pm20) cc_final: 0.8537 (pt0)
REVERT: D  794 SER cc_start: 0.9166 (p) cc_final: 0.8381 (m)
REVERT: D  796 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8720 (mp0)
REVERT: D  812 LEU cc_start: 0.9114 (pp) cc_final: 0.8606 (pp)
REVERT: D  966 TRP cc_start: 0.7855 (m100) cc_final: 0.7132 (m100)
REVERT: D 1006 ILE cc_start: 0.8983 (mp) cc_final: 0.8540 (mt)
REVERT: D 1011 TYR cc_start: 0.9034 (m-10) cc_final: 0.8687 (m-80)
REVERT: D 1126 PHE cc_start: 0.8922 (t80) cc_final: 0.8474 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1968
  time to fit residues: 68.9822
Evaluate side-chains
  210 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8801  Z= 0.202
  Angle     :  0.661   9.025  12005  Z= 0.333
  Chirality :  0.041   0.214   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  6.974  52.448   1710
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.16 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.26), residues: 1046
  helix:  0.50 (0.23), residues: 530
  sheet: -3.48 (0.59), residues: 58
  loop : -2.73 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 651 
 HIS   0.002   0.001   HIS D 779 
 PHE   0.022   0.002   PHE D 533 
 TYR   0.017   0.001   TYR D 499 
 ARG   0.006   0.000   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 246
  time to evaluate  : 0.946 
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: G   80 TYR cc_start: 0.9240 (m-10) cc_final: 0.8945 (m-10)
REVERT: G   98 MET cc_start: 0.8925 (ptt) cc_final: 0.8685 (ptt)
REVERT: G  102 CYS cc_start: 0.9019 (t) cc_final: 0.8007 (t)
REVERT: G  141 TYR cc_start: 0.8257 (m-10) cc_final: 0.7838 (m-80)
REVERT: G  175 TYR cc_start: 0.7410 (t80) cc_final: 0.7016 (t80)
REVERT: G  186 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8217 (ttmt)
REVERT: D  454 LEU cc_start: 0.8382 (tp) cc_final: 0.8168 (tp)
REVERT: D  460 LYS cc_start: 0.9076 (pttp) cc_final: 0.8767 (pttm)
REVERT: D  502 MET cc_start: 0.8240 (tmm) cc_final: 0.7888 (tpp)
REVERT: D  530 MET cc_start: 0.9054 (tpp) cc_final: 0.8294 (tpp)
REVERT: D  575 PHE cc_start: 0.8802 (m-10) cc_final: 0.7953 (m-80)
REVERT: D  595 GLU cc_start: 0.8985 (mp0) cc_final: 0.8461 (mp0)
REVERT: D  739 ASN cc_start: 0.7332 (t0) cc_final: 0.7111 (t0)
REVERT: D  796 GLU cc_start: 0.8938 (mt-10) cc_final: 0.7999 (tm-30)
REVERT: D  805 LYS cc_start: 0.9145 (pttm) cc_final: 0.8830 (pttm)
REVERT: D  966 TRP cc_start: 0.7780 (m100) cc_final: 0.7059 (m100)
REVERT: D 1006 ILE cc_start: 0.8911 (mp) cc_final: 0.8468 (mt)
REVERT: D 1011 TYR cc_start: 0.8941 (m-10) cc_final: 0.8666 (m-80)
REVERT: D 1097 MET cc_start: 0.9002 (ppp) cc_final: 0.8798 (ppp)
REVERT: D 1126 PHE cc_start: 0.8880 (t80) cc_final: 0.8435 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1957
  time to fit residues: 66.9598
Evaluate side-chains
  203 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 75 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 51 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8801  Z= 0.249
  Angle     :  0.682  10.789  12005  Z= 0.346
  Chirality :  0.041   0.215   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  7.093  53.616   1710
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.26), residues: 1046
  helix:  0.62 (0.23), residues: 522
  sheet: -3.56 (0.57), residues: 58
  loop : -2.62 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 352 
 HIS   0.003   0.001   HIS D 941 
 PHE   0.033   0.002   PHE D 996 
 TYR   0.012   0.001   TYR G  62 
 ARG   0.006   0.000   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.869 
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: G   80 TYR cc_start: 0.9244 (m-10) cc_final: 0.8953 (m-10)
REVERT: G   98 MET cc_start: 0.8982 (ptt) cc_final: 0.8726 (ptt)
REVERT: G  102 CYS cc_start: 0.9143 (t) cc_final: 0.8171 (t)
REVERT: G  141 TYR cc_start: 0.8323 (m-10) cc_final: 0.7847 (m-80)
REVERT: G  144 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8267 (mtp180)
REVERT: G  150 THR cc_start: 0.7886 (t) cc_final: 0.7659 (t)
REVERT: G  175 TYR cc_start: 0.7670 (t80) cc_final: 0.7229 (t80)
REVERT: G  186 LYS cc_start: 0.8494 (ttmt) cc_final: 0.7995 (ttmt)
REVERT: D  460 LYS cc_start: 0.9132 (pttp) cc_final: 0.8889 (pttm)
REVERT: D  502 MET cc_start: 0.8193 (tmm) cc_final: 0.7841 (tpp)
REVERT: D  518 MET cc_start: 0.8782 (mtm) cc_final: 0.8415 (mtm)
REVERT: D  530 MET cc_start: 0.9101 (tpp) cc_final: 0.8265 (tpp)
REVERT: D  575 PHE cc_start: 0.8827 (m-10) cc_final: 0.8030 (m-80)
REVERT: D  595 GLU cc_start: 0.9008 (mp0) cc_final: 0.8473 (mp0)
REVERT: D  796 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8045 (tm-30)
REVERT: D 1006 ILE cc_start: 0.8944 (mp) cc_final: 0.8526 (mt)
REVERT: D 1011 TYR cc_start: 0.8969 (m-10) cc_final: 0.8639 (m-80)
REVERT: D 1126 PHE cc_start: 0.8926 (t80) cc_final: 0.8458 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1909
  time to fit residues: 64.1981
Evaluate side-chains
  202 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0050
   chunk 25 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:   30.0000
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0170
   overall best weight:    0.8036

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8801  Z= 0.179
  Angle     :  0.667  10.179  12005  Z= 0.335
  Chirality :  0.041   0.211   1383
  Planarity :  0.004   0.042   1465
  Dihedral  :  6.783  56.783   1710
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.26), residues: 1046
  helix:  0.70 (0.23), residues: 522
  sheet: -3.59 (0.56), residues: 58
  loop : -2.56 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 651 
 HIS   0.002   0.000   HIS D 429 
 PHE   0.029   0.002   PHE D 996 
 TYR   0.015   0.001   TYR D 499 
 ARG   0.009   0.000   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 PHE cc_start: 0.9353 (t80) cc_final: 0.9128 (t80)
REVERT: G   80 TYR cc_start: 0.9192 (m-10) cc_final: 0.8875 (m-10)
REVERT: G   98 MET cc_start: 0.9008 (ptt) cc_final: 0.8735 (ptt)
REVERT: G  102 CYS cc_start: 0.9128 (t) cc_final: 0.8108 (t)
REVERT: G  141 TYR cc_start: 0.8187 (m-10) cc_final: 0.7859 (m-80)
REVERT: G  150 THR cc_start: 0.7922 (t) cc_final: 0.7677 (t)
REVERT: G  160 MET cc_start: 0.8493 (tpt) cc_final: 0.8261 (tpp)
REVERT: G  175 TYR cc_start: 0.7592 (t80) cc_final: 0.7127 (t80)
REVERT: G  186 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7755 (ttmt)
REVERT: D  218 ASP cc_start: 0.8511 (m-30) cc_final: 0.8300 (m-30)
REVERT: D  460 LYS cc_start: 0.9076 (pttp) cc_final: 0.8776 (pttm)
REVERT: D  502 MET cc_start: 0.8086 (tmm) cc_final: 0.7754 (tpp)
REVERT: D  518 MET cc_start: 0.8765 (mtm) cc_final: 0.8291 (mtt)
REVERT: D  530 MET cc_start: 0.9110 (tpp) cc_final: 0.8509 (tpp)
REVERT: D  575 PHE cc_start: 0.8770 (m-10) cc_final: 0.7993 (m-80)
REVERT: D  579 ASP cc_start: 0.8527 (m-30) cc_final: 0.8320 (m-30)
REVERT: D  747 LEU cc_start: 0.9059 (mm) cc_final: 0.8857 (mm)
REVERT: D  796 GLU cc_start: 0.8900 (mt-10) cc_final: 0.7992 (tm-30)
REVERT: D  896 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8304 (mt-10)
REVERT: D  966 TRP cc_start: 0.7694 (m100) cc_final: 0.7039 (m100)
REVERT: D 1006 ILE cc_start: 0.8801 (mp) cc_final: 0.8339 (mt)
REVERT: D 1011 TYR cc_start: 0.8853 (m-10) cc_final: 0.8648 (m-80)
REVERT: D 1126 PHE cc_start: 0.9012 (t80) cc_final: 0.8578 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1818
  time to fit residues: 65.0545
Evaluate side-chains
  208 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 101 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 466 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8801  Z= 0.174
  Angle     :  0.660   9.747  12005  Z= 0.330
  Chirality :  0.040   0.216   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  6.681  58.388   1710
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.25 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.26), residues: 1046
  helix:  0.80 (0.23), residues: 526
  sheet: -3.65 (0.54), residues: 57
  loop : -2.49 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 352 
 HIS   0.003   0.000   HIS D 692 
 PHE   0.022   0.002   PHE D 292 
 TYR   0.012   0.001   TYR G  62 
 ARG   0.004   0.000   ARG G 144 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9183 (m-10) cc_final: 0.8834 (m-10)
REVERT: G   98 MET cc_start: 0.8999 (ptt) cc_final: 0.8768 (ptt)
REVERT: G  102 CYS cc_start: 0.9110 (t) cc_final: 0.8169 (t)
REVERT: G  141 TYR cc_start: 0.8193 (m-10) cc_final: 0.7920 (m-80)
REVERT: G  160 MET cc_start: 0.8475 (tpt) cc_final: 0.8267 (tpp)
REVERT: G  175 TYR cc_start: 0.7563 (t80) cc_final: 0.7281 (t80)
REVERT: D  218 ASP cc_start: 0.8537 (m-30) cc_final: 0.8316 (m-30)
REVERT: D  460 LYS cc_start: 0.9095 (pttp) cc_final: 0.8794 (pttm)
REVERT: D  502 MET cc_start: 0.8039 (tmm) cc_final: 0.7796 (tpp)
REVERT: D  530 MET cc_start: 0.9049 (tpp) cc_final: 0.8708 (tpp)
REVERT: D  575 PHE cc_start: 0.8841 (m-10) cc_final: 0.8059 (m-80)
REVERT: D  579 ASP cc_start: 0.8633 (m-30) cc_final: 0.8404 (m-30)
REVERT: D  595 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8975 (pt0)
REVERT: D  725 PHE cc_start: 0.8724 (m-10) cc_final: 0.8472 (m-80)
REVERT: D  747 LEU cc_start: 0.9095 (mm) cc_final: 0.8866 (mm)
REVERT: D  796 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8037 (tm-30)
REVERT: D  896 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8292 (mt-10)
REVERT: D  966 TRP cc_start: 0.7629 (m100) cc_final: 0.6965 (m100)
REVERT: D  986 ILE cc_start: 0.9187 (tp) cc_final: 0.8986 (tp)
REVERT: D 1006 ILE cc_start: 0.8816 (mp) cc_final: 0.8410 (mt)
REVERT: D 1011 TYR cc_start: 0.8947 (m-10) cc_final: 0.8717 (m-80)
REVERT: D 1126 PHE cc_start: 0.8774 (t80) cc_final: 0.8442 (t80)
REVERT: D 1129 CYS cc_start: 0.8957 (t) cc_final: 0.8525 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1877
  time to fit residues: 68.8752
Evaluate side-chains
  201 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 977 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   8801  Z= 0.381
  Angle     :  0.788  11.781  12005  Z= 0.401
  Chirality :  0.045   0.232   1383
  Planarity :  0.005   0.041   1465
  Dihedral  :  7.391  57.030   1710
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.26), residues: 1046
  helix:  0.32 (0.22), residues: 534
  sheet: -3.76 (0.55), residues: 57
  loop : -2.50 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 352 
 HIS   0.008   0.002   HIS D1055 
 PHE   0.021   0.002   PHE D 772 
 TYR   0.020   0.002   TYR D1060 
 ARG   0.006   0.001   ARG D 661 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9248 (m-10) cc_final: 0.8978 (m-10)
REVERT: G   98 MET cc_start: 0.9065 (ptt) cc_final: 0.8690 (ptt)
REVERT: G  102 CYS cc_start: 0.9114 (t) cc_final: 0.8091 (t)
REVERT: G  139 LEU cc_start: 0.8526 (mm) cc_final: 0.8242 (mm)
REVERT: G  141 TYR cc_start: 0.8360 (m-10) cc_final: 0.8088 (m-80)
REVERT: G  150 THR cc_start: 0.7864 (t) cc_final: 0.7574 (t)
REVERT: G  175 TYR cc_start: 0.7482 (t80) cc_final: 0.7087 (t80)
REVERT: D  218 ASP cc_start: 0.8550 (m-30) cc_final: 0.8325 (m-30)
REVERT: D  460 LYS cc_start: 0.9155 (pttp) cc_final: 0.8915 (pttm)
REVERT: D  502 MET cc_start: 0.8202 (tmm) cc_final: 0.7774 (tpp)
REVERT: D  530 MET cc_start: 0.9077 (tpp) cc_final: 0.8379 (tpp)
REVERT: D  575 PHE cc_start: 0.8923 (m-10) cc_final: 0.8522 (m-80)
REVERT: D  595 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9063 (mp0)
REVERT: D  648 MET cc_start: 0.9186 (tpt) cc_final: 0.8969 (tpp)
REVERT: D  767 GLU cc_start: 0.8767 (mp0) cc_final: 0.8538 (mp0)
REVERT: D  796 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8104 (tm-30)
REVERT: D  896 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8282 (mt-10)
REVERT: D  926 GLU cc_start: 0.7806 (pm20) cc_final: 0.7577 (pm20)
REVERT: D 1006 ILE cc_start: 0.9057 (mp) cc_final: 0.8675 (mt)
REVERT: D 1011 TYR cc_start: 0.9076 (m-10) cc_final: 0.8757 (m-80)
REVERT: D 1122 PHE cc_start: 0.8219 (t80) cc_final: 0.7980 (t80)
REVERT: D 1126 PHE cc_start: 0.8901 (t80) cc_final: 0.8482 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1726
  time to fit residues: 59.4426
Evaluate side-chains
  193 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 41 optimal weight:    0.5980
   chunk 74 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8801  Z= 0.228
  Angle     :  0.717  11.202  12005  Z= 0.358
  Chirality :  0.042   0.210   1383
  Planarity :  0.004   0.041   1465
  Dihedral  :  7.121  57.086   1710
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.26), residues: 1046
  helix:  0.48 (0.23), residues: 533
  sheet: -3.78 (0.53), residues: 58
  loop : -2.51 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 352 
 HIS   0.007   0.001   HIS D1055 
 PHE   0.037   0.002   PHE D 996 
 TYR   0.023   0.001   TYR G  62 
 ARG   0.004   0.000   ARG D 373 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9173 (m-10) cc_final: 0.8842 (m-10)
REVERT: G   98 MET cc_start: 0.9029 (ptt) cc_final: 0.8623 (ptt)
REVERT: G  102 CYS cc_start: 0.9105 (t) cc_final: 0.8013 (t)
REVERT: G  139 LEU cc_start: 0.8451 (mm) cc_final: 0.8157 (mm)
REVERT: G  141 TYR cc_start: 0.8235 (m-10) cc_final: 0.7996 (m-80)
REVERT: G  150 THR cc_start: 0.7914 (t) cc_final: 0.7617 (t)
REVERT: G  175 TYR cc_start: 0.7324 (t80) cc_final: 0.6970 (t80)
REVERT: D  460 LYS cc_start: 0.9135 (pttp) cc_final: 0.8811 (pttm)
REVERT: D  502 MET cc_start: 0.8177 (tmm) cc_final: 0.7782 (tpp)
REVERT: D  530 MET cc_start: 0.9071 (tpp) cc_final: 0.8377 (tpp)
REVERT: D  575 PHE cc_start: 0.8867 (m-10) cc_final: 0.8193 (m-80)
REVERT: D  579 ASP cc_start: 0.8689 (m-30) cc_final: 0.8486 (m-30)
REVERT: D  595 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9039 (mp0)
REVERT: D  648 MET cc_start: 0.9179 (tpt) cc_final: 0.8942 (tpp)
REVERT: D  767 GLU cc_start: 0.8752 (mp0) cc_final: 0.8519 (mp0)
REVERT: D  796 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8090 (tm-30)
REVERT: D  926 GLU cc_start: 0.7696 (pm20) cc_final: 0.7426 (pm20)
REVERT: D  966 TRP cc_start: 0.7815 (m100) cc_final: 0.7269 (m100)
REVERT: D 1006 ILE cc_start: 0.8999 (mp) cc_final: 0.8630 (mt)
REVERT: D 1011 TYR cc_start: 0.9134 (m-10) cc_final: 0.8806 (m-80)
REVERT: D 1126 PHE cc_start: 0.8817 (t80) cc_final: 0.8437 (t80)
REVERT: D 1130 MET cc_start: 0.8965 (tmm) cc_final: 0.8733 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1702
  time to fit residues: 58.5645
Evaluate side-chains
  193 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0020
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   overall best weight:    1.3794

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8801  Z= 0.196
  Angle     :  0.721  11.402  12005  Z= 0.354
  Chirality :  0.041   0.214   1383
  Planarity :  0.004   0.067   1465
  Dihedral  :  6.949  57.424   1710
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.26), residues: 1046
  helix:  0.60 (0.23), residues: 530
  sheet: -3.75 (0.52), residues: 58
  loop : -2.45 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 352 
 HIS   0.010   0.001   HIS D1055 
 PHE   0.038   0.002   PHE D 996 
 TYR   0.028   0.001   TYR D 499 
 ARG   0.004   0.000   ARG D 373 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8855 (mp0)
REVERT: G   80 TYR cc_start: 0.9143 (m-10) cc_final: 0.8807 (m-10)
REVERT: G   98 MET cc_start: 0.9045 (ptt) cc_final: 0.8722 (ptt)
REVERT: G  102 CYS cc_start: 0.9081 (t) cc_final: 0.7929 (t)
REVERT: G  139 LEU cc_start: 0.8417 (mm) cc_final: 0.8113 (mm)
REVERT: G  141 TYR cc_start: 0.8195 (m-10) cc_final: 0.7960 (m-80)
REVERT: G  150 THR cc_start: 0.7923 (t) cc_final: 0.7623 (t)
REVERT: G  175 TYR cc_start: 0.7292 (t80) cc_final: 0.7068 (t80)
REVERT: G  188 GLU cc_start: 0.9083 (mp0) cc_final: 0.8877 (mp0)
REVERT: D  460 LYS cc_start: 0.9126 (pttp) cc_final: 0.8804 (pttm)
REVERT: D  502 MET cc_start: 0.8175 (tmm) cc_final: 0.7826 (tpp)
REVERT: D  530 MET cc_start: 0.9062 (tpp) cc_final: 0.8371 (tpp)
REVERT: D  575 PHE cc_start: 0.8954 (m-10) cc_final: 0.8255 (m-80)
REVERT: D  579 ASP cc_start: 0.8669 (m-30) cc_final: 0.8445 (m-30)
REVERT: D  595 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9027 (mp0)
REVERT: D  648 MET cc_start: 0.9140 (tpt) cc_final: 0.8904 (tpp)
REVERT: D  725 PHE cc_start: 0.8670 (m-10) cc_final: 0.8440 (m-10)
REVERT: D  747 LEU cc_start: 0.9100 (mm) cc_final: 0.8897 (mm)
REVERT: D  767 GLU cc_start: 0.8748 (mp0) cc_final: 0.8510 (mp0)
REVERT: D  796 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8104 (tm-30)
REVERT: D  896 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: D  926 GLU cc_start: 0.7637 (pm20) cc_final: 0.7343 (pm20)
REVERT: D  966 TRP cc_start: 0.7687 (m100) cc_final: 0.7163 (m100)
REVERT: D 1006 ILE cc_start: 0.8993 (mp) cc_final: 0.8625 (mt)
REVERT: D 1126 PHE cc_start: 0.8851 (t80) cc_final: 0.8465 (t80)
REVERT: D 1129 CYS cc_start: 0.8898 (t) cc_final: 0.8627 (p)
REVERT: D 1130 MET cc_start: 0.8871 (tmm) cc_final: 0.8669 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1774
  time to fit residues: 60.6105
Evaluate side-chains
  201 residues out of total 926 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 76 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 83 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 10 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 73 optimal weight:    5.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 862 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 = 0.3711 r_free = 0.3711 target = 0.114301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.086303 restraints weight = 22759.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088961 restraints weight = 12798.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090699 restraints weight = 8798.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8801  Z= 0.296
  Angle     :  0.754  11.082  12005  Z= 0.378
  Chirality :  0.043   0.221   1383
  Planarity :  0.005   0.051   1465
  Dihedral  :  7.199  57.067   1710
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.26), residues: 1046
  helix:  0.47 (0.23), residues: 533
  sheet: -3.81 (0.52), residues: 58
  loop : -2.48 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 721 
 HIS   0.007   0.001   HIS D1055 
 PHE   0.019   0.002   PHE D 533 
 TYR   0.039   0.002   TYR D1011 
 ARG   0.004   0.000   ARG D 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1947.77 seconds
wall clock time: 36 minutes 32.61 seconds (2192.61 seconds total)