Starting phenix.real_space_refine
on Wed Mar  4 10:31:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_0446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_0446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_0446.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_0446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nmc_0446/03_2026/6nmc_0446.map"
  }
  resolution = 4.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.73, per 1000 atoms: 0.21
  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: 1.04
  Conformation dependent library (CDL) restraints added in 512.5 milliseconds
  

  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: 1.56
  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: 2.07

  Time building geometry restraints manager: 1.38 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:             0.290
  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:          0.200
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     13.140
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.890
-------------------------------------------------------------------------------
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 : 20.03
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG A 508 
 TYR   0.029   0.003   TYR A 237 
 PHE   0.033   0.004   PHE A1161 
 TRP   0.037   0.003   TRP C 100 
 HIS   0.008   0.002   HIS B  42 

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

*********************** 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  : 0.514 
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: 0.8995 (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: 0.9064 (p0)
REVERT: A  325 PHE cc_start: 0.8755 (m-80) cc_final: 0.8357 (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: 0.8910 (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: 0.8839 (mm-40) cc_final: 0.8125 (mm110)
REVERT: B  152 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8616 (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: 0.1328
  time to fit residues: 69.5245
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  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    4.0026

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 849 ASN
** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
A 873 HIS
** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1186 ASN
B  18 GLN
** 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.077801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.051521 restraints weight = 55455.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.053521 restraints weight = 29369.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.054794 restraints weight = 19793.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.055578 restraints weight = 15438.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.056024 restraints weight = 13262.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13121  Z= 0.200
  Angle     :  0.692   9.160  17756  Z= 0.377
  Chirality :  0.045   0.232   1889
  Planarity :  0.004   0.052   2188
  Dihedral  : 12.051 169.356   1978
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.81 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.16 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.20), residues: 1462
  helix: -0.87 (0.18), residues: 718
  sheet: -2.71 (0.48), residues: 103
  loop : -2.64 (0.23), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 883 
 TYR   0.031   0.002   TYR A 840 
 PHE   0.022   0.002   PHE A  61 
 TRP   0.039   0.003   TRP B 100 
 HIS   0.005   0.001   HIS A 797 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (13121)
  covalent geometry    : angle       0.69175 (17756)
  hydrogen bonds       : bond        0.04108 (  516)
  hydrogen bonds       : angle       5.24477 ( 1469)

*********************** 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
  268 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 266
  time to evaluate  : 0.505 
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: A   13 LEU cc_start: 0.9697 (tp) cc_final: 0.9463 (tt)
REVERT: A   81 PHE cc_start: 0.9486 (t80) cc_final: 0.9275 (t80)
REVERT: A  120 LYS cc_start: 0.9338 (mppt) cc_final: 0.9055 (mmtm)
REVERT: A  161 MET cc_start: 0.9448 (mtm) cc_final: 0.9069 (mtp)
REVERT: A  179 ASN cc_start: 0.9286 (m110) cc_final: 0.8965 (m110)
REVERT: A  350 ASP cc_start: 0.9314 (t0) cc_final: 0.9077 (t0)
REVERT: A  355 TRP cc_start: 0.7914 (m-90) cc_final: 0.7218 (m-10)
REVERT: A  384 ASP cc_start: 0.9594 (t0) cc_final: 0.9270 (m-30)
REVERT: A  386 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8918 (mmm-85)
REVERT: A  390 LYS cc_start: 0.9658 (mmpt) cc_final: 0.9268 (ptpp)
REVERT: A  407 ASP cc_start: 0.9002 (m-30) cc_final: 0.8796 (t0)
REVERT: A  427 LYS cc_start: 0.9730 (tmtt) cc_final: 0.9498 (tptp)
REVERT: A  490 PHE cc_start: 0.9332 (t80) cc_final: 0.8955 (t80)
REVERT: A  498 LEU cc_start: 0.9266 (mt) cc_final: 0.8965 (mt)
REVERT: A  531 MET cc_start: 0.8979 (mtm) cc_final: 0.8723 (mtm)
REVERT: A  671 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8852 (ttm110)
REVERT: A  675 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8641 (tm-30)
REVERT: A  795 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8447 (mt-10)
REVERT: A  832 ASP cc_start: 0.8364 (t0) cc_final: 0.8019 (t0)
REVERT: A  938 VAL cc_start: 0.4654 (OUTLIER) cc_final: 0.3446 (t)
REVERT: A  939 GLU cc_start: 0.7415 (mp0) cc_final: 0.6948 (mp0)
REVERT: A  971 LEU cc_start: 0.9436 (mt) cc_final: 0.9045 (mp)
REVERT: A  986 MET cc_start: 0.8076 (ppp) cc_final: 0.7649 (ppp)
REVERT: A 1035 MET cc_start: 0.8881 (ptm) cc_final: 0.7845 (ppp)
REVERT: B   36 GLN cc_start: 0.9553 (pt0) cc_final: 0.9319 (pt0)
REVERT: B   47 ASN cc_start: 0.8842 (p0) cc_final: 0.8503 (p0)
REVERT: B   71 ASN cc_start: 0.9443 (m-40) cc_final: 0.8910 (m-40)
REVERT: B   84 TRP cc_start: 0.9258 (m100) cc_final: 0.9033 (m100)
REVERT: B  100 TRP cc_start: 0.8146 (p90) cc_final: 0.7872 (p90)
REVERT: B  106 TYR cc_start: 0.8995 (t80) cc_final: 0.8774 (t80)
REVERT: B  136 TYR cc_start: 0.9638 (t80) cc_final: 0.9271 (t80)
REVERT: B  145 GLU cc_start: 0.9238 (tp30) cc_final: 0.8946 (tp30)
REVERT: B  146 LEU cc_start: 0.9603 (mt) cc_final: 0.9268 (mt)
REVERT: C   45 HIS cc_start: 0.9698 (p-80) cc_final: 0.9480 (p-80)
REVERT: C  105 ASN cc_start: 0.8962 (m-40) cc_final: 0.8025 (p0)
REVERT: C  125 ASP cc_start: 0.7778 (m-30) cc_final: 0.7382 (m-30)
REVERT: C  132 TYR cc_start: 0.9430 (t80) cc_final: 0.9224 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 268
  average time/residue: 0.1246
  time to fit residues: 46.6509
Evaluate side-chains
  204 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 39 optimal weight:   40.0000
   chunk 98 optimal weight:    9.9990
   chunk 104 optimal weight:    2.9990
   chunk 100 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 117 optimal weight:    0.0470
   chunk 76 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0170
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.4122

-------------------------------------------------------------------------------
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 142 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
A 468 ASN
A 797 HIS
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 944 GLN
A1136 GLN
A1139 ASN
** B  20 ASN ** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.077953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.051857 restraints weight = 55507.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.053879 restraints weight = 28624.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.055056 restraints weight = 19073.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.055917 restraints weight = 14976.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.056375 restraints weight = 12811.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13121  Z= 0.140
  Angle     :  0.605   8.969  17756  Z= 0.330
  Chirality :  0.043   0.238   1889
  Planarity :  0.004   0.062   2188
  Dihedral  : 11.685 171.149   1978
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.13 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.09 %
    Favored  : 95.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.22), residues: 1462
  helix: -0.09 (0.19), residues: 717
  sheet: -2.54 (0.50), residues: 93
  loop : -2.26 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  98 
 TYR   0.039   0.002   TYR C 106 
 PHE   0.025   0.002   PHE A1161 
 TRP   0.021   0.002   TRP A1086 
 HIS   0.003   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13121)
  covalent geometry    : angle       0.60513 (17756)
  hydrogen bonds       : bond        0.03421 (  516)
  hydrogen bonds       : angle       4.96511 ( 1469)

*********************** 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
  258 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 0.480 
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: A   13 LEU cc_start: 0.9603 (tp) cc_final: 0.9372 (tt)
REVERT: A   62 ILE cc_start: 0.9655 (mm) cc_final: 0.9369 (pt)
REVERT: A   64 ASP cc_start: 0.9483 (t70) cc_final: 0.9216 (m-30)
REVERT: A   71 LEU cc_start: 0.9040 (tp) cc_final: 0.8601 (tp)
REVERT: A   81 PHE cc_start: 0.9408 (t80) cc_final: 0.9192 (t80)
REVERT: A  162 PHE cc_start: 0.8849 (m-80) cc_final: 0.8509 (m-80)
REVERT: A  200 HIS cc_start: 0.9705 (m-70) cc_final: 0.9497 (m-70)
REVERT: A  256 ASN cc_start: 0.9558 (m-40) cc_final: 0.9061 (p0)
REVERT: A  321 LEU cc_start: 0.9775 (mt) cc_final: 0.9572 (mt)
REVERT: A  355 TRP cc_start: 0.7971 (m-90) cc_final: 0.7570 (m-10)
REVERT: A  387 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9261 (ptpt)
REVERT: A  390 LYS cc_start: 0.9687 (mmpt) cc_final: 0.9323 (ptpp)
REVERT: A  427 LYS cc_start: 0.9756 (tmtt) cc_final: 0.9532 (tptp)
REVERT: A  490 PHE cc_start: 0.9271 (t80) cc_final: 0.9022 (t80)
REVERT: A  498 LEU cc_start: 0.9390 (mt) cc_final: 0.9107 (mt)
REVERT: A  531 MET cc_start: 0.8906 (mtm) cc_final: 0.8671 (mtm)
REVERT: A  558 MET cc_start: 0.8896 (mpp) cc_final: 0.8381 (mpp)
REVERT: A  675 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8476 (tp30)
REVERT: A  832 ASP cc_start: 0.8366 (t0) cc_final: 0.8019 (t0)
REVERT: A  939 GLU cc_start: 0.7549 (mp0) cc_final: 0.7307 (mp0)
REVERT: A  971 LEU cc_start: 0.9400 (mt) cc_final: 0.8858 (tp)
REVERT: A  986 MET cc_start: 0.7960 (ppp) cc_final: 0.7645 (ppp)
REVERT: A 1035 MET cc_start: 0.8777 (ptm) cc_final: 0.8008 (ppp)
REVERT: A 1128 MET cc_start: 0.9168 (mmp) cc_final: 0.8141 (tpp)
REVERT: A 1135 LEU cc_start: 0.9559 (mm) cc_final: 0.9317 (mm)
REVERT: A 1151 ILE cc_start: 0.8635 (mm) cc_final: 0.7818 (mm)
REVERT: B   36 GLN cc_start: 0.9535 (pt0) cc_final: 0.9319 (pt0)
REVERT: B   71 ASN cc_start: 0.9453 (m-40) cc_final: 0.8838 (m110)
REVERT: B  145 GLU cc_start: 0.9249 (tp30) cc_final: 0.8972 (tp30)
REVERT: B  146 LEU cc_start: 0.9643 (mt) cc_final: 0.9280 (mt)
REVERT: C   94 ASP cc_start: 0.8324 (p0) cc_final: 0.8109 (p0)
REVERT: C  105 ASN cc_start: 0.9019 (m-40) cc_final: 0.8264 (p0)
REVERT: C  109 LEU cc_start: 0.8341 (mt) cc_final: 0.8052 (mt)
REVERT: C  132 TYR cc_start: 0.9441 (t80) cc_final: 0.9227 (t80)
REVERT: C  144 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9415 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1219
  time to fit residues: 44.1741
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  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0050
   chunk 136 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    2.6002

-------------------------------------------------------------------------------
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 142 ASN
** 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**
C  91 HIS
** C 147 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 = 0.3527 r_free = 0.3527 target = 0.077665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.051339 restraints weight = 56185.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.053335 restraints weight = 29446.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.054549 restraints weight = 19887.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.055311 restraints weight = 15673.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.055718 restraints weight = 13557.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13121  Z= 0.141
  Angle     :  0.587   8.698  17756  Z= 0.319
  Chirality :  0.042   0.207   1889
  Planarity :  0.004   0.062   2188
  Dihedral  : 11.503 172.481   1978
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.22), residues: 1462
  helix:  0.23 (0.20), residues: 717
  sheet: -2.33 (0.50), residues: 93
  loop : -2.04 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  41 
 TYR   0.020   0.001   TYR C 106 
 PHE   0.019   0.001   PHE A1161 
 TRP   0.036   0.002   TRP A1218 
 HIS   0.011   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (13121)
  covalent geometry    : angle       0.58668 (17756)
  hydrogen bonds       : bond        0.03294 (  516)
  hydrogen bonds       : angle       4.85337 ( 1469)

*********************** 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
  247 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.462 
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: A   55 ASP cc_start: 0.9116 (t0) cc_final: 0.8876 (t0)
REVERT: A   62 ILE cc_start: 0.9645 (mm) cc_final: 0.9327 (pt)
REVERT: A   64 ASP cc_start: 0.9438 (t70) cc_final: 0.8989 (m-30)
REVERT: A   71 LEU cc_start: 0.9054 (tp) cc_final: 0.8592 (tp)
REVERT: A  162 PHE cc_start: 0.9239 (m-80) cc_final: 0.8367 (m-80)
REVERT: A  256 ASN cc_start: 0.9579 (m-40) cc_final: 0.9081 (p0)
REVERT: A  321 LEU cc_start: 0.9781 (mt) cc_final: 0.9578 (mt)
REVERT: A  355 TRP cc_start: 0.8168 (m-90) cc_final: 0.7764 (m-10)
REVERT: A  384 ASP cc_start: 0.9610 (t0) cc_final: 0.9259 (m-30)
REVERT: A  390 LYS cc_start: 0.9684 (mmpt) cc_final: 0.9255 (ptpp)
REVERT: A  407 ASP cc_start: 0.8751 (t70) cc_final: 0.8478 (t70)
REVERT: A  427 LYS cc_start: 0.9789 (tmtt) cc_final: 0.9525 (tptp)
REVERT: A  490 PHE cc_start: 0.9336 (t80) cc_final: 0.9053 (t80)
REVERT: A  498 LEU cc_start: 0.9508 (mt) cc_final: 0.9153 (mt)
REVERT: A  531 MET cc_start: 0.8905 (mtm) cc_final: 0.8638 (mtm)
REVERT: A  558 MET cc_start: 0.8951 (mpp) cc_final: 0.8515 (mpp)
REVERT: A  722 MET cc_start: 0.8952 (tpp) cc_final: 0.8703 (tpp)
REVERT: A  832 ASP cc_start: 0.8408 (t0) cc_final: 0.8028 (t0)
REVERT: A  939 GLU cc_start: 0.7751 (mp0) cc_final: 0.7491 (mp0)
REVERT: A  944 GLN cc_start: 0.9262 (pt0) cc_final: 0.8847 (pt0)
REVERT: A 1035 MET cc_start: 0.8765 (ptm) cc_final: 0.7985 (ppp)
REVERT: A 1128 MET cc_start: 0.9140 (mmp) cc_final: 0.8131 (tpp)
REVERT: A 1135 LEU cc_start: 0.9559 (mm) cc_final: 0.9325 (mm)
REVERT: B   17 MET cc_start: 0.9605 (mmp) cc_final: 0.9320 (mmp)
REVERT: B   36 GLN cc_start: 0.9543 (pt0) cc_final: 0.9315 (pt0)
REVERT: B   71 ASN cc_start: 0.9429 (m-40) cc_final: 0.8690 (m-40)
REVERT: B  119 GLU cc_start: 0.8323 (mp0) cc_final: 0.8120 (mp0)
REVERT: B  145 GLU cc_start: 0.9241 (tp30) cc_final: 0.8962 (tp30)
REVERT: B  146 LEU cc_start: 0.9652 (mt) cc_final: 0.9320 (mt)
REVERT: B  158 ASP cc_start: 0.8429 (t0) cc_final: 0.8206 (t0)
REVERT: C   94 ASP cc_start: 0.8449 (p0) cc_final: 0.8131 (p0)
REVERT: C   97 PHE cc_start: 0.9221 (p90) cc_final: 0.8899 (p90)
REVERT: C  105 ASN cc_start: 0.9077 (m-40) cc_final: 0.8462 (p0)
REVERT: C  109 LEU cc_start: 0.8626 (mt) cc_final: 0.8077 (mt)
REVERT: C  144 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9375 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1225
  time to fit residues: 42.2502
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  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 48 optimal weight:   20.0000
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 144 optimal weight:    9.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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**
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 HIS
C  91 HIS
** C 147 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 = 0.3492 r_free = 0.3492 target = 0.076035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.050247 restraints weight = 55317.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.052127 restraints weight = 29008.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.053323 restraints weight = 19619.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.054085 restraints weight = 15339.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.054390 restraints weight = 13216.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.5477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13121  Z= 0.167
  Angle     :  0.608   8.830  17756  Z= 0.329
  Chirality :  0.043   0.199   1889
  Planarity :  0.004   0.048   2188
  Dihedral  : 11.438 172.943   1978
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.67 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.22), residues: 1462
  helix:  0.33 (0.20), residues: 730
  sheet: -2.19 (0.51), residues: 87
  loop : -2.02 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  41 
 TYR   0.029   0.002   TYR A 429 
 PHE   0.020   0.002   PHE A1161 
 TRP   0.041   0.002   TRP A1218 
 HIS   0.010   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13121)
  covalent geometry    : angle       0.60798 (17756)
  hydrogen bonds       : bond        0.03280 (  516)
  hydrogen bonds       : angle       4.97023 ( 1469)

*********************** 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
  236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.516 
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   71 LEU cc_start: 0.9023 (tp) cc_final: 0.8563 (tp)
REVERT: A  120 LYS cc_start: 0.9330 (mppt) cc_final: 0.9091 (mmtm)
REVERT: A  161 MET cc_start: 0.9418 (mtm) cc_final: 0.9121 (mtp)
REVERT: A  162 PHE cc_start: 0.9096 (m-80) cc_final: 0.8430 (m-80)
REVERT: A  179 ASN cc_start: 0.9154 (m110) cc_final: 0.8861 (m110)
REVERT: A  256 ASN cc_start: 0.9607 (m-40) cc_final: 0.9117 (p0)
REVERT: A  407 ASP cc_start: 0.8858 (t70) cc_final: 0.8571 (t70)
REVERT: A  427 LYS cc_start: 0.9822 (tmtt) cc_final: 0.9532 (tptp)
REVERT: A  487 TYR cc_start: 0.8889 (m-80) cc_final: 0.8683 (m-80)
REVERT: A  498 LEU cc_start: 0.9334 (mt) cc_final: 0.8931 (mt)
REVERT: A  531 MET cc_start: 0.8913 (mtm) cc_final: 0.8630 (mtm)
REVERT: A  558 MET cc_start: 0.9038 (mpp) cc_final: 0.8561 (mpp)
REVERT: A  675 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: A  832 ASP cc_start: 0.8507 (t0) cc_final: 0.8122 (t0)
REVERT: A  944 GLN cc_start: 0.9367 (pt0) cc_final: 0.8950 (pt0)
REVERT: A  986 MET cc_start: 0.7933 (ppp) cc_final: 0.7725 (ptm)
REVERT: A 1035 MET cc_start: 0.8733 (ptm) cc_final: 0.7973 (ppp)
REVERT: A 1128 MET cc_start: 0.9130 (mmp) cc_final: 0.8124 (tpp)
REVERT: B   32 ASP cc_start: 0.9170 (t0) cc_final: 0.8952 (t70)
REVERT: B   36 GLN cc_start: 0.9558 (pt0) cc_final: 0.9331 (pt0)
REVERT: B  145 GLU cc_start: 0.9190 (tp30) cc_final: 0.8905 (tp30)
REVERT: B  146 LEU cc_start: 0.9667 (mt) cc_final: 0.9345 (mt)
REVERT: B  158 ASP cc_start: 0.8552 (t0) cc_final: 0.8260 (t0)
REVERT: B  164 GLN cc_start: 0.9548 (mm-40) cc_final: 0.9337 (mm-40)
REVERT: C   45 HIS cc_start: 0.9755 (p-80) cc_final: 0.9529 (p-80)
REVERT: C   86 PHE cc_start: 0.7704 (p90) cc_final: 0.7330 (p90)
REVERT: C   94 ASP cc_start: 0.8505 (p0) cc_final: 0.8091 (p0)
REVERT: C  125 ASP cc_start: 0.8558 (p0) cc_final: 0.8277 (p0)
REVERT: C  144 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9333 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1200
  time to fit residues: 39.9129
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  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:   20.0000
   chunk 125 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 23 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 20 optimal weight:   40.0000
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 HIS
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 HIS
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 = 0.3455 r_free = 0.3455 target = 0.074154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.048013 restraints weight = 55070.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.049804 restraints weight = 29509.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.050881 restraints weight = 20184.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.051588 restraints weight = 16034.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.051865 restraints weight = 13961.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13121  Z= 0.231
  Angle     :  0.662   8.718  17756  Z= 0.361
  Chirality :  0.044   0.210   1889
  Planarity :  0.004   0.049   2188
  Dihedral  : 11.533 172.376   1978
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.08 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.22), residues: 1462
  helix:  0.37 (0.19), residues: 732
  sheet: -2.55 (0.45), residues: 99
  loop : -2.09 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  41 
 TYR   0.018   0.002   TYR A1102 
 PHE   0.025   0.002   PHE A1161 
 TRP   0.025   0.002   TRP A1086 
 HIS   0.011   0.002   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (13121)
  covalent geometry    : angle       0.66225 (17756)
  hydrogen bonds       : bond        0.03501 (  516)
  hydrogen bonds       : angle       5.11273 ( 1469)

*********************** 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
  224 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.367 
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   71 LEU cc_start: 0.8928 (tp) cc_final: 0.8475 (tp)
REVERT: A  120 LYS cc_start: 0.9440 (mppt) cc_final: 0.9155 (mmtm)
REVERT: A  178 GLU cc_start: 0.9176 (pm20) cc_final: 0.8642 (pm20)
REVERT: A  179 ASN cc_start: 0.8925 (m110) cc_final: 0.7665 (m110)
REVERT: A  256 ASN cc_start: 0.9660 (m-40) cc_final: 0.9187 (p0)
REVERT: A  328 PHE cc_start: 0.9348 (t80) cc_final: 0.9107 (t80)
REVERT: A  384 ASP cc_start: 0.9670 (t0) cc_final: 0.9350 (m-30)
REVERT: A  390 LYS cc_start: 0.9705 (mmpt) cc_final: 0.9316 (ptpp)
REVERT: A  407 ASP cc_start: 0.8904 (t70) cc_final: 0.8664 (t70)
REVERT: A  427 LYS cc_start: 0.9818 (tmtt) cc_final: 0.9547 (tptp)
REVERT: A  487 TYR cc_start: 0.8880 (m-80) cc_final: 0.8621 (m-80)
REVERT: A  498 LEU cc_start: 0.9378 (mt) cc_final: 0.9069 (mt)
REVERT: A  531 MET cc_start: 0.9052 (mtm) cc_final: 0.8768 (mtm)
REVERT: A  558 MET cc_start: 0.9092 (mpp) cc_final: 0.8621 (mpp)
REVERT: A  675 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: A  722 MET cc_start: 0.8938 (tpp) cc_final: 0.8637 (tpp)
REVERT: A  832 ASP cc_start: 0.8716 (t0) cc_final: 0.8318 (t0)
REVERT: A  944 GLN cc_start: 0.9464 (pt0) cc_final: 0.9044 (pt0)
REVERT: A  952 ASP cc_start: 0.9096 (m-30) cc_final: 0.8865 (m-30)
REVERT: A  986 MET cc_start: 0.7833 (ppp) cc_final: 0.7574 (ptm)
REVERT: A 1035 MET cc_start: 0.8843 (ptm) cc_final: 0.8125 (ppp)
REVERT: A 1128 MET cc_start: 0.9174 (mmp) cc_final: 0.8171 (tpp)
REVERT: B   47 ASN cc_start: 0.8843 (p0) cc_final: 0.8612 (p0)
REVERT: B   82 ILE cc_start: 0.9051 (mm) cc_final: 0.8087 (mm)
REVERT: B  106 TYR cc_start: 0.8782 (t80) cc_final: 0.8546 (t80)
REVERT: B  136 TYR cc_start: 0.9417 (t80) cc_final: 0.9177 (t80)
REVERT: B  145 GLU cc_start: 0.9263 (tp30) cc_final: 0.8953 (tp30)
REVERT: B  146 LEU cc_start: 0.9755 (mt) cc_final: 0.9435 (mt)
REVERT: B  148 GLN cc_start: 0.9606 (mm110) cc_final: 0.9353 (mm-40)
REVERT: B  152 LYS cc_start: 0.9335 (tptp) cc_final: 0.9066 (tptp)
REVERT: C   45 HIS cc_start: 0.9756 (p-80) cc_final: 0.9545 (p-80)
REVERT: C   86 PHE cc_start: 0.7734 (p90) cc_final: 0.7433 (p90)
REVERT: C  109 LEU cc_start: 0.9418 (mp) cc_final: 0.8948 (mt)
REVERT: C  144 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9350 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 0.1218
  time to fit residues: 38.3123
Evaluate side-chains
  189 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0000
   chunk 120 optimal weight:   10.0000
   chunk 124 optimal weight:    0.7980
   chunk 122 optimal weight:    0.0970
   chunk 146 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
C  91 HIS
** C 147 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 = 0.3493 r_free = 0.3493 target = 0.075968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.050022 restraints weight = 55469.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.051936 restraints weight = 29035.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.053146 restraints weight = 19642.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.053847 restraints weight = 15464.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 71)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.054342 restraints weight = 13436.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.6043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13121  Z= 0.131
  Angle     :  0.605   8.432  17756  Z= 0.322
  Chirality :  0.043   0.271   1889
  Planarity :  0.003   0.039   2188
  Dihedral  : 11.374 173.387   1978
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.22), residues: 1462
  helix:  0.49 (0.19), residues: 734
  sheet: -2.10 (0.50), residues: 87
  loop : -1.97 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  41 
 TYR   0.031   0.001   TYR A 494 
 PHE   0.018   0.001   PHE A1161 
 TRP   0.031   0.002   TRP A 355 
 HIS   0.011   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13121)
  covalent geometry    : angle       0.60472 (17756)
  hydrogen bonds       : bond        0.03176 (  516)
  hydrogen bonds       : angle       4.88310 ( 1469)

*********************** 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: 0
    poor density    : 236
  time to evaluate  : 0.371 
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: 0.8875 (tp) cc_final: 0.8396 (tp)
REVERT: A  120 LYS cc_start: 0.9422 (mppt) cc_final: 0.9106 (mmtm)
REVERT: A  162 PHE cc_start: 0.9263 (m-80) cc_final: 0.8352 (m-80)
REVERT: A  256 ASN cc_start: 0.9629 (m-40) cc_final: 0.9152 (p0)
REVERT: A  328 PHE cc_start: 0.9321 (t80) cc_final: 0.9074 (t80)
REVERT: A  384 ASP cc_start: 0.9657 (t0) cc_final: 0.9322 (m-30)
REVERT: A  390 LYS cc_start: 0.9699 (mmpt) cc_final: 0.9294 (ptpp)
REVERT: A  407 ASP cc_start: 0.8940 (t70) cc_final: 0.8696 (t70)
REVERT: A  427 LYS cc_start: 0.9815 (tmtt) cc_final: 0.9520 (tptp)
REVERT: A  476 GLU cc_start: 0.9150 (pp20) cc_final: 0.8181 (pp20)
REVERT: A  487 TYR cc_start: 0.8840 (m-80) cc_final: 0.8639 (m-80)
REVERT: A  505 ASP cc_start: 0.9230 (m-30) cc_final: 0.9014 (m-30)
REVERT: A  531 MET cc_start: 0.8884 (mtm) cc_final: 0.8592 (mtm)
REVERT: A  535 ASP cc_start: 0.9172 (m-30) cc_final: 0.8905 (t70)
REVERT: A  558 MET cc_start: 0.9189 (mpp) cc_final: 0.8651 (mpp)
REVERT: A  675 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8605 (tm-30)
REVERT: A  722 MET cc_start: 0.8928 (tpp) cc_final: 0.8583 (tpp)
REVERT: A  832 ASP cc_start: 0.8499 (t0) cc_final: 0.8057 (t0)
REVERT: A  944 GLN cc_start: 0.9434 (pt0) cc_final: 0.9041 (pt0)
REVERT: A  952 ASP cc_start: 0.8948 (m-30) cc_final: 0.8688 (m-30)
REVERT: A  986 MET cc_start: 0.7721 (ppp) cc_final: 0.7355 (ptm)
REVERT: A 1035 MET cc_start: 0.8775 (ptm) cc_final: 0.7998 (ppp)
REVERT: A 1128 MET cc_start: 0.9098 (mmp) cc_final: 0.8231 (tpp)
REVERT: B   32 ASP cc_start: 0.9173 (t0) cc_final: 0.8701 (t0)
REVERT: B   36 GLN cc_start: 0.9545 (pt0) cc_final: 0.9224 (pt0)
REVERT: B  106 TYR cc_start: 0.8809 (t80) cc_final: 0.8601 (t80)
REVERT: B  136 TYR cc_start: 0.9395 (t80) cc_final: 0.9109 (t80)
REVERT: B  145 GLU cc_start: 0.9191 (tp30) cc_final: 0.8905 (tp30)
REVERT: B  146 LEU cc_start: 0.9735 (mt) cc_final: 0.9431 (mt)
REVERT: B  152 LYS cc_start: 0.9271 (tptp) cc_final: 0.9035 (tptp)
REVERT: B  158 ASP cc_start: 0.8476 (t0) cc_final: 0.8143 (t0)
REVERT: C   45 HIS cc_start: 0.9780 (p-80) cc_final: 0.9470 (p-80)
REVERT: C   94 ASP cc_start: 0.8622 (p0) cc_final: 0.8244 (p0)
REVERT: C  144 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9325 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1172
  time to fit residues: 39.5190
Evaluate side-chains
  184 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 108 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 113 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   overall best weight:    4.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
** B  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.073895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.047962 restraints weight = 56191.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.049799 restraints weight = 29933.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.050929 restraints weight = 20369.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.051637 restraints weight = 16148.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.052047 restraints weight = 14006.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.6304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13121  Z= 0.208
  Angle     :  0.667   9.259  17756  Z= 0.361
  Chirality :  0.045   0.277   1889
  Planarity :  0.004   0.040   2188
  Dihedral  : 11.462 172.451   1978
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.19 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.22), residues: 1462
  helix:  0.50 (0.19), residues: 740
  sheet: -2.45 (0.44), residues: 103
  loop : -1.95 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 671 
 TYR   0.045   0.002   TYR A 840 
 PHE   0.021   0.002   PHE A1161 
 TRP   0.060   0.003   TRP A1218 
 HIS   0.011   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (13121)
  covalent geometry    : angle       0.66703 (17756)
  hydrogen bonds       : bond        0.03387 (  516)
  hydrogen bonds       : angle       5.15333 ( 1469)

*********************** 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
  225 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.485 
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: 0.8925 (tp) cc_final: 0.8468 (tp)
REVERT: A  120 LYS cc_start: 0.9440 (mppt) cc_final: 0.9132 (mmtm)
REVERT: A  179 ASN cc_start: 0.9291 (m110) cc_final: 0.8952 (m110)
REVERT: A  187 MET cc_start: 0.9283 (mtp) cc_final: 0.9076 (mtp)
REVERT: A  256 ASN cc_start: 0.9655 (m-40) cc_final: 0.9202 (p0)
REVERT: A  328 PHE cc_start: 0.9332 (t80) cc_final: 0.9039 (t80)
REVERT: A  384 ASP cc_start: 0.9655 (t0) cc_final: 0.9451 (p0)
REVERT: A  390 LYS cc_start: 0.9701 (mmpt) cc_final: 0.9294 (ptpp)
REVERT: A  407 ASP cc_start: 0.9075 (t70) cc_final: 0.8841 (t70)
REVERT: A  427 LYS cc_start: 0.9819 (tmtt) cc_final: 0.9552 (tptp)
REVERT: A  490 PHE cc_start: 0.9310 (t80) cc_final: 0.8887 (t80)
REVERT: A  498 LEU cc_start: 0.9256 (mt) cc_final: 0.9042 (mt)
REVERT: A  531 MET cc_start: 0.8935 (mtm) cc_final: 0.8647 (mtm)
REVERT: A  832 ASP cc_start: 0.8634 (t0) cc_final: 0.8195 (t0)
REVERT: A  952 ASP cc_start: 0.9037 (m-30) cc_final: 0.8807 (m-30)
REVERT: A  986 MET cc_start: 0.7630 (ppp) cc_final: 0.7264 (ptm)
REVERT: A 1035 MET cc_start: 0.8824 (ptm) cc_final: 0.7991 (ppp)
REVERT: A 1121 LYS cc_start: 0.9155 (tppt) cc_final: 0.8850 (tppt)
REVERT: A 1128 MET cc_start: 0.9132 (mmp) cc_final: 0.8260 (tpp)
REVERT: A 1182 ASN cc_start: 0.9302 (t0) cc_final: 0.9045 (t0)
REVERT: B   32 ASP cc_start: 0.9230 (t0) cc_final: 0.8777 (t0)
REVERT: B   36 GLN cc_start: 0.9544 (pt0) cc_final: 0.9236 (pt0)
REVERT: B   73 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9198 (ptpp)
REVERT: B  136 TYR cc_start: 0.9449 (t80) cc_final: 0.9119 (t80)
REVERT: B  145 GLU cc_start: 0.9185 (tp30) cc_final: 0.8913 (tp30)
REVERT: B  146 LEU cc_start: 0.9754 (mt) cc_final: 0.9298 (mt)
REVERT: B  148 GLN cc_start: 0.9591 (mm110) cc_final: 0.9352 (mm-40)
REVERT: B  158 ASP cc_start: 0.8514 (t0) cc_final: 0.8214 (t0)
REVERT: B  164 GLN cc_start: 0.9581 (mm-40) cc_final: 0.9356 (mp10)
REVERT: C   45 HIS cc_start: 0.9809 (p-80) cc_final: 0.9524 (p-80)
REVERT: C   86 PHE cc_start: 0.8429 (p90) cc_final: 0.8089 (p90)
REVERT: C   94 ASP cc_start: 0.8569 (p0) cc_final: 0.8136 (p0)
REVERT: C  105 ASN cc_start: 0.9245 (p0) cc_final: 0.9020 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1146
  time to fit residues: 36.6398
Evaluate side-chains
  173 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 142 optimal weight:   30.0000
   chunk 137 optimal weight:   50.0000
   chunk 74 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 114 optimal weight:   10.0000
   chunk 147 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 ASN
B  47 ASN
C  91 HIS
** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.073939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.047835 restraints weight = 55133.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.049704 restraints weight = 29322.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.050802 restraints weight = 19869.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.051507 restraints weight = 15781.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.051980 restraints weight = 13655.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.6501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13121  Z= 0.194
  Angle     :  0.664   9.452  17756  Z= 0.359
  Chirality :  0.045   0.259   1889
  Planarity :  0.004   0.039   2188
  Dihedral  : 11.441 172.567   1978
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.74 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.22), residues: 1462
  helix:  0.43 (0.19), residues: 741
  sheet: -2.48 (0.44), residues: 103
  loop : -1.90 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 174 
 TYR   0.039   0.002   TYR A 840 
 PHE   0.023   0.002   PHE A 931 
 TRP   0.045   0.003   TRP B  84 
 HIS   0.011   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (13121)
  covalent geometry    : angle       0.66417 (17756)
  hydrogen bonds       : bond        0.03381 (  516)
  hydrogen bonds       : angle       5.16042 ( 1469)

*********************** 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
  225 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.499 
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   71 LEU cc_start: 0.8923 (tp) cc_final: 0.8500 (tp)
REVERT: A  120 LYS cc_start: 0.9414 (mptt) cc_final: 0.9199 (mmtm)
REVERT: A  256 ASN cc_start: 0.9677 (m-40) cc_final: 0.9233 (p0)
REVERT: A  313 GLU cc_start: 0.9295 (pm20) cc_final: 0.9026 (pm20)
REVERT: A  328 PHE cc_start: 0.9344 (t80) cc_final: 0.8944 (t80)
REVERT: A  384 ASP cc_start: 0.9697 (t0) cc_final: 0.9491 (p0)
REVERT: A  390 LYS cc_start: 0.9712 (mmpt) cc_final: 0.9314 (ptpp)
REVERT: A  427 LYS cc_start: 0.9815 (tmtt) cc_final: 0.9552 (tptp)
REVERT: A  531 MET cc_start: 0.8955 (mtm) cc_final: 0.8693 (mtm)
REVERT: A  832 ASP cc_start: 0.8660 (t0) cc_final: 0.8273 (t0)
REVERT: A  952 ASP cc_start: 0.8986 (m-30) cc_final: 0.8760 (m-30)
REVERT: A  986 MET cc_start: 0.7596 (ppp) cc_final: 0.7099 (ptm)
REVERT: A 1035 MET cc_start: 0.8855 (ptm) cc_final: 0.8019 (ppp)
REVERT: A 1121 LYS cc_start: 0.9115 (tppt) cc_final: 0.8827 (tppt)
REVERT: A 1128 MET cc_start: 0.9086 (mmp) cc_final: 0.8303 (tpp)
REVERT: A 1182 ASN cc_start: 0.9284 (t0) cc_final: 0.9075 (t0)
REVERT: B   32 ASP cc_start: 0.9200 (t0) cc_final: 0.8718 (t0)
REVERT: B   36 GLN cc_start: 0.9537 (pt0) cc_final: 0.9211 (pt0)
REVERT: B   66 MET cc_start: 0.4802 (mmm) cc_final: 0.4059 (mmm)
REVERT: B   73 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9205 (ptpp)
REVERT: B  145 GLU cc_start: 0.9228 (tp30) cc_final: 0.8950 (tp30)
REVERT: B  146 LEU cc_start: 0.9689 (mt) cc_final: 0.9364 (mt)
REVERT: B  148 GLN cc_start: 0.9559 (mm110) cc_final: 0.9325 (mm-40)
REVERT: B  158 ASP cc_start: 0.8583 (t0) cc_final: 0.8287 (t0)
REVERT: B  164 GLN cc_start: 0.9610 (mm-40) cc_final: 0.9364 (mp10)
REVERT: C   45 HIS cc_start: 0.9815 (p-80) cc_final: 0.9602 (p90)
REVERT: C   86 PHE cc_start: 0.8393 (p90) cc_final: 0.8102 (p90)
REVERT: C   94 ASP cc_start: 0.8669 (p0) cc_final: 0.8242 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1135
  time to fit residues: 36.8446
Evaluate side-chains
  170 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:   20.0000
   chunk 122 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 134 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 146 optimal weight:   20.0000
   chunk 77 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 238 ASN
** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3462 r_free = 0.3462 target = 0.074516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.048519 restraints weight = 55154.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.050350 restraints weight = 29346.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.051489 restraints weight = 20009.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.052157 restraints weight = 15865.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.052411 restraints weight = 13781.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.6666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111  13121  Z= 0.165
  Angle     :  0.650   9.223  17756  Z= 0.350
  Chirality :  0.044   0.249   1889
  Planarity :  0.003   0.038   2188
  Dihedral  : 11.392 172.768   1978
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.37 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.22), residues: 1462
  helix:  0.52 (0.19), residues: 738
  sheet: -2.39 (0.45), residues: 103
  loop : -1.78 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  41 
 TYR   0.035   0.002   TYR A 429 
 PHE   0.018   0.002   PHE A1161 
 TRP   0.038   0.002   TRP B  84 
 HIS   0.003   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13121)
  covalent geometry    : angle       0.64976 (17756)
  hydrogen bonds       : bond        0.03238 (  516)
  hydrogen bonds       : angle       5.13317 ( 1469)

********************** 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
  228 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 0.358 
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: 0.8938 (tp) cc_final: 0.8513 (tp)
REVERT: A  256 ASN cc_start: 0.9682 (m-40) cc_final: 0.9235 (p0)
REVERT: A  313 GLU cc_start: 0.9299 (pm20) cc_final: 0.9058 (pm20)
REVERT: A  328 PHE cc_start: 0.9352 (t80) cc_final: 0.8907 (t80)
REVERT: A  390 LYS cc_start: 0.9733 (mmpt) cc_final: 0.9329 (ptpp)
REVERT: A  427 LYS cc_start: 0.9844 (tmtt) cc_final: 0.9587 (tptp)
REVERT: A  498 LEU cc_start: 0.9275 (mt) cc_final: 0.9063 (mt)
REVERT: A  505 ASP cc_start: 0.9306 (m-30) cc_final: 0.9098 (m-30)
REVERT: A  531 MET cc_start: 0.8903 (mtm) cc_final: 0.8637 (mtm)
REVERT: A  606 TYR cc_start: 0.8886 (t80) cc_final: 0.8412 (t80)
REVERT: A  832 ASP cc_start: 0.8703 (t0) cc_final: 0.8297 (t0)
REVERT: A  952 ASP cc_start: 0.8924 (m-30) cc_final: 0.8709 (m-30)
REVERT: A 1035 MET cc_start: 0.8842 (ptm) cc_final: 0.7980 (ppp)
REVERT: A 1121 LYS cc_start: 0.9151 (tppt) cc_final: 0.8876 (tppt)
REVERT: A 1128 MET cc_start: 0.9082 (mmp) cc_final: 0.8322 (tpp)
REVERT: A 1182 ASN cc_start: 0.9023 (t0) cc_final: 0.8532 (p0)
REVERT: A 1186 ASN cc_start: 0.9131 (m110) cc_final: 0.8839 (m110)
REVERT: B   73 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9219 (ptpp)
REVERT: B  133 ASP cc_start: 0.9515 (p0) cc_final: 0.9307 (p0)
REVERT: B  145 GLU cc_start: 0.9214 (tp30) cc_final: 0.8931 (tp30)
REVERT: B  146 LEU cc_start: 0.9683 (mt) cc_final: 0.9384 (mt)
REVERT: B  148 GLN cc_start: 0.9585 (mm110) cc_final: 0.9368 (mm-40)
REVERT: B  158 ASP cc_start: 0.8657 (t0) cc_final: 0.8349 (t0)
REVERT: B  164 GLN cc_start: 0.9567 (mm-40) cc_final: 0.9297 (mm-40)
REVERT: C   45 HIS cc_start: 0.9817 (p-80) cc_final: 0.9479 (p-80)
REVERT: C   86 PHE cc_start: 0.8355 (p90) cc_final: 0.8140 (p90)
REVERT: C   94 ASP cc_start: 0.8766 (p0) cc_final: 0.8363 (p0)
REVERT: C  140 MET cc_start: 0.9213 (mmp) cc_final: 0.8924 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1114
  time to fit residues: 37.1124
Evaluate side-chains
  178 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 140 optimal weight:   50.0000
   chunk 123 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 128 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
B  47 ASN
** C  42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 HIS
C 147 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.076021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.050317 restraints weight = 54964.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.052250 restraints weight = 29018.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.053402 restraints weight = 19603.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.054171 restraints weight = 15501.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.054613 restraints weight = 13342.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.6840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.146  13121  Z= 0.134
  Angle     :  0.639   9.793  17756  Z= 0.342
  Chirality :  0.044   0.234   1889
  Planarity :  0.003   0.035   2188
  Dihedral  : 11.275 173.390   1978
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.07 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.22), residues: 1462
  helix:  0.57 (0.19), residues: 730
  sheet: -1.87 (0.51), residues: 91
  loop : -1.56 (0.25), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 543 
 TYR   0.034   0.001   TYR B  12 
 PHE   0.015   0.001   PHE A1161 
 TRP   0.035   0.002   TRP B  84 
 HIS   0.007   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (13121)
  covalent geometry    : angle       0.63867 (17756)
  hydrogen bonds       : bond        0.03169 (  516)
  hydrogen bonds       : angle       5.03358 ( 1469)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2353.70 seconds
wall clock time: 41 minutes 30.85 seconds (2490.85 seconds total)