Starting phenix.real_space_refine
on Thu Jul 31 00:50:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nmc_0446/07_2025/6nmc_0446.cif"
  }
  resolution = 4.24
  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=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     P      25      5.49       5
     Mg      2      5.21       5
     S      39      5.16       5
     C    8096      2.51       5
     N    2098      2.21       5
     O    2548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12808
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 9931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1202, 9931
          Classifications: {'peptide': 1202}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 1172}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 535
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 8, 'rna3p': 16}
    Chain: "B"
      Number of atoms: 1305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1305
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 2, 'TRANS': 153}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1029
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 7.95, per 1000 atoms: 0.62
  Number of scatterers: 12808
  At special positions: 0
  Unit cell: (132.184, 108.732, 105.534, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      25     15.00
     Mg      2     11.99
     O    2548      8.00
     N    2098      7.00
     C    8096      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.25
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2838

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 13 sheets defined
      53.0% alpha, 4.8% beta
      4 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 4.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 37 through 66
      removed outlier: 5.043A  pdb=" N   TYR A  47 " --> pdb=" O   ARG A  43 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   LYS A  48 " --> pdb=" O   ALA A  44 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLY A  49 " --> pdb=" O   GLU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 69
      No H-bonds generated for 'chain 'A' and resid 67 through 69'
    Processing helix  chain 'A' and resid 73 through 83
      removed outlier: 4.073A  pdb=" N   LEU A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 111
      removed outlier: 3.737A  pdb=" N   GLU A  93 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 119
      removed outlier: 4.475A  pdb=" N   PHE A 119 " --> pdb=" O   LYS A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 124
      removed outlier: 3.881A  pdb=" N   ILE A 123 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 124 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 120 through 124'
    Processing helix  chain 'A' and resid 136 through 142
      removed outlier: 4.147A  pdb=" N   LEU A 140 " --> pdb=" O   ASP A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 4.162A  pdb=" N   GLY A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 161
    Processing helix  chain 'A' and resid 170 through 178
      removed outlier: 3.846A  pdb=" N   ARG A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 3.927A  pdb=" N   SER A 185 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 216 through 221
      removed outlier: 3.856A  pdb=" N   PHE A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 254 through 261
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 3.719A  pdb=" N   LYS A 265 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'A' and resid 312 through 327
    Processing helix  chain 'A' and resid 328 through 331
    Processing helix  chain 'A' and resid 341 through 353
      removed outlier: 4.155A  pdb=" N   SER A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   THR A 346 " --> pdb=" O   PRO A 342 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 371
      removed outlier: 4.142A  pdb=" N   ILE A 369 " --> pdb=" O   GLU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 390
    Processing helix  chain 'A' and resid 396 through 404
    Processing helix  chain 'A' and resid 409 through 433
      removed outlier: 4.363A  pdb=" N   LYS A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 471
    Processing helix  chain 'A' and resid 483 through 498
      removed outlier: 4.623A  pdb=" N   ASP A 489 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU A 492 " --> pdb=" O   GLY A 488 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE A 496 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 3.702A  pdb=" N   ALA A 506 " --> pdb=" O   HIS A 502 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ASN A 509 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 543
    Processing helix  chain 'A' and resid 560 through 563
      removed outlier: 4.068A  pdb=" N   ALA A 563 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 563'
    Processing helix  chain 'A' and resid 592 through 597
    Processing helix  chain 'A' and resid 609 through 619
    Processing helix  chain 'A' and resid 628 through 646
      removed outlier: 4.445A  pdb=" N   LYS A 634 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A 635 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 652
      removed outlier: 3.940A  pdb=" N   ASN A 651 " --> pdb=" O   PRO A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 663
      removed outlier: 3.882A  pdb=" N   TYR A 663 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 677
    Processing helix  chain 'A' and resid 687 through 697
    Processing helix  chain 'A' and resid 718 through 727
    Processing helix  chain 'A' and resid 786 through 790
      removed outlier: 3.800A  pdb=" N   PHE A 789 " --> pdb=" O   ASP A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 823
      removed outlier: 4.058A  pdb=" N   ARG A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   HIS A 822 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 886
      removed outlier: 3.711A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 4.443A  pdb=" N   VAL A 908 " --> pdb=" O   ILE A 904 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   HIS A 909 " --> pdb=" O   SER A 905 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LYS A 910 " --> pdb=" O   GLN A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 952
      removed outlier: 3.702A  pdb=" N   TYR A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 956
    Processing helix  chain 'A' and resid 1020 through 1030
      removed outlier: 4.398A  pdb=" N   LYS A1026 " --> pdb=" O   ALA A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1102
    Processing helix  chain 'A' and resid 1111 through 1116
    Processing helix  chain 'A' and resid 1120 through 1136
      removed outlier: 4.183A  pdb=" N   TYR A1124 " --> pdb=" O   ASP A1120 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA A1129 " --> pdb=" O   SER A1125 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU A1130 " --> pdb=" O   SER A1126 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU A1133 " --> pdb=" O   ALA A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1169
      removed outlier: 4.165A  pdb=" N   ALA A1169 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1199
      removed outlier: 3.774A  pdb=" N   ILE A1187 " --> pdb=" O   GLY A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1214 through 1225
    Processing helix  chain 'B' and resid 3 through 20
      removed outlier: 3.508A  pdb=" N   GLU B  10 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B  13 " --> pdb=" O   LYS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 45
      removed outlier: 4.287A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 67 through 76
      removed outlier: 3.529A  pdb=" N   GLU B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 112
    Processing helix  chain 'B' and resid 124 through 162
      removed outlier: 4.589A  pdb=" N   GLU B 129 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   GLU B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP B 149 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 150 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   HIS B 161 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 4.288A  pdb=" N   ALA C  33 " --> pdb=" O   GLU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 52
    Processing helix  chain 'C' and resid 67 through 76
      removed outlier: 3.528A  pdb=" N   GLU C  76 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 112
      removed outlier: 3.741A  pdb=" N   THR C 112 " --> pdb=" O   GLU C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 162
      removed outlier: 3.815A  pdb=" N   LEU C 130 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU C 145 " --> pdb=" O   GLY C 141 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP C 149 " --> pdb=" O   GLU C 145 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE C 150 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS C 161 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 580
      removed outlier: 3.853A  pdb=" N   TYR A 794 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339
    Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522
      removed outlier: 3.642A  pdb=" N   PHE A 521 " --> pdb=" O   MET A 746 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 746 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585
    Processing sheet with id=AA5, first strand: chain 'A' and resid 736 through 738
      removed outlier: 3.657A  pdb=" N   ARG A 737 " --> pdb=" O   ALA A 801 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 759
      removed outlier: 3.692A  pdb=" N   HIS A 759 " --> pdb=" O   VAL A 783 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 783 " --> pdb=" O   HIS A 759 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 765
    Processing sheet with id=AA8, first strand: chain 'A' and resid 828 through 832
      removed outlier: 3.594A  pdb=" N   VAL A 842 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ILE A 841 " --> pdb=" O   GLN A 853 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLN A 853 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 843 " --> pdb=" O   VAL A 851 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 862
      removed outlier: 4.332A  pdb=" N   ILE A 868 " --> pdb=" O   ASN A 861 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 922 through 925
      removed outlier: 6.708A  pdb=" N   ILE A 922 " --> pdb=" O   PHE A 994 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE A 996 " --> pdb=" O   ILE A 922 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   LEU A 924 " --> pdb=" O   ILE A 996 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1047 through 1048
      removed outlier: 3.845A  pdb=" N   LEU A1047 " --> pdb=" O   TRP A1063 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TRP A1063 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1070 through 1073
      removed outlier: 3.878A  pdb=" N   ARG A1071 " --> pdb=" O   VAL A1089 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A1089 " --> pdb=" O   ARG A1071 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140

    506 hydrogen bonds defined for protein.
    1449 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      10 hydrogen bonds
      20 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 4.77

  Time building geometry restraints manager: 3.84 seconds

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

  Histogram of bond lengths:
        1.20 -     1.35: 4109
        1.35 -     1.50: 4532
        1.50 -     1.66: 4415
        1.66 -     1.81: 24
        1.81 -     1.96: 41
  Bond restraints: 13121
  Sorted by residual:
  bond pdb=" SD  MET A 531 "
       pdb=" CE  MET A 531 "
    ideal  model  delta    sigma   weight residual
    1.791  1.963 -0.172 2.50e-02 1.60e+03 4.74e+01
  bond pdb=" SD  MET A 626 "
       pdb=" CE  MET A 626 "
    ideal  model  delta    sigma   weight residual
    1.791  1.963 -0.172 2.50e-02 1.60e+03 4.73e+01
  bond pdb=" CG  MET A 531 "
       pdb=" SD  MET A 531 "
    ideal  model  delta    sigma   weight residual
    1.803  1.963 -0.160 2.50e-02 1.60e+03 4.11e+01
  bond pdb=" SD  MET A 603 "
       pdb=" CE  MET A 603 "
    ideal  model  delta    sigma   weight residual
    1.791  1.951 -0.160 2.50e-02 1.60e+03 4.08e+01
  bond pdb=" CG  MET A 626 "
       pdb=" SD  MET A 626 "
    ideal  model  delta    sigma   weight residual
    1.803  1.962 -0.159 2.50e-02 1.60e+03 4.04e+01
  ... (remaining 13116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 16769
        2.34 -     4.68: 862
        4.68 -     7.01: 90
        7.01 -     9.35: 28
        9.35 -    11.69: 7
  Bond angle restraints: 17756
  Sorted by residual:
  angle pdb=" N   MET A 626 "
        pdb=" CA  MET A 626 "
        pdb=" C   MET A 626 "
      ideal   model   delta    sigma   weight residual
     113.16  105.09    8.07 1.24e+00 6.50e-01 4.23e+01
  angle pdb=" C   GLY A 477 "
        pdb=" N   LYS A 478 "
        pdb=" CA  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     121.70  133.39  -11.69 1.80e+00 3.09e-01 4.22e+01
  angle pdb=" C   PHE A 220 "
        pdb=" CA  PHE A 220 "
        pdb=" CB  PHE A 220 "
      ideal   model   delta    sigma   weight residual
     109.29  119.29  -10.00 1.82e+00 3.02e-01 3.02e+01
  angle pdb=" CA  TRP B 100 "
        pdb=" C   TRP B 100 "
        pdb=" O   TRP B 100 "
      ideal   model   delta    sigma   weight residual
     121.10  115.55    5.55 1.10e+00 8.26e-01 2.55e+01
  angle pdb=" CA  TRP C 100 "
        pdb=" C   TRP C 100 "
        pdb=" O   TRP C 100 "
      ideal   model   delta    sigma   weight residual
     121.10  115.60    5.50 1.10e+00 8.26e-01 2.50e+01
  ... (remaining 17751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.60: 7688
       35.60 -    71.19: 238
       71.19 -   106.79: 13
      106.79 -   142.38: 0
      142.38 -   177.98: 1
  Dihedral angle restraints: 7940
    sinusoidal: 3542
      harmonic: 4398
  Sorted by residual:
  dihedral pdb=" O4'   U G  16 "
           pdb=" C1'   U G  16 "
           pdb=" N1    U G  16 "
           pdb=" C2    U G  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.02  177.98     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" C   ASP A 625 "
           pdb=" N   ASP A 625 "
           pdb=" CA  ASP A 625 "
           pdb=" CB  ASP A 625 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.57   14.97     0      2.50e+00 1.60e-01 3.59e+01
  dihedral pdb=" CA  GLU A 476 "
           pdb=" C   GLU A 476 "
           pdb=" N   GLY A 477 "
           pdb=" CA  GLY A 477 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.39  -29.61     0      5.00e+00 4.00e-02 3.51e+01
  ... (remaining 7937 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1597
       0.098 -    0.196: 267
       0.196 -    0.293: 18
       0.293 -    0.391: 5
       0.391 -    0.489: 2
  Chirality restraints: 1889
  Sorted by residual:
  chirality pdb=" CA  ASP A 625 "
            pdb=" N   ASP A 625 "
            pdb=" C   ASP A 625 "
            pdb=" CB  ASP A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.98e+00
  chirality pdb=" CB  ILE A 798 "
            pdb=" CA  ILE A 798 "
            pdb=" CG1 ILE A 798 "
            pdb=" CG2 ILE A 798 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.00e+00
  chirality pdb=" CB  ILE B 113 "
            pdb=" CA  ILE B 113 "
            pdb=" CG1 ILE B 113 "
            pdb=" CG2 ILE B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.64e+00
  ... (remaining 1886 not shown)

  Planarity restraints: 2188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 102 "    0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   ASN C 102 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ASN C 102 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PHE C 103 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 128 "   -0.044 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO A 129 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 599 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.80e+00
        pdb=" C   SER A 599 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   SER A 599 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS A 600 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2185 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 266
        2.59 -     3.17: 11018
        3.17 -     3.75: 20420
        3.75 -     4.32: 26700
        4.32 -     4.90: 42382
  Nonbonded interactions: 100786
  Sorted by model distance:
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 202 "
     model   vdw
     2.015 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 201 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" OP2   A G  19 "
            pdb="MG    MG A1301 "
     model   vdw
     2.032 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 203 "
     model   vdw
     2.036 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH A1401 "
     model   vdw
     2.045 2.170
  ... (remaining 100781 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     35.300
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
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      :  0.014   0.172  13121  Z= 0.640
  Angle     :  1.162  11.689  17756  Z= 0.685
  Chirality :  0.073   0.489   1889
  Planarity :  0.007   0.065   2188
  Dihedral  : 16.981 177.976   5102
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 10.19 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.04 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.42 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    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: -4.23 (0.17), residues: 1462
  helix: -2.34 (0.15), residues: 695
  sheet: -3.03 (0.45), residues: 112
  loop : -3.24 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP C 100 
 HIS   0.008   0.002   HIS B  42 
 PHE   0.033   0.004   PHE A1161 
 TYR   0.029   0.003   TYR A 237 
 ARG   0.004   0.001   ARG A 508 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12769 (  516)
  hydrogen bonds       : angle       6.64998 ( 1469)
  covalent geometry    : bond        0.01361 (13121)
  covalent geometry    : angle       1.16157 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 359
  time to evaluate  : 1.385 
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: A   81 PHE cc_start: 0.9173 (t80) cc_final: 0.8924 (t80)
REVERT: A  142 ASN cc_start: 0.8986 (t0) cc_final: 0.8695 (t0)
REVERT: A  173 PHE cc_start: 0.9203 (t80) cc_final: 0.8996 (t80)
REVERT: A  200 HIS cc_start: 0.9264 (m-70) cc_final: 0.9020 (m-70)
REVERT: A  231 GLN cc_start: 0.9530 (pt0) cc_final: 0.8739 (pp30)
REVERT: A  256 ASN cc_start: 0.9400 (m-40) cc_final: 0.9065 (p0)
REVERT: A  325 PHE cc_start: 0.8755 (m-80) cc_final: 0.8358 (m-80)
REVERT: A  407 ASP cc_start: 0.8416 (m-30) cc_final: 0.8190 (t0)
REVERT: A  420 GLN cc_start: 0.9315 (tt0) cc_final: 0.9091 (tm-30)
REVERT: A  435 LEU cc_start: 0.9605 (tp) cc_final: 0.9219 (tt)
REVERT: A  459 LEU cc_start: 0.9348 (mt) cc_final: 0.8923 (mm)
REVERT: A  490 PHE cc_start: 0.8855 (t80) cc_final: 0.8499 (t80)
REVERT: A  498 LEU cc_start: 0.9226 (mt) cc_final: 0.8527 (mt)
REVERT: A  555 LEU cc_start: 0.9372 (tp) cc_final: 0.8911 (tt)
REVERT: A  675 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8431 (tm-30)
REVERT: A  914 LEU cc_start: 0.9523 (tp) cc_final: 0.9159 (mt)
REVERT: A 1013 LEU cc_start: 0.9050 (mp) cc_final: 0.8850 (mm)
REVERT: A 1035 MET cc_start: 0.8363 (ptm) cc_final: 0.7682 (ppp)
REVERT: A 1049 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: A 1186 ASN cc_start: 0.8612 (m-40) cc_final: 0.8398 (m110)
REVERT: A 1195 ILE cc_start: 0.9621 (mt) cc_final: 0.9393 (tp)
REVERT: B   97 PHE cc_start: 0.8225 (m-10) cc_final: 0.7792 (m-10)
REVERT: B  100 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7696 (p90)
REVERT: B  140 MET cc_start: 0.9227 (mmp) cc_final: 0.8907 (mmp)
REVERT: B  148 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8125 (mm110)
REVERT: B  152 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8615 (tptp)
REVERT: C  105 ASN cc_start: 0.8370 (m-40) cc_final: 0.8104 (m-40)
REVERT: C  108 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7930 (mm-30)
  outliers start: 33
  outliers final: 9
  residues processed: 385
  average time/residue: 0.3146
  time to fit residues: 162.8526
Evaluate side-chains
  219 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 135 optimal weight:    5.9990
   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  30 ASN
A  33 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 577 ASN
A 613 GLN
A 797 HIS
A 849 ASN
** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1186 ASN
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.080269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.054234 restraints weight = 53752.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.056393 restraints weight = 27908.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.057716 restraints weight = 18473.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13121  Z= 0.147
  Angle     :  0.661   8.849  17756  Z= 0.359
  Chirality :  0.044   0.230   1889
  Planarity :  0.004   0.053   2188
  Dihedral  : 12.018 169.318   1978
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.27 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.79 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.70 (0.20), residues: 1462
  helix: -0.96 (0.18), residues: 710
  sheet: -2.11 (0.55), residues: 93
  loop : -2.69 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 100 
 HIS   0.004   0.001   HIS B  31 
 PHE   0.024   0.002   PHE A  61 
 TYR   0.028   0.002   TYR A 840 
 ARG   0.004   0.001   ARG A 935 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  516)
  hydrogen bonds       : angle       5.16202 ( 1469)
  covalent geometry    : bond        0.00305 (13121)
  covalent geometry    : angle       0.66054 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 288
  time to evaluate  : 1.496 
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: A   13 LEU cc_start: 0.9616 (tp) cc_final: 0.9393 (tt)
REVERT: A   64 ASP cc_start: 0.9521 (t70) cc_final: 0.9178 (m-30)
REVERT: A   81 PHE cc_start: 0.9499 (t80) cc_final: 0.9263 (t80)
REVERT: A  120 LYS cc_start: 0.9316 (mppt) cc_final: 0.9008 (mmtm)
REVERT: A  147 PHE cc_start: 0.8251 (t80) cc_final: 0.7739 (t80)
REVERT: A  161 MET cc_start: 0.9467 (mtm) cc_final: 0.9051 (mtp)
REVERT: A  179 ASN cc_start: 0.9311 (m110) cc_final: 0.9076 (m110)
REVERT: A  235 ASP cc_start: 0.9177 (m-30) cc_final: 0.8920 (m-30)
REVERT: A  256 ASN cc_start: 0.9612 (m-40) cc_final: 0.9224 (p0)
REVERT: A  276 LEU cc_start: 0.9382 (mt) cc_final: 0.8647 (tp)
REVERT: A  321 LEU cc_start: 0.9813 (mt) cc_final: 0.9574 (mt)
REVERT: A  355 TRP cc_start: 0.7582 (m-90) cc_final: 0.7052 (m-10)
REVERT: A  384 ASP cc_start: 0.9608 (t0) cc_final: 0.9291 (m-30)
REVERT: A  390 LYS cc_start: 0.9644 (mmpt) cc_final: 0.9316 (pttm)
REVERT: A  407 ASP cc_start: 0.8975 (m-30) cc_final: 0.8734 (t0)
REVERT: A  420 GLN cc_start: 0.9623 (tt0) cc_final: 0.9414 (tm-30)
REVERT: A  427 LYS cc_start: 0.9716 (tmtt) cc_final: 0.9511 (tptp)
REVERT: A  435 LEU cc_start: 0.9716 (tp) cc_final: 0.9074 (tt)
REVERT: A  490 PHE cc_start: 0.9371 (t80) cc_final: 0.8811 (t80)
REVERT: A  497 LEU cc_start: 0.9813 (tp) cc_final: 0.9600 (tp)
REVERT: A  498 LEU cc_start: 0.9235 (mt) cc_final: 0.8963 (mt)
REVERT: A  531 MET cc_start: 0.8905 (mtm) cc_final: 0.8569 (mtm)
REVERT: A  671 ARG cc_start: 0.9176 (ttm110) cc_final: 0.8887 (ttm110)
REVERT: A  795 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8467 (mt-10)
REVERT: A  832 ASP cc_start: 0.8140 (t0) cc_final: 0.7809 (t0)
REVERT: A  938 VAL cc_start: 0.4157 (OUTLIER) cc_final: 0.2972 (t)
REVERT: A  971 LEU cc_start: 0.9396 (mt) cc_final: 0.8788 (tp)
REVERT: A  986 MET cc_start: 0.7989 (ppp) cc_final: 0.7634 (ppp)
REVERT: A 1035 MET cc_start: 0.8788 (ptm) cc_final: 0.7896 (ppp)
REVERT: A 1128 MET cc_start: 0.9234 (mmp) cc_final: 0.9031 (mmm)
REVERT: B   32 ASP cc_start: 0.9342 (t0) cc_final: 0.8942 (t0)
REVERT: B   36 GLN cc_start: 0.9557 (pt0) cc_final: 0.9338 (pt0)
REVERT: B   47 ASN cc_start: 0.8755 (p0) cc_final: 0.8389 (p0)
REVERT: B   58 PHE cc_start: 0.5065 (m-80) cc_final: 0.4641 (m-80)
REVERT: B   71 ASN cc_start: 0.9444 (m-40) cc_final: 0.8799 (m110)
REVERT: B  136 TYR cc_start: 0.9607 (t80) cc_final: 0.9252 (t80)
REVERT: B  145 GLU cc_start: 0.9257 (tp30) cc_final: 0.8767 (tm-30)
REVERT: B  146 LEU cc_start: 0.9586 (mt) cc_final: 0.9108 (mt)
REVERT: C   45 HIS cc_start: 0.9688 (p-80) cc_final: 0.9473 (p-80)
REVERT: C  105 ASN cc_start: 0.8892 (m-40) cc_final: 0.8068 (p0)
REVERT: C  109 LEU cc_start: 0.7620 (mt) cc_final: 0.7393 (mt)
REVERT: C  125 ASP cc_start: 0.7615 (m-30) cc_final: 0.7211 (m-30)
REVERT: C  132 TYR cc_start: 0.9418 (t80) cc_final: 0.9190 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 289
  average time/residue: 0.3015
  time to fit residues: 121.8211
Evaluate side-chains
  209 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 26 optimal weight:   40.0000
   chunk 126 optimal weight:    9.9990
   chunk 111 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 9 optimal weight:   40.0000
   chunk 99 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    6.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 944 GLN
** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  18 GLN
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.074089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.048086 restraints weight = 56699.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.049924 restraints weight = 29772.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.051085 restraints weight = 20232.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  13121  Z= 0.294
  Angle     :  0.738   9.549  17756  Z= 0.403
  Chirality :  0.046   0.254   1889
  Planarity :  0.005   0.060   2188
  Dihedral  : 11.863 171.179   1978
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.18 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.90 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.00 (0.21), residues: 1462
  helix: -0.27 (0.19), residues: 732
  sheet: -2.62 (0.54), residues: 88
  loop : -2.40 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A1218 
 HIS   0.006   0.002   HIS C  42 
 PHE   0.033   0.003   PHE A1161 
 TYR   0.049   0.002   TYR C 106 
 ARG   0.006   0.001   ARG A 833 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  516)
  hydrogen bonds       : angle       5.40048 ( 1469)
  covalent geometry    : bond        0.00599 (13121)
  covalent geometry    : angle       0.73811 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 1.519 
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: A   13 LEU cc_start: 0.9660 (tp) cc_final: 0.9459 (tt)
REVERT: A   55 ASP cc_start: 0.9148 (t0) cc_final: 0.8895 (t0)
REVERT: A   71 LEU cc_start: 0.9104 (tp) cc_final: 0.8616 (tp)
REVERT: A  162 PHE cc_start: 0.9088 (m-80) cc_final: 0.8705 (m-80)
REVERT: A  179 ASN cc_start: 0.9285 (m110) cc_final: 0.8847 (m110)
REVERT: A  192 LYS cc_start: 0.9656 (mmtm) cc_final: 0.9452 (mmtm)
REVERT: A  256 ASN cc_start: 0.9662 (m-40) cc_final: 0.9256 (p0)
REVERT: A  355 TRP cc_start: 0.8529 (m-90) cc_final: 0.7573 (m-10)
REVERT: A  383 ASP cc_start: 0.9294 (t70) cc_final: 0.8825 (t0)
REVERT: A  387 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9155 (ptpt)
REVERT: A  390 LYS cc_start: 0.9700 (mmpt) cc_final: 0.9372 (pttm)
REVERT: A  424 GLU cc_start: 0.9493 (tp30) cc_final: 0.9226 (tp30)
REVERT: A  427 LYS cc_start: 0.9784 (tmtt) cc_final: 0.9520 (tptp)
REVERT: A  487 TYR cc_start: 0.9026 (m-80) cc_final: 0.8572 (m-80)
REVERT: A  490 PHE cc_start: 0.9280 (t80) cc_final: 0.9022 (t80)
REVERT: A  497 LEU cc_start: 0.9815 (tp) cc_final: 0.9599 (tp)
REVERT: A  498 LEU cc_start: 0.9431 (mt) cc_final: 0.9204 (mt)
REVERT: A  505 ASP cc_start: 0.9109 (m-30) cc_final: 0.8894 (m-30)
REVERT: A  558 MET cc_start: 0.9048 (mpp) cc_final: 0.8485 (mpp)
REVERT: A  722 MET cc_start: 0.9022 (tpp) cc_final: 0.8741 (tpp)
REVERT: A  832 ASP cc_start: 0.8677 (t0) cc_final: 0.8273 (t0)
REVERT: A  986 MET cc_start: 0.7985 (ppp) cc_final: 0.7637 (ppp)
REVERT: A  992 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8693 (m-10)
REVERT: A 1023 ASP cc_start: 0.9298 (t0) cc_final: 0.8928 (m-30)
REVERT: A 1035 MET cc_start: 0.8865 (ptm) cc_final: 0.7810 (ppp)
REVERT: A 1128 MET cc_start: 0.9243 (mmp) cc_final: 0.8280 (tpp)
REVERT: B   36 GLN cc_start: 0.9564 (pt0) cc_final: 0.9356 (pt0)
REVERT: B   47 ASN cc_start: 0.8966 (p0) cc_final: 0.8713 (p0)
REVERT: B   94 ASP cc_start: 0.9185 (p0) cc_final: 0.8963 (p0)
REVERT: B  125 ASP cc_start: 0.9155 (p0) cc_final: 0.8634 (p0)
REVERT: B  145 GLU cc_start: 0.9268 (tp30) cc_final: 0.8990 (tp30)
REVERT: B  146 LEU cc_start: 0.9683 (mt) cc_final: 0.9388 (mt)
REVERT: B  155 ARG cc_start: 0.9331 (mmm-85) cc_final: 0.8848 (ttm-80)
REVERT: C   92 ILE cc_start: 0.6982 (mp) cc_final: 0.6630 (mp)
REVERT: C   94 ASP cc_start: 0.8422 (p0) cc_final: 0.8085 (p0)
REVERT: C  105 ASN cc_start: 0.9059 (m-40) cc_final: 0.8284 (p0)
REVERT: C  109 LEU cc_start: 0.8709 (mt) cc_final: 0.7871 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2811
  time to fit residues: 94.5101
Evaluate side-chains
  185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 1.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 26 optimal weight:   50.0000
   chunk 61 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 77 optimal weight:    9.9990
   chunk 111 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 468 ASN
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 ASN
** B  20 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 = 0.3525 r_free = 0.3525 target = 0.077197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.050966 restraints weight = 55133.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.052934 restraints weight = 29121.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.054162 restraints weight = 19754.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.5266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13121  Z= 0.127
  Angle     :  0.597   8.195  17756  Z= 0.323
  Chirality :  0.043   0.241   1889
  Planarity :  0.004   0.060   2188
  Dihedral  : 11.516 173.132   1978
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.47 (0.22), residues: 1462
  helix:  0.19 (0.20), residues: 726
  sheet: -2.31 (0.53), residues: 88
  loop : -2.17 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 100 
 HIS   0.010   0.001   HIS C  42 
 PHE   0.021   0.002   PHE A 147 
 TYR   0.017   0.001   TYR B   6 
 ARG   0.003   0.000   ARG A 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  516)
  hydrogen bonds       : angle       4.95224 ( 1469)
  covalent geometry    : bond        0.00267 (13121)
  covalent geometry    : angle       0.59727 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.596 
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: A   55 ASP cc_start: 0.9163 (t0) cc_final: 0.8759 (t0)
REVERT: A   64 ASP cc_start: 0.9531 (t0) cc_final: 0.9294 (m-30)
REVERT: A   71 LEU cc_start: 0.9041 (tp) cc_final: 0.8627 (tp)
REVERT: A  162 PHE cc_start: 0.9131 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  179 ASN cc_start: 0.9305 (m110) cc_final: 0.8963 (m110)
REVERT: A  355 TRP cc_start: 0.8512 (m-90) cc_final: 0.8127 (m-10)
REVERT: A  384 ASP cc_start: 0.9652 (t0) cc_final: 0.9310 (m-30)
REVERT: A  390 LYS cc_start: 0.9695 (mmpt) cc_final: 0.9264 (ptpp)
REVERT: A  407 ASP cc_start: 0.8861 (t70) cc_final: 0.8585 (t70)
REVERT: A  427 LYS cc_start: 0.9785 (tmtt) cc_final: 0.9505 (tptp)
REVERT: A  471 LYS cc_start: 0.9505 (mtmt) cc_final: 0.9243 (mtmm)
REVERT: A  476 GLU cc_start: 0.8641 (pm20) cc_final: 0.8226 (pp20)
REVERT: A  490 PHE cc_start: 0.9269 (t80) cc_final: 0.9026 (t80)
REVERT: A  498 LEU cc_start: 0.9216 (mt) cc_final: 0.8891 (mt)
REVERT: A  505 ASP cc_start: 0.9059 (m-30) cc_final: 0.8858 (m-30)
REVERT: A  558 MET cc_start: 0.8979 (mpp) cc_final: 0.8460 (mpp)
REVERT: A  675 GLU cc_start: 0.9166 (tp30) cc_final: 0.8811 (tm-30)
REVERT: A  832 ASP cc_start: 0.8302 (t0) cc_final: 0.7939 (t0)
REVERT: A  916 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: A  944 GLN cc_start: 0.9364 (mt0) cc_final: 0.9088 (mt0)
REVERT: A  986 MET cc_start: 0.8063 (ppp) cc_final: 0.7563 (ptm)
REVERT: A 1023 ASP cc_start: 0.9260 (t0) cc_final: 0.8912 (m-30)
REVERT: A 1035 MET cc_start: 0.8772 (ptm) cc_final: 0.7989 (ppp)
REVERT: A 1128 MET cc_start: 0.9184 (mmp) cc_final: 0.8206 (tpp)
REVERT: A 1151 ILE cc_start: 0.8607 (mm) cc_final: 0.8147 (mm)
REVERT: B   36 GLN cc_start: 0.9533 (pt0) cc_final: 0.9304 (pt0)
REVERT: B   47 ASN cc_start: 0.8851 (p0) cc_final: 0.8573 (p0)
REVERT: B  106 TYR cc_start: 0.9021 (t80) cc_final: 0.8760 (t80)
REVERT: B  145 GLU cc_start: 0.9253 (tp30) cc_final: 0.8977 (tp30)
REVERT: B  146 LEU cc_start: 0.9706 (mt) cc_final: 0.9445 (mt)
REVERT: B  155 ARG cc_start: 0.9278 (mmm-85) cc_final: 0.9010 (ttm-80)
REVERT: B  158 ASP cc_start: 0.8471 (t0) cc_final: 0.8154 (t0)
REVERT: C   52 PHE cc_start: 0.8129 (t80) cc_final: 0.7863 (t80)
REVERT: C   86 PHE cc_start: 0.8843 (p90) cc_final: 0.8422 (p90)
REVERT: C   94 ASP cc_start: 0.8620 (p0) cc_final: 0.8397 (p0)
REVERT: C   97 PHE cc_start: 0.9195 (p90) cc_final: 0.8916 (p90)
REVERT: C  105 ASN cc_start: 0.9128 (m-40) cc_final: 0.8673 (p0)
REVERT: C  109 LEU cc_start: 0.8450 (mt) cc_final: 0.7611 (mt)
REVERT: C  125 ASP cc_start: 0.8602 (p0) cc_final: 0.8338 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2824
  time to fit residues: 103.1043
Evaluate side-chains
  192 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 64 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   chunk 116 optimal weight:    7.9990
   chunk 133 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 115 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.074881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.048951 restraints weight = 56309.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.050797 restraints weight = 29610.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.051962 restraints weight = 20087.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13121  Z= 0.189
  Angle     :  0.631  10.293  17756  Z= 0.343
  Chirality :  0.043   0.215   1889
  Planarity :  0.004   0.049   2188
  Dihedral  : 11.469 172.981   1978
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.23 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.22), residues: 1462
  helix:  0.34 (0.20), residues: 723
  sheet: -2.06 (0.54), residues: 85
  loop : -2.05 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1086 
 HIS   0.010   0.001   HIS C  42 
 PHE   0.023   0.002   PHE A1161 
 TYR   0.028   0.002   TYR A 429 
 ARG   0.005   0.001   ARG C  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  516)
  hydrogen bonds       : angle       5.06401 ( 1469)
  covalent geometry    : bond        0.00394 (13121)
  covalent geometry    : angle       0.63077 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 1.535 
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: A   55 ASP cc_start: 0.9131 (t0) cc_final: 0.8919 (t0)
REVERT: A   64 ASP cc_start: 0.9585 (t0) cc_final: 0.9328 (m-30)
REVERT: A   71 LEU cc_start: 0.8928 (tp) cc_final: 0.8483 (tp)
REVERT: A  120 LYS cc_start: 0.9214 (mppt) cc_final: 0.8957 (mmtm)
REVERT: A  162 PHE cc_start: 0.9234 (m-80) cc_final: 0.8422 (m-80)
REVERT: A  179 ASN cc_start: 0.9251 (m110) cc_final: 0.8967 (m110)
REVERT: A  328 PHE cc_start: 0.9379 (t80) cc_final: 0.9175 (t80)
REVERT: A  390 LYS cc_start: 0.9702 (mmpt) cc_final: 0.9278 (ptpp)
REVERT: A  407 ASP cc_start: 0.8969 (t70) cc_final: 0.8708 (t70)
REVERT: A  427 LYS cc_start: 0.9813 (tmtt) cc_final: 0.9538 (tptp)
REVERT: A  461 ASP cc_start: 0.9484 (t0) cc_final: 0.9172 (p0)
REVERT: A  471 LYS cc_start: 0.9534 (mtmt) cc_final: 0.9334 (mtmt)
REVERT: A  476 GLU cc_start: 0.8887 (pm20) cc_final: 0.8674 (pp20)
REVERT: A  478 LYS cc_start: 0.9549 (ptpp) cc_final: 0.9130 (mtmm)
REVERT: A  487 TYR cc_start: 0.8920 (m-80) cc_final: 0.8642 (m-80)
REVERT: A  490 PHE cc_start: 0.9378 (t80) cc_final: 0.8915 (t80)
REVERT: A  498 LEU cc_start: 0.9357 (mt) cc_final: 0.9098 (mt)
REVERT: A  531 MET cc_start: 0.9057 (mtm) cc_final: 0.8854 (mtm)
REVERT: A  558 MET cc_start: 0.9083 (mpp) cc_final: 0.8614 (mpp)
REVERT: A  675 GLU cc_start: 0.9231 (tp30) cc_final: 0.8908 (tm-30)
REVERT: A  832 ASP cc_start: 0.8604 (t0) cc_final: 0.8115 (t0)
REVERT: A  916 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8556 (tm-30)
REVERT: A  986 MET cc_start: 0.7899 (ppp) cc_final: 0.7508 (ptm)
REVERT: A 1023 ASP cc_start: 0.9332 (t0) cc_final: 0.9042 (m-30)
REVERT: A 1035 MET cc_start: 0.8786 (ptm) cc_final: 0.7995 (ppp)
REVERT: A 1128 MET cc_start: 0.9189 (mmp) cc_final: 0.8217 (tpp)
REVERT: B   36 GLN cc_start: 0.9553 (pt0) cc_final: 0.9338 (pt0)
REVERT: B   71 ASN cc_start: 0.9469 (m-40) cc_final: 0.8683 (m-40)
REVERT: B   94 ASP cc_start: 0.8846 (p0) cc_final: 0.8640 (p0)
REVERT: B  106 TYR cc_start: 0.9002 (t80) cc_final: 0.8750 (t80)
REVERT: B  136 TYR cc_start: 0.9447 (t80) cc_final: 0.9131 (t80)
REVERT: B  145 GLU cc_start: 0.9316 (tp30) cc_final: 0.9012 (tp30)
REVERT: B  146 LEU cc_start: 0.9730 (mt) cc_final: 0.9419 (mt)
REVERT: B  155 ARG cc_start: 0.9302 (mmm-85) cc_final: 0.8982 (ttm170)
REVERT: B  158 ASP cc_start: 0.8563 (t0) cc_final: 0.8287 (t0)
REVERT: C   45 HIS cc_start: 0.9749 (p-80) cc_final: 0.9539 (p-80)
REVERT: C   86 PHE cc_start: 0.8745 (p90) cc_final: 0.8356 (p90)
REVERT: C   94 ASP cc_start: 0.8649 (p0) cc_final: 0.8181 (p0)
REVERT: C  105 ASN cc_start: 0.9167 (m-40) cc_final: 0.8822 (p0)
REVERT: C  109 LEU cc_start: 0.9030 (mt) cc_final: 0.7958 (mt)
REVERT: C  144 GLU cc_start: 0.9500 (tp30) cc_final: 0.9193 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 229
  average time/residue: 0.2726
  time to fit residues: 87.5757
Evaluate side-chains
  186 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 111 optimal weight:   20.0000
   chunk 100 optimal weight:    4.9990
   chunk 21 optimal weight:   30.0000
   chunk 145 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 127 optimal weight:    0.0670
   chunk 107 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    5.2126

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 ASN
A 279 GLN
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 ASN
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.074003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.048068 restraints weight = 57441.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.049915 restraints weight = 29965.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.051060 restraints weight = 20252.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.5943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13121  Z= 0.221
  Angle     :  0.646   9.387  17756  Z= 0.353
  Chirality :  0.044   0.200   1889
  Planarity :  0.004   0.048   2188
  Dihedral  : 11.495 172.455   1978
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.75 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.32 (0.22), residues: 1462
  helix:  0.30 (0.19), residues: 724
  sheet: -2.39 (0.48), residues: 97
  loop : -2.02 (0.25), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A1218 
 HIS   0.010   0.001   HIS C  42 
 PHE   0.024   0.002   PHE A1161 
 TYR   0.021   0.002   TYR A 494 
 ARG   0.005   0.001   ARG C  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  516)
  hydrogen bonds       : angle       5.16492 ( 1469)
  covalent geometry    : bond        0.00458 (13121)
  covalent geometry    : angle       0.64649 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 1.525 
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: A   64 ASP cc_start: 0.9571 (t0) cc_final: 0.9311 (m-30)
REVERT: A   71 LEU cc_start: 0.8830 (tp) cc_final: 0.8391 (tp)
REVERT: A  116 LYS cc_start: 0.9361 (mptt) cc_final: 0.9135 (mmtt)
REVERT: A  120 LYS cc_start: 0.9309 (mppt) cc_final: 0.9005 (mmtm)
REVERT: A  161 MET cc_start: 0.9448 (mtm) cc_final: 0.9232 (mtp)
REVERT: A  328 PHE cc_start: 0.9386 (t80) cc_final: 0.9153 (t80)
REVERT: A  355 TRP cc_start: 0.8768 (m-10) cc_final: 0.8198 (m-10)
REVERT: A  390 LYS cc_start: 0.9703 (mmpt) cc_final: 0.9298 (ptpt)
REVERT: A  407 ASP cc_start: 0.8991 (t70) cc_final: 0.8744 (t70)
REVERT: A  427 LYS cc_start: 0.9833 (tmtt) cc_final: 0.9555 (tptp)
REVERT: A  478 LYS cc_start: 0.9526 (ptpp) cc_final: 0.9204 (ptpp)
REVERT: A  487 TYR cc_start: 0.8926 (m-80) cc_final: 0.8562 (m-80)
REVERT: A  490 PHE cc_start: 0.9342 (t80) cc_final: 0.8789 (t80)
REVERT: A  531 MET cc_start: 0.9025 (mtm) cc_final: 0.8781 (mtm)
REVERT: A  707 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9224 (mtmm)
REVERT: A  722 MET cc_start: 0.9008 (tpp) cc_final: 0.8683 (tpp)
REVERT: A  832 ASP cc_start: 0.8617 (t0) cc_final: 0.8169 (t0)
REVERT: A  986 MET cc_start: 0.7893 (ppp) cc_final: 0.7623 (ptm)
REVERT: A 1035 MET cc_start: 0.8814 (ptm) cc_final: 0.8056 (ppp)
REVERT: A 1128 MET cc_start: 0.9203 (mmp) cc_final: 0.8230 (tpp)
REVERT: A 1135 LEU cc_start: 0.9619 (mm) cc_final: 0.9388 (mm)
REVERT: B   71 ASN cc_start: 0.9462 (m-40) cc_final: 0.8683 (m-40)
REVERT: B  106 TYR cc_start: 0.8926 (t80) cc_final: 0.8657 (t80)
REVERT: B  145 GLU cc_start: 0.9306 (tp30) cc_final: 0.9015 (tp30)
REVERT: B  146 LEU cc_start: 0.9755 (mt) cc_final: 0.9437 (mt)
REVERT: B  155 ARG cc_start: 0.9238 (mmm-85) cc_final: 0.8917 (ttm170)
REVERT: C   45 HIS cc_start: 0.9767 (p-80) cc_final: 0.9513 (p-80)
REVERT: C   86 PHE cc_start: 0.8699 (p90) cc_final: 0.8293 (p90)
REVERT: C   94 ASP cc_start: 0.8788 (p0) cc_final: 0.8302 (p0)
REVERT: C  105 ASN cc_start: 0.9245 (m-40) cc_final: 0.9030 (p0)
REVERT: C  109 LEU cc_start: 0.9089 (mt) cc_final: 0.8685 (mt)
REVERT: C  144 GLU cc_start: 0.9471 (tp30) cc_final: 0.9157 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 228
  average time/residue: 0.2840
  time to fit residues: 91.3351
Evaluate side-chains
  172 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 35 optimal weight:   30.0000
   chunk 137 optimal weight:   50.0000
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 144 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 797 HIS
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
B  47 ASN
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.076983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.051323 restraints weight = 54303.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.053331 restraints weight = 28371.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.054566 restraints weight = 19033.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.6113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13121  Z= 0.119
  Angle     :  0.610   9.453  17756  Z= 0.325
  Chirality :  0.043   0.220   1889
  Planarity :  0.003   0.038   2188
  Dihedral  : 11.338 173.856   1978
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.11 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.09 (0.22), residues: 1462
  helix:  0.40 (0.20), residues: 721
  sheet: -1.95 (0.53), residues: 85
  loop : -1.86 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.003   TRP A 355 
 HIS   0.011   0.001   HIS C  42 
 PHE   0.026   0.001   PHE A 931 
 TYR   0.018   0.001   TYR A1068 
 ARG   0.004   0.000   ARG C  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  516)
  hydrogen bonds       : angle       4.92568 ( 1469)
  covalent geometry    : bond        0.00252 (13121)
  covalent geometry    : angle       0.61020 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 1.444 
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: A   64 ASP cc_start: 0.9480 (t0) cc_final: 0.9244 (m-30)
REVERT: A   71 LEU cc_start: 0.8839 (tp) cc_final: 0.8373 (tp)
REVERT: A  116 LYS cc_start: 0.9347 (mptt) cc_final: 0.9126 (mmtt)
REVERT: A  120 LYS cc_start: 0.9291 (mppt) cc_final: 0.8986 (mmtm)
REVERT: A  178 GLU cc_start: 0.9080 (pm20) cc_final: 0.8616 (pm20)
REVERT: A  179 ASN cc_start: 0.8859 (m110) cc_final: 0.7633 (m110)
REVERT: A  200 HIS cc_start: 0.9745 (m-70) cc_final: 0.9544 (m90)
REVERT: A  328 PHE cc_start: 0.9365 (t80) cc_final: 0.9102 (t80)
REVERT: A  384 ASP cc_start: 0.9690 (t0) cc_final: 0.9434 (p0)
REVERT: A  407 ASP cc_start: 0.8859 (t70) cc_final: 0.8599 (t70)
REVERT: A  427 LYS cc_start: 0.9832 (tmtt) cc_final: 0.9533 (tptp)
REVERT: A  487 TYR cc_start: 0.8873 (m-80) cc_final: 0.8618 (m-80)
REVERT: A  490 PHE cc_start: 0.9355 (t80) cc_final: 0.8736 (t80)
REVERT: A  498 LEU cc_start: 0.9241 (mt) cc_final: 0.8858 (mt)
REVERT: A  505 ASP cc_start: 0.9169 (m-30) cc_final: 0.8951 (m-30)
REVERT: A  558 MET cc_start: 0.9098 (mpp) cc_final: 0.8559 (mpp)
REVERT: A  707 LYS cc_start: 0.9475 (mtpt) cc_final: 0.9249 (mtmm)
REVERT: A  832 ASP cc_start: 0.8424 (t0) cc_final: 0.8090 (t0)
REVERT: A  952 ASP cc_start: 0.8955 (m-30) cc_final: 0.8630 (m-30)
REVERT: A  986 MET cc_start: 0.7869 (ppp) cc_final: 0.7173 (ptm)
REVERT: A 1023 ASP cc_start: 0.9287 (t0) cc_final: 0.9029 (m-30)
REVERT: A 1035 MET cc_start: 0.8732 (ptm) cc_final: 0.7988 (ppp)
REVERT: A 1128 MET cc_start: 0.9132 (mmp) cc_final: 0.8197 (tpp)
REVERT: A 1151 ILE cc_start: 0.8478 (mm) cc_final: 0.8016 (mm)
REVERT: B   71 ASN cc_start: 0.9421 (m-40) cc_final: 0.8699 (m110)
REVERT: B  106 TYR cc_start: 0.8919 (t80) cc_final: 0.8711 (t80)
REVERT: B  129 GLU cc_start: 0.9354 (pt0) cc_final: 0.9014 (pp20)
REVERT: B  130 LEU cc_start: 0.9584 (mt) cc_final: 0.8802 (mt)
REVERT: B  145 GLU cc_start: 0.9244 (tp30) cc_final: 0.8946 (tp30)
REVERT: B  146 LEU cc_start: 0.9714 (mt) cc_final: 0.9299 (mt)
REVERT: B  155 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.9008 (ttm170)
REVERT: B  164 GLN cc_start: 0.9554 (mm-40) cc_final: 0.9343 (mm-40)
REVERT: C   45 HIS cc_start: 0.9776 (p-80) cc_final: 0.9520 (p-80)
REVERT: C  144 GLU cc_start: 0.9378 (tp30) cc_final: 0.9104 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2779
  time to fit residues: 91.7885
Evaluate side-chains
  190 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0070
   chunk 68 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 143 optimal weight:    0.3980
   chunk 6 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 HIS
C 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.078233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.052475 restraints weight = 54610.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.054438 restraints weight = 28938.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055651 restraints weight = 19513.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.6366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.086  13121  Z= 0.115
  Angle     :  0.607   9.066  17756  Z= 0.321
  Chirality :  0.043   0.215   1889
  Planarity :  0.003   0.039   2188
  Dihedral  : 11.251 174.894   1978
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.02 (0.22), residues: 1462
  helix:  0.38 (0.19), residues: 728
  sheet: -1.68 (0.56), residues: 85
  loop : -1.77 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 355 
 HIS   0.011   0.001   HIS C  42 
 PHE   0.016   0.001   PHE A1149 
 TYR   0.022   0.001   TYR C 106 
 ARG   0.005   0.000   ARG A 935 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  516)
  hydrogen bonds       : angle       4.80036 ( 1469)
  covalent geometry    : bond        0.00249 (13121)
  covalent geometry    : angle       0.60723 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.433 
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: A   64 ASP cc_start: 0.9490 (t0) cc_final: 0.9248 (m-30)
REVERT: A   71 LEU cc_start: 0.8851 (tp) cc_final: 0.8392 (tp)
REVERT: A  116 LYS cc_start: 0.9375 (mptt) cc_final: 0.9137 (mmtt)
REVERT: A  120 LYS cc_start: 0.9240 (mppt) cc_final: 0.8993 (mmtm)
REVERT: A  187 MET cc_start: 0.9262 (mtp) cc_final: 0.9045 (mtp)
REVERT: A  328 PHE cc_start: 0.9350 (t80) cc_final: 0.9075 (t80)
REVERT: A  390 LYS cc_start: 0.9701 (mmpt) cc_final: 0.9218 (ptpp)
REVERT: A  407 ASP cc_start: 0.8795 (t70) cc_final: 0.8536 (t70)
REVERT: A  427 LYS cc_start: 0.9822 (tmtt) cc_final: 0.9522 (tptp)
REVERT: A  487 TYR cc_start: 0.8924 (m-80) cc_final: 0.8714 (m-80)
REVERT: A  490 PHE cc_start: 0.9421 (t80) cc_final: 0.8810 (t80)
REVERT: A  498 LEU cc_start: 0.9212 (mt) cc_final: 0.8976 (mt)
REVERT: A  505 ASP cc_start: 0.9148 (m-30) cc_final: 0.8934 (m-30)
REVERT: A  535 ASP cc_start: 0.9052 (m-30) cc_final: 0.8708 (t70)
REVERT: A  558 MET cc_start: 0.9127 (mpp) cc_final: 0.8570 (mpp)
REVERT: A  703 GLN cc_start: 0.8766 (tt0) cc_final: 0.8315 (tm-30)
REVERT: A  707 LYS cc_start: 0.9466 (mtpt) cc_final: 0.9143 (mtmm)
REVERT: A  832 ASP cc_start: 0.8283 (t0) cc_final: 0.7863 (t0)
REVERT: A  952 ASP cc_start: 0.8913 (m-30) cc_final: 0.8533 (m-30)
REVERT: A  986 MET cc_start: 0.7861 (ppp) cc_final: 0.7261 (ptm)
REVERT: A 1003 LYS cc_start: 0.9233 (mtmm) cc_final: 0.8892 (mppt)
REVERT: A 1023 ASP cc_start: 0.9324 (t0) cc_final: 0.9080 (m-30)
REVERT: A 1035 MET cc_start: 0.8661 (ptm) cc_final: 0.7936 (ppp)
REVERT: A 1128 MET cc_start: 0.9073 (mmp) cc_final: 0.8179 (tpp)
REVERT: A 1151 ILE cc_start: 0.8262 (mm) cc_final: 0.7825 (mm)
REVERT: A 1186 ASN cc_start: 0.8888 (m110) cc_final: 0.8607 (m110)
REVERT: B   71 ASN cc_start: 0.9416 (m-40) cc_final: 0.8714 (m110)
REVERT: B  106 TYR cc_start: 0.8944 (t80) cc_final: 0.8739 (t80)
REVERT: B  129 GLU cc_start: 0.9379 (pt0) cc_final: 0.8937 (pp20)
REVERT: B  130 LEU cc_start: 0.9535 (mt) cc_final: 0.8714 (mt)
REVERT: B  136 TYR cc_start: 0.9436 (t80) cc_final: 0.8927 (t80)
REVERT: B  145 GLU cc_start: 0.9256 (tp30) cc_final: 0.8954 (tp30)
REVERT: B  146 LEU cc_start: 0.9693 (mt) cc_final: 0.9234 (mt)
REVERT: B  155 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.9089 (ttt180)
REVERT: C   45 HIS cc_start: 0.9783 (p-80) cc_final: 0.9526 (p-80)
REVERT: C   86 PHE cc_start: 0.8793 (p90) cc_final: 0.8578 (p90)
REVERT: C  144 GLU cc_start: 0.9272 (tp30) cc_final: 0.9065 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2777
  time to fit residues: 93.2763
Evaluate side-chains
  202 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 121 optimal weight:   10.0000
   chunk 92 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 147 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   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  30 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 797 HIS
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
B 164 GLN
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.077017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.050805 restraints weight = 55428.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.052721 restraints weight = 29503.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.053952 restraints weight = 20133.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.6478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  13121  Z= 0.145
  Angle     :  0.615   9.142  17756  Z= 0.331
  Chirality :  0.043   0.211   1889
  Planarity :  0.003   0.037   2188
  Dihedral  : 11.275 174.834   1978
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.59 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.90 (0.22), residues: 1462
  helix:  0.47 (0.20), residues: 728
  sheet: -1.73 (0.54), residues: 85
  loop : -1.68 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B  84 
 HIS   0.004   0.001   HIS C  42 
 PHE   0.016   0.001   PHE A1161 
 TYR   0.037   0.001   TYR A 840 
 ARG   0.003   0.000   ARG A1144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03083 (  516)
  hydrogen bonds       : angle       4.86384 ( 1469)
  covalent geometry    : bond        0.00318 (13121)
  covalent geometry    : angle       0.61513 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 1.627 
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: A   64 ASP cc_start: 0.9526 (t0) cc_final: 0.9290 (m-30)
REVERT: A   71 LEU cc_start: 0.8871 (tp) cc_final: 0.8393 (tp)
REVERT: A  187 MET cc_start: 0.9317 (mtp) cc_final: 0.9080 (mtp)
REVERT: A  325 PHE cc_start: 0.9311 (m-80) cc_final: 0.8827 (m-80)
REVERT: A  328 PHE cc_start: 0.9375 (t80) cc_final: 0.8882 (t80)
REVERT: A  390 LYS cc_start: 0.9712 (mmpt) cc_final: 0.9209 (ptpp)
REVERT: A  407 ASP cc_start: 0.8836 (t70) cc_final: 0.8589 (t70)
REVERT: A  427 LYS cc_start: 0.9829 (tmtt) cc_final: 0.9546 (tptp)
REVERT: A  490 PHE cc_start: 0.9355 (t80) cc_final: 0.8745 (t80)
REVERT: A  498 LEU cc_start: 0.9227 (mt) cc_final: 0.9002 (mt)
REVERT: A  505 ASP cc_start: 0.9182 (m-30) cc_final: 0.8978 (m-30)
REVERT: A  707 LYS cc_start: 0.9478 (mtpt) cc_final: 0.9116 (mtmm)
REVERT: A  832 ASP cc_start: 0.8440 (t0) cc_final: 0.7999 (t0)
REVERT: A  952 ASP cc_start: 0.8891 (m-30) cc_final: 0.8601 (m-30)
REVERT: A  986 MET cc_start: 0.7770 (ppp) cc_final: 0.7232 (ptm)
REVERT: A 1035 MET cc_start: 0.8719 (ptm) cc_final: 0.8053 (ppp)
REVERT: A 1128 MET cc_start: 0.9079 (mmp) cc_final: 0.8182 (tpp)
REVERT: A 1151 ILE cc_start: 0.8551 (mm) cc_final: 0.8013 (mm)
REVERT: A 1186 ASN cc_start: 0.8825 (m110) cc_final: 0.8480 (m110)
REVERT: B   32 ASP cc_start: 0.9263 (t0) cc_final: 0.8672 (t0)
REVERT: B   36 GLN cc_start: 0.9542 (pt0) cc_final: 0.9172 (pm20)
REVERT: B   71 ASN cc_start: 0.9404 (m-40) cc_final: 0.8604 (m110)
REVERT: B  129 GLU cc_start: 0.9381 (pt0) cc_final: 0.8993 (pp20)
REVERT: B  130 LEU cc_start: 0.9562 (mt) cc_final: 0.8732 (mt)
REVERT: B  136 TYR cc_start: 0.9458 (t80) cc_final: 0.8910 (t80)
REVERT: B  145 GLU cc_start: 0.9245 (tp30) cc_final: 0.8973 (tp30)
REVERT: B  146 LEU cc_start: 0.9650 (mt) cc_final: 0.9323 (mt)
REVERT: B  155 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.9020 (ttm170)
REVERT: C   45 HIS cc_start: 0.9783 (p-80) cc_final: 0.9514 (p-80)
REVERT: C   86 PHE cc_start: 0.8788 (p90) cc_final: 0.8453 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.3009
  time to fit residues: 98.0107
Evaluate side-chains
  194 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 148 optimal weight:   40.0000
   chunk 53 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 70 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0000
   overall best weight:    3.3992

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  63 ASN
A 145 ASN
A 238 ASN
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
B 164 GLN
C  91 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.075482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.049633 restraints weight = 54841.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.051589 restraints weight = 28812.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.052802 restraints weight = 19409.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.6604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  13121  Z= 0.167
  Angle     :  0.641   8.905  17756  Z= 0.348
  Chirality :  0.045   0.233   1889
  Planarity :  0.003   0.037   2188
  Dihedral  : 11.320 174.612   1978
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.22), residues: 1462
  helix:  0.42 (0.19), residues: 726
  sheet: -1.94 (0.51), residues: 90
  loop : -1.62 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  84 
 HIS   0.012   0.001   HIS C  42 
 PHE   0.017   0.002   PHE A1161 
 TYR   0.040   0.002   TYR A 840 
 ARG   0.004   0.000   ARG C  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  516)
  hydrogen bonds       : angle       5.05511 ( 1469)
  covalent geometry    : bond        0.00367 (13121)
  covalent geometry    : angle       0.64068 (17756)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 215
  time to evaluate  : 1.502 
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: A   71 LEU cc_start: 0.8892 (tp) cc_final: 0.8434 (tp)
REVERT: A  116 LYS cc_start: 0.9432 (mptt) cc_final: 0.9217 (mmtt)
REVERT: A  179 ASN cc_start: 0.9252 (m110) cc_final: 0.8934 (m110)
REVERT: A  325 PHE cc_start: 0.9352 (m-80) cc_final: 0.8874 (m-80)
REVERT: A  328 PHE cc_start: 0.9412 (t80) cc_final: 0.8876 (t80)
REVERT: A  390 LYS cc_start: 0.9695 (mmpt) cc_final: 0.9236 (ptpp)
REVERT: A  407 ASP cc_start: 0.8848 (t70) cc_final: 0.8608 (t70)
REVERT: A  427 LYS cc_start: 0.9837 (tmtt) cc_final: 0.9556 (tptp)
REVERT: A  490 PHE cc_start: 0.9401 (t80) cc_final: 0.8735 (t80)
REVERT: A  498 LEU cc_start: 0.9279 (mt) cc_final: 0.9049 (mt)
REVERT: A  505 ASP cc_start: 0.9249 (m-30) cc_final: 0.9026 (m-30)
REVERT: A  832 ASP cc_start: 0.8537 (t0) cc_final: 0.8076 (t0)
REVERT: A  842 VAL cc_start: 0.9651 (t) cc_final: 0.9373 (m)
REVERT: A  952 ASP cc_start: 0.8909 (m-30) cc_final: 0.8627 (m-30)
REVERT: A  986 MET cc_start: 0.7589 (ppp) cc_final: 0.6985 (ptm)
REVERT: A 1035 MET cc_start: 0.8802 (ptm) cc_final: 0.8143 (ppp)
REVERT: A 1128 MET cc_start: 0.9039 (mmp) cc_final: 0.8332 (tpp)
REVERT: A 1186 ASN cc_start: 0.8816 (m110) cc_final: 0.8472 (m110)
REVERT: B   20 ASN cc_start: 0.8849 (m110) cc_final: 0.8039 (m110)
REVERT: B   71 ASN cc_start: 0.9435 (m-40) cc_final: 0.8535 (m110)
REVERT: B   82 ILE cc_start: 0.8637 (mp) cc_final: 0.8406 (tp)
REVERT: B  145 GLU cc_start: 0.9293 (tp30) cc_final: 0.8971 (tp30)
REVERT: B  146 LEU cc_start: 0.9687 (mt) cc_final: 0.9339 (mt)
REVERT: B  155 ARG cc_start: 0.9309 (mmm-85) cc_final: 0.8949 (ttt90)
  outliers start: 2
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2745
  time to fit residues: 84.1881
Evaluate side-chains
  180 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 136 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 106 optimal weight:    7.9990
   chunk 8 optimal weight:    0.4980
   chunk 91 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 19 optimal weight:   30.0000
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A 238 ASN
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 797 HIS
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
B 164 GLN
C  91 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.074736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.048943 restraints weight = 55316.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.050845 restraints weight = 29108.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.052038 restraints weight = 19592.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.6776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13121  Z= 0.186
  Angle     :  0.655   8.380  17756  Z= 0.355
  Chirality :  0.045   0.247   1889
  Planarity :  0.004   0.056   2188
  Dihedral  : 11.347 174.175   1978
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.37 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.89 (0.22), residues: 1462
  helix:  0.40 (0.19), residues: 726
  sheet: -2.05 (0.50), residues: 91
  loop : -1.50 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  84 
 HIS   0.013   0.002   HIS C  42 
 PHE   0.019   0.002   PHE A1161 
 TYR   0.039   0.002   TYR A 840 
 ARG   0.004   0.001   ARG C  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  516)
  hydrogen bonds       : angle       5.19500 ( 1469)
  covalent geometry    : bond        0.00397 (13121)
  covalent geometry    : angle       0.65542 (17756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4793.93 seconds
wall clock time: 84 minutes 4.76 seconds (5044.76 seconds total)