Starting phenix.real_space_refine
on Tue Aug 26 15:49:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cg4_16630/08_2025/8cg4_16630.map"
  }
  resolution = 2.6
  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=   0.000 sd=   0.014
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: 5
    Type Number    sf(0)   Gaussians
     S     128      5.16       5
     C   12166      2.51       5
     N    3386      2.21       5
     O    3642      1.98       5
     H   19118      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 158 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 38440
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 19220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1252, 19220
          Classifications: {'peptide': 1252}
          Link IDs: {'PTRANS': 77, 'TRANS': 1174}
    Chain: "B"
      Number of atoms: 19220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1252, 19220
          Classifications: {'peptide': 1252}
          Link IDs: {'PTRANS': 77, 'TRANS': 1174}
  Time building chain proxies: 5.71, per 1000 atoms: 0.15
  Number of scatterers: 38440
  At special positions: 0
  Unit cell: (99.22, 202.54, 125.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     128     16.00
     O    3642      8.00
     N    3386      7.00
     C   12166      6.00
     H   19118      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 2.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4660

  Finding SS restraints...
    Secondary structure from input PDB file:
      112 helices and 16 sheets defined
      48.5% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 30 through 51
      removed outlier: 3.876A  pdb=" N   LEU A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A  51 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 61
      removed outlier: 3.661A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 74
      removed outlier: 3.574A  pdb=" N   VAL A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 101
      removed outlier: 3.865A  pdb=" N   THR A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 109
      No H-bonds generated for 'chain 'A' and resid 107 through 109'
    Processing helix  chain 'A' and resid 119 through 128
      removed outlier: 3.637A  pdb=" N   ALA A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 161
      removed outlier: 3.603A  pdb=" N   LEU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      Proline residue:  A 137  - end of helix
    Processing helix  chain 'A' and resid 162 through 165
      removed outlier: 3.886A  pdb=" N   ASP A 165 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 162 through 165'
    Processing helix  chain 'A' and resid 179 through 195
    Processing helix  chain 'A' and resid 197 through 201
      removed outlier: 3.697A  pdb=" N   ARG A 201 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 226
    Processing helix  chain 'A' and resid 251 through 259
      removed outlier: 3.570A  pdb=" N   ILE A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
      removed outlier: 4.345A  pdb=" N   LEU A 270 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.792A  pdb=" N   GLU A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 324
      Proline residue:  A 316  - end of helix
      removed outlier: 3.541A  pdb=" N   ARG A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 349
    Processing helix  chain 'A' and resid 388 through 399
      removed outlier: 3.575A  pdb=" N   LYS A 398 " --> pdb=" O   ASP A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 417
      removed outlier: 4.255A  pdb=" N   HIS A 416 " --> pdb=" O   ASP A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 457 through 474
    Processing helix  chain 'A' and resid 481 through 487
      removed outlier: 3.812A  pdb=" N   GLN A 485 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ARG A 486 " --> pdb=" O   SER A 483 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP A 487 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 541 through 543
      No H-bonds generated for 'chain 'A' and resid 541 through 543'
    Processing helix  chain 'A' and resid 544 through 560
    Processing helix  chain 'A' and resid 575 through 577
      No H-bonds generated for 'chain 'A' and resid 575 through 577'
    Processing helix  chain 'A' and resid 578 through 583
      removed outlier: 3.538A  pdb=" N   LEU A 582 " --> pdb=" O   GLY A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 624
    Processing helix  chain 'A' and resid 650 through 666
    Processing helix  chain 'A' and resid 668 through 670
      No H-bonds generated for 'chain 'A' and resid 668 through 670'
    Processing helix  chain 'A' and resid 684 through 698
      removed outlier: 3.714A  pdb=" N   GLU A 689 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 718
    Processing helix  chain 'A' and resid 725 through 741
    Processing helix  chain 'A' and resid 762 through 765
    Processing helix  chain 'A' and resid 827 through 845
    Processing helix  chain 'A' and resid 849 through 859
    Processing helix  chain 'A' and resid 874 through 889
    Processing helix  chain 'A' and resid 890 through 893
      removed outlier: 4.310A  pdb=" N   SER A 893 " --> pdb=" O   ASP A 890 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 890 through 893'
    Processing helix  chain 'A' and resid 916 through 923
    Processing helix  chain 'A' and resid 923 through 940
    Processing helix  chain 'A' and resid 945 through 951
      removed outlier: 4.181A  pdb=" N   CYS A 949 " --> pdb=" O   PHE A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 982
      removed outlier: 3.568A  pdb=" N   VAL A 964 " --> pdb=" O   ALA A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1003
    Processing helix  chain 'A' and resid 1007 through 1026
    Processing helix  chain 'A' and resid 1039 through 1042
    Processing helix  chain 'A' and resid 1043 through 1050
      removed outlier: 3.535A  pdb=" N   HIS A1050 " --> pdb=" O   TRP A1046 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1082
    Processing helix  chain 'A' and resid 1097 through 1101
      removed outlier: 3.534A  pdb=" N   VAL A1100 " --> pdb=" O   SER A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1111
      removed outlier: 4.756A  pdb=" N   ASP A1106 " --> pdb=" O   PRO A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1114
      No H-bonds generated for 'chain 'A' and resid 1112 through 1114'
    Processing helix  chain 'A' and resid 1139 through 1147
      removed outlier: 3.802A  pdb=" N   CYS A1147 " --> pdb=" O   VAL A1143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1163
    Processing helix  chain 'A' and resid 1180 through 1189
      removed outlier: 3.616A  pdb=" N   MET A1184 " --> pdb=" O   LEU A1180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1204 through 1220
      removed outlier: 4.422A  pdb=" N   SER A1208 " --> pdb=" O   ALA A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1224 through 1230
    Processing helix  chain 'A' and resid 1232 through 1236
      removed outlier: 3.538A  pdb=" N   SER A1235 " --> pdb=" O   PHE A1232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 30 through 51
      removed outlier: 3.874A  pdb=" N   LEU B  49 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLN B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B  51 " --> pdb=" O   GLN B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 61
      removed outlier: 3.639A  pdb=" N   LEU B  59 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 74
      removed outlier: 3.572A  pdb=" N   VAL B  73 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 101
      removed outlier: 3.970A  pdb=" N   ARG B  82 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR B  83 " --> pdb=" O   PRO B  79 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER B 101 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 109
      No H-bonds generated for 'chain 'B' and resid 107 through 109'
    Processing helix  chain 'B' and resid 119 through 128
      removed outlier: 3.643A  pdb=" N   ALA B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 161
      removed outlier: 3.579A  pdb=" N   LEU B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      Proline residue:  B 137  - end of helix
    Processing helix  chain 'B' and resid 162 through 165
      removed outlier: 3.808A  pdb=" N   ASP B 165 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 162 through 165'
    Processing helix  chain 'B' and resid 179 through 195
    Processing helix  chain 'B' and resid 197 through 201
      removed outlier: 3.706A  pdb=" N   ARG B 201 " --> pdb=" O   GLN B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 226
    Processing helix  chain 'B' and resid 251 through 259
      removed outlier: 3.574A  pdb=" N   ILE B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
      removed outlier: 4.342A  pdb=" N   LEU B 270 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 304
      removed outlier: 3.518A  pdb=" N   VAL B 296 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU B 304 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 324
      Proline residue:  B 316  - end of helix
      removed outlier: 3.562A  pdb=" N   ARG B 322 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 349
      removed outlier: 3.955A  pdb=" N   ASP B 346 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 399
      removed outlier: 3.866A  pdb=" N   LYS B 398 " --> pdb=" O   ASP B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 417
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 452 through 456
    Processing helix  chain 'B' and resid 457 through 474
    Processing helix  chain 'B' and resid 481 through 487
      removed outlier: 3.812A  pdb=" N   GLN B 485 " --> pdb=" O   PRO B 482 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ARG B 486 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ASP B 487 " --> pdb=" O   THR B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 531
    Processing helix  chain 'B' and resid 541 through 543
      No H-bonds generated for 'chain 'B' and resid 541 through 543'
    Processing helix  chain 'B' and resid 544 through 560
    Processing helix  chain 'B' and resid 576 through 583
      removed outlier: 4.362A  pdb=" N   THR B 580 " --> pdb=" O   PRO B 576 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY B 581 " --> pdb=" O   ASP B 577 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B 582 " --> pdb=" O   GLY B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 624
    Processing helix  chain 'B' and resid 650 through 666
    Processing helix  chain 'B' and resid 668 through 670
      No H-bonds generated for 'chain 'B' and resid 668 through 670'
    Processing helix  chain 'B' and resid 684 through 698
      removed outlier: 3.675A  pdb=" N   GLU B 689 " --> pdb=" O   GLY B 685 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 718
    Processing helix  chain 'B' and resid 725 through 741
    Processing helix  chain 'B' and resid 762 through 765
    Processing helix  chain 'B' and resid 827 through 845
    Processing helix  chain 'B' and resid 849 through 859
    Processing helix  chain 'B' and resid 874 through 889
    Processing helix  chain 'B' and resid 916 through 923
    Processing helix  chain 'B' and resid 923 through 940
    Processing helix  chain 'B' and resid 945 through 951
      removed outlier: 4.160A  pdb=" N   CYS B 949 " --> pdb=" O   PHE B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 982
      removed outlier: 3.582A  pdb=" N   VAL B 964 " --> pdb=" O   ALA B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 995 through 1003
    Processing helix  chain 'B' and resid 1007 through 1026
    Processing helix  chain 'B' and resid 1039 through 1042
    Processing helix  chain 'B' and resid 1043 through 1051
      removed outlier: 3.615A  pdb=" N   HIS B1050 " --> pdb=" O   TRP B1046 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1069 through 1081
    Processing helix  chain 'B' and resid 1097 through 1101
      removed outlier: 3.531A  pdb=" N   VAL B1100 " --> pdb=" O   SER B1097 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1111
    Processing helix  chain 'B' and resid 1112 through 1114
      No H-bonds generated for 'chain 'B' and resid 1112 through 1114'
    Processing helix  chain 'B' and resid 1139 through 1147
      removed outlier: 3.783A  pdb=" N   CYS B1147 " --> pdb=" O   VAL B1143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1163
    Processing helix  chain 'B' and resid 1180 through 1189
      removed outlier: 3.646A  pdb=" N   MET B1184 " --> pdb=" O   LEU B1180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1204 through 1220
      removed outlier: 4.247A  pdb=" N   SER B1208 " --> pdb=" O   ALA B1204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1224 through 1229
    Processing helix  chain 'B' and resid 1232 through 1236
      removed outlier: 3.550A  pdb=" N   SER B1235 " --> pdb=" O   PHE B1232 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 277
      removed outlier: 8.436A  pdb=" N   ILE A 277 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL A 113 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLN A   6 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   LEU A 114 " --> pdb=" O   GLN A   6 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   PHE A   8 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ARG A   5 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ARG A 335 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   LEU A   7 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 207
      removed outlier: 6.487A  pdb=" N   THR A 213 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   ILE A 207 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ALA A 211 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER A 172 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 539
      removed outlier: 9.003A  pdb=" N   TYR A 537 " --> pdb=" O   ILE A 489 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL A 491 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   ASN A 539 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   HIS A 493 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A 378 " --> pdb=" O   PHE A 614 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LYS A 616 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ILE A 376 " --> pdb=" O   LYS A 616 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A 630 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 631 " --> pdb=" O   GLU A 802 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE A 800 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ALA A 635 " --> pdb=" O   ALA A 798 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA A 798 " --> pdb=" O   ALA A 635 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 637 " --> pdb=" O   ASN A 796 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN A 796 " --> pdb=" O   THR A 637 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ARG A 784 " --> pdb=" O   PHE A 672 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TYR A 674 " --> pdb=" O   ARG A 784 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   LEU A 710 " --> pdb=" O   HIS A 768 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441
    Processing sheet with id=AA5, first strand: chain 'A' and resid 742 through 743
    Processing sheet with id=AA6, first strand: chain 'A' and resid 819 through 825
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1130 through 1132
      removed outlier: 6.797A  pdb=" N   THR A 989 " --> pdb=" O   LEU A1124 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A 988 " --> pdb=" O   ILE A 901 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A1172 " --> pdb=" O   LEU A1196 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1053 through 1059
      removed outlier: 6.568A  pdb=" N   VAL A1064 " --> pdb=" O   ALA A1055 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   ILE A1057 " --> pdb=" O   ASP A1062 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ASP A1062 " --> pdb=" O   ILE A1057 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277
      removed outlier: 8.445A  pdb=" N   ILE B 277 " --> pdb=" O   SER B 111 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B 113 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLN B   6 " --> pdb=" O   TYR B 112 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   LEU B 114 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   PHE B   8 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ARG B   5 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ARG B 335 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   LEU B   7 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   PHE B 332 " --> pdb=" O   ARG B 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 207
      removed outlier: 6.514A  pdb=" N   THR B 213 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   ILE B 207 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ALA B 211 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   SER B 172 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 536 through 539
      removed outlier: 9.011A  pdb=" N   TYR B 537 " --> pdb=" O   ILE B 489 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL B 491 " --> pdb=" O   TYR B 537 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   ASN B 539 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   HIS B 493 " --> pdb=" O   ASN B 539 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER B 378 " --> pdb=" O   PHE B 614 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LYS B 616 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   ILE B 376 " --> pdb=" O   LYS B 616 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY B 630 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL B 631 " --> pdb=" O   GLU B 802 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ILE B 800 " --> pdb=" O   LEU B 633 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA B 635 " --> pdb=" O   ALA B 798 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ALA B 798 " --> pdb=" O   ALA B 635 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   THR B 637 " --> pdb=" O   ASN B 796 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ASN B 796 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ARG B 784 " --> pdb=" O   PHE B 672 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR B 674 " --> pdb=" O   ARG B 784 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   LEU B 710 " --> pdb=" O   HIS B 768 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 441
    Processing sheet with id=AB4, first strand: chain 'B' and resid 742 through 743
    Processing sheet with id=AB5, first strand: chain 'B' and resid 819 through 825
    Processing sheet with id=AB6, first strand: chain 'B' and resid 1130 through 1132
      removed outlier: 6.787A  pdb=" N   THR B 989 " --> pdb=" O   LEU B1124 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 988 " --> pdb=" O   ILE B 901 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B1172 " --> pdb=" O   LEU B1196 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1053 through 1059
      removed outlier: 5.467A  pdb=" N   VAL B1054 " --> pdb=" O   SER B1066 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   SER B1066 " --> pdb=" O   VAL B1054 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASP B1062 " --> pdb=" O   ASN B1058 " (cutoff:3.500A)

    882 hydrogen bonds defined for protein.
    2508 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 9.07

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 19062
        1.03 -     1.23: 82
        1.23 -     1.42: 8114
        1.42 -     1.61: 11428
        1.61 -     1.81: 200
  Bond restraints: 38886
  Sorted by residual:
  bond pdb=" N   GLN A   3 "
       pdb=" CA  GLN A   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.77e+00
  bond pdb=" N   GLN B   3 "
       pdb=" CA  GLN B   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.56e+00
  bond pdb=" N   GLN A   3 "
       pdb=" H   GLN A   3 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" N   GLN B   3 "
       pdb=" H   GLN B   3 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C   ILE A 361 "
       pdb=" N   PRO A 362 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.07e+00
  ... (remaining 38881 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.16: 70296
        7.16 -    14.31: 2
       14.31 -    21.47: 0
       21.47 -    28.63: 0
       28.63 -    35.78: 18
  Bond angle restraints: 70316
  Sorted by residual:
  angle pdb=" CB  SER A 350 "
        pdb=" CA  SER A 350 "
        pdb=" HA  SER A 350 "
      ideal   model   delta    sigma   weight residual
     109.00   73.22   35.78 3.00e+00 1.11e-01 1.42e+02
  angle pdb=" C   THR A 505 "
        pdb=" CA  THR A 505 "
        pdb=" HA  THR A 505 "
      ideal   model   delta    sigma   weight residual
     109.00   73.59   35.41 3.00e+00 1.11e-01 1.39e+02
  angle pdb=" C   ARG A 354 "
        pdb=" CA  ARG A 354 "
        pdb=" HA  ARG A 354 "
      ideal   model   delta    sigma   weight residual
     109.00   73.73   35.27 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" C   THR B 505 "
        pdb=" CA  THR B 505 "
        pdb=" HA  THR B 505 "
      ideal   model   delta    sigma   weight residual
     109.00   73.78   35.22 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" N   THR B 505 "
        pdb=" CA  THR B 505 "
        pdb=" HA  THR B 505 "
      ideal   model   delta    sigma   weight residual
     110.00   74.84   35.16 3.00e+00 1.11e-01 1.37e+02
  ... (remaining 70311 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 16118
       17.95 -    35.90: 1525
       35.90 -    53.85: 618
       53.85 -    71.80: 149
       71.80 -    89.75: 50
  Dihedral angle restraints: 18460
    sinusoidal: 10112
      harmonic: 8348
  Sorted by residual:
  dihedral pdb=" CA  THR B 541 "
           pdb=" C   THR B 541 "
           pdb=" N   ALA B 542 "
           pdb=" CA  ALA B 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -130.73  -49.27     0      5.00e+00 4.00e-02 9.71e+01
  dihedral pdb=" CA  THR A 541 "
           pdb=" C   THR A 541 "
           pdb=" N   ALA A 542 "
           pdb=" CA  ALA A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.92  -49.08     0      5.00e+00 4.00e-02 9.63e+01
  dihedral pdb=" CA  GLU A 338 "
           pdb=" C   GLU A 338 "
           pdb=" N   THR A 339 "
           pdb=" CA  THR A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.87   33.13     0      5.00e+00 4.00e-02 4.39e+01
  ... (remaining 18457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 2734
       0.070 -    0.141: 300
       0.141 -    0.211: 2
       0.211 -    0.281: 0
       0.281 -    0.352: 6
  Chirality restraints: 3042
  Sorted by residual:
  chirality pdb=" CA  THR B 505 "
            pdb=" N   THR B 505 "
            pdb=" C   THR B 505 "
            pdb=" CB  THR B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  SER A 350 "
            pdb=" N   SER A 350 "
            pdb=" C   SER A 350 "
            pdb=" CB  SER A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CA  THR A 505 "
            pdb=" N   THR A 505 "
            pdb=" C   THR A 505 "
            pdb=" CB  THR A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.18    0.35 2.00e-01 2.50e+01 3.05e+00
  ... (remaining 3039 not shown)

  Planarity restraints: 5846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 335 "    0.228 9.50e-02 1.11e+02   7.62e-02 6.40e+00
        pdb=" NE  ARG A 335 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 335 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 335 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 335 "    0.008 2.00e-02 2.50e+03
        pdb="HH11 ARG A 335 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A 335 "    0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 335 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 335 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 898 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO B 899 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 899 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 899 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 366 "    0.036 5.00e-02 4.00e+02   5.51e-02 4.85e+00
        pdb=" N   PRO A 367 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 367 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 367 "    0.030 5.00e-02 4.00e+02
  ... (remaining 5843 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 527
        2.05 -     2.69: 59634
        2.69 -     3.33: 111563
        3.33 -     3.96: 146036
        3.96 -     4.60: 230927
  Nonbonded interactions: 548687
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 348 "
            pdb=" H   THR B 351 "
     model   vdw
     1.418 2.450
  nonbonded pdb=" O   ASP A 626 "
            pdb="HH22 ARG A 807 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" O   ASP B 626 "
            pdb="HH22 ARG B 807 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" HG  SER A 546 "
            pdb=" O   GLY A 724 "
     model   vdw
     1.557 2.450
  nonbonded pdb=" O   ILE B 204 "
            pdb="HE21 GLN B 305 "
     model   vdw
     1.572 2.450
  ... (remaining 548682 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             5.580
  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:             0.240
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     32.110
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
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      :  0.004   0.048  19768  Z= 0.193
  Angle     :  0.621   8.561  26888  Z= 0.358
  Chirality :  0.045   0.352   3042
  Planarity :  0.006   0.102   3502
  Dihedral  : 17.740  89.753   7262
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.20 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 22.12 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -0.42 (0.17), residues: 2500
  helix:  0.98 (0.16), residues: 1012
  sheet:  0.47 (0.32), residues: 280
  loop : -1.61 (0.17), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 366 
 TYR   0.020   0.002   TYR A 468 
 PHE   0.011   0.001   PHE A 190 
 TRP   0.011   0.001   TRP A 393 
 HIS   0.007   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (19768)
  covalent geometry    : angle       0.62128 (26888)
  hydrogen bonds       : bond        0.18317 (  882)
  hydrogen bonds       : angle       6.43554 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 153
  time to evaluate  : 0.866 
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: A  518 ASN cc_start: 0.5576 (OUTLIER) cc_final: 0.5041 (m-40)
REVERT: B  518 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.4751 (m-40)
  outliers start: 92
  outliers final: 63
  residues processed: 238
  average time/residue: 1.2189
  time to fit residues: 329.5564
Evaluate side-chains
  186 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 121
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  518 ASN
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  645 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1159 SER
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  278 SER
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  433 CYS
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  518 ASN
Chi-restraints excluded: chain B residue  522 ILE
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  725 VAL
Chi-restraints excluded: chain B residue  726 SER
Chi-restraints excluded: chain B residue  728 VAL
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  989 THR
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1106 ASP
Chi-restraints excluded: chain B residue 1159 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 216 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    2.9990
   chunk 227 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 247 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 527 ASN
A1133 HIS
B 107 GLN
B 527 ASN
B1048 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.103992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075275 restraints weight = 109621.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.81
r_work: 0.3004 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  19768  Z= 0.199
  Angle     :  0.607   7.184  26888  Z= 0.318
  Chirality :  0.046   0.412   3042
  Planarity :  0.005   0.055   3502
  Dihedral  :  7.880  64.021   2782
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.24 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.04 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole: -0.07 (0.17), residues: 2500
  helix:  1.38 (0.16), residues: 1024
  sheet:  1.06 (0.33), residues: 240
  loop : -1.58 (0.17), residues: 1236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 880 
 TYR   0.019   0.002   TYR B 468 
 PHE   0.009   0.001   PHE A 437 
 TRP   0.012   0.001   TRP B 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (19768)
  covalent geometry    : angle       0.60720 (26888)
  hydrogen bonds       : bond        0.05393 (  882)
  hydrogen bonds       : angle       4.95329 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 128
  time to evaluate  : 0.893 
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: A   97 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8212 (tp30)
REVERT: A  323 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.2947 (mp10)
REVERT: A  705 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5547 (mttt)
REVERT: A  928 GLU cc_start: 0.8278 (mp0) cc_final: 0.7885 (mp0)
REVERT: A 1121 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8788 (pp)
REVERT: B  167 ARG cc_start: 0.3354 (OUTLIER) cc_final: 0.2269 (tpp80)
REVERT: B  351 THR cc_start: 0.6089 (OUTLIER) cc_final: 0.5704 (m)
REVERT: B  928 GLU cc_start: 0.8268 (mp0) cc_final: 0.7877 (mp0)
  outliers start: 105
  outliers final: 56
  residues processed: 217
  average time/residue: 1.1692
  time to fit residues: 290.0226
Evaluate side-chains
  184 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 122
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain B residue   23 SER
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  522 ILE
Chi-restraints excluded: chain B residue  594 CYS
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  725 VAL
Chi-restraints excluded: chain B residue  726 SER
Chi-restraints excluded: chain B residue  728 VAL
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  980 THR
Chi-restraints excluded: chain B residue  989 THR
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1087 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 179 optimal weight:    2.9990
   chunk 169 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 191 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 164 optimal weight:    1.9990
   chunk 157 optimal weight:    0.0570
   chunk 98 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.2504

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
A 527 ASN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.103077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.073683 restraints weight = 108373.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.84
r_work: 0.2959 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  19768  Z= 0.150
  Angle     :  0.561   7.117  26888  Z= 0.291
  Chirality :  0.044   0.414   3042
  Planarity :  0.005   0.051   3502
  Dihedral  :  7.278  65.839   2757
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.00 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.70 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.21 (0.17), residues: 2500
  helix:  1.72 (0.16), residues: 1028
  sheet:  0.97 (0.33), residues: 240
  loop : -1.50 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 366 
 TYR   0.018   0.001   TYR B 468 
 PHE   0.007   0.001   PHE A 437 
 TRP   0.012   0.001   TRP A 393 
 HIS   0.005   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (19768)
  covalent geometry    : angle       0.56130 (26888)
  hydrogen bonds       : bond        0.04528 (  882)
  hydrogen bonds       : angle       4.63527 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 127
  time to evaluate  : 0.759 
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: A  167 ARG cc_start: 0.3038 (OUTLIER) cc_final: 0.2045 (tpp80)
REVERT: A  323 GLN cc_start: 0.4066 (OUTLIER) cc_final: 0.2711 (mp10)
REVERT: A  705 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5821 (mttm)
REVERT: A 1121 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8642 (pp)
REVERT: B   43 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8396 (m)
REVERT: B  167 ARG cc_start: 0.3231 (OUTLIER) cc_final: 0.2274 (tpp80)
REVERT: B  351 THR cc_start: 0.5717 (OUTLIER) cc_final: 0.5418 (m)
REVERT: B  723 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7391 (tt0)
REVERT: B 1121 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8648 (pp)
  outliers start: 81
  outliers final: 52
  residues processed: 196
  average time/residue: 1.1784
  time to fit residues: 261.0836
Evaluate side-chains
  181 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 121
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  725 VAL
Chi-restraints excluded: chain B residue  726 SER
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  980 THR
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1087 THR
Chi-restraints excluded: chain B residue 1121 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 202 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 151 optimal weight:    0.0870
   chunk 76 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 167 optimal weight:   20.0000
   chunk 123 optimal weight:    2.9990
   chunk 158 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 221 optimal weight:    2.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 460 GLN
A 527 ASN
B 107 GLN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072250 restraints weight = 106583.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.89
r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  19768  Z= 0.166
  Angle     :  0.563   6.907  26888  Z= 0.291
  Chirality :  0.044   0.410   3042
  Planarity :  0.005   0.047   3502
  Dihedral  :  6.998  64.735   2746
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.28 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.56 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.23 (0.17), residues: 2500
  helix:  1.79 (0.16), residues: 1032
  sheet:  0.80 (0.33), residues: 244
  loop : -1.52 (0.17), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1077 
 TYR   0.019   0.002   TYR B 468 
 PHE   0.009   0.001   PHE A 348 
 TRP   0.011   0.001   TRP A 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (19768)
  covalent geometry    : angle       0.56304 (26888)
  hydrogen bonds       : bond        0.04384 (  882)
  hydrogen bonds       : angle       4.52700 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 127
  time to evaluate  : 1.250 
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: A  167 ARG cc_start: 0.3133 (OUTLIER) cc_final: 0.2092 (tpp80)
REVERT: A  323 GLN cc_start: 0.4147 (OUTLIER) cc_final: 0.2811 (mp10)
REVERT: A  705 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5851 (mttm)
REVERT: A  723 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7444 (tt0)
REVERT: A 1121 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8637 (pp)
REVERT: B   43 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (m)
REVERT: B  167 ARG cc_start: 0.3223 (OUTLIER) cc_final: 0.2307 (tpp80)
REVERT: B  723 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7429 (tt0)
REVERT: B 1121 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8609 (pp)
  outliers start: 78
  outliers final: 54
  residues processed: 195
  average time/residue: 1.5556
  time to fit residues: 341.6669
Evaluate side-chains
  183 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 122
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1167 ASP
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  505 THR
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  725 VAL
Chi-restraints excluded: chain B residue  726 SER
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  980 THR
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1121 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 248 optimal weight:    0.0980
   chunk 128 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 174 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 240 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 221 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 460 GLN
A 527 ASN
B 107 GLN
B 527 ASN
B1050 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.102752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.072517 restraints weight = 106698.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.90
r_work: 0.2955 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  19768  Z= 0.150
  Angle     :  0.550   6.906  26888  Z= 0.283
  Chirality :  0.044   0.417   3042
  Planarity :  0.005   0.053   3502
  Dihedral  :  6.743  64.986   2741
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.00 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.70 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.31 (0.17), residues: 2500
  helix:  1.86 (0.16), residues: 1036
  sheet:  0.82 (0.33), residues: 244
  loop : -1.48 (0.17), residues: 1220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1077 
 TYR   0.019   0.001   TYR B 468 
 PHE   0.008   0.001   PHE B 437 
 TRP   0.011   0.001   TRP A 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (19768)
  covalent geometry    : angle       0.55022 (26888)
  hydrogen bonds       : bond        0.04145 (  882)
  hydrogen bonds       : angle       4.42265 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 125
  time to evaluate  : 1.129 
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: A  167 ARG cc_start: 0.3072 (OUTLIER) cc_final: 0.2119 (tpp80)
REVERT: A  323 GLN cc_start: 0.4162 (OUTLIER) cc_final: 0.2793 (mp10)
REVERT: A  705 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5821 (mttm)
REVERT: A  723 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7411 (tt0)
REVERT: A 1121 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8580 (pp)
REVERT: B   43 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8354 (m)
REVERT: B  167 ARG cc_start: 0.3171 (OUTLIER) cc_final: 0.2262 (tpp80)
REVERT: B  723 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7404 (tt0)
REVERT: B 1121 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8584 (pp)
  outliers start: 72
  outliers final: 53
  residues processed: 185
  average time/residue: 1.5967
  time to fit residues: 333.2002
Evaluate side-chains
  183 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 123
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1122 LEU
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  433 CYS
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  779 THR
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  980 THR
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1087 THR
Chi-restraints excluded: chain B residue 1121 LEU
Chi-restraints excluded: chain B residue 1122 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 167 optimal weight:   20.0000
   chunk 76 optimal weight:    0.0570
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 184 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 206 optimal weight:    2.9990
   overall best weight:    2.0104

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
A 527 ASN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071359 restraints weight = 107166.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.92
r_work: 0.2933 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  19768  Z= 0.197
  Angle     :  0.573   6.830  26888  Z= 0.296
  Chirality :  0.045   0.410   3042
  Planarity :  0.005   0.123   3502
  Dihedral  :  6.600  62.970   2734
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.44 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.32 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.22 (0.17), residues: 2500
  helix:  1.75 (0.16), residues: 1046
  sheet:  0.64 (0.33), residues: 250
  loop : -1.50 (0.17), residues: 1204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1077 
 TYR   0.019   0.002   TYR B 468 
 PHE   0.009   0.001   PHE B 437 
 TRP   0.011   0.001   TRP B 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (19768)
  covalent geometry    : angle       0.57281 (26888)
  hydrogen bonds       : bond        0.04455 (  882)
  hydrogen bonds       : angle       4.46705 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 123
  time to evaluate  : 1.139 
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: A  167 ARG cc_start: 0.3205 (OUTLIER) cc_final: 0.2121 (tpp80)
REVERT: A  323 GLN cc_start: 0.4218 (OUTLIER) cc_final: 0.2902 (mp10)
REVERT: A  705 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5895 (mttm)
REVERT: A  723 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7529 (tt0)
REVERT: A 1121 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8571 (pp)
REVERT: B   43 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8385 (m)
REVERT: B  723 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7515 (tt0)
REVERT: B 1121 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8547 (pp)
  outliers start: 77
  outliers final: 57
  residues processed: 191
  average time/residue: 1.5665
  time to fit residues: 338.2369
Evaluate side-chains
  184 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 121
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  910 SER
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1122 LEU
Chi-restraints excluded: chain A residue 1167 ASP
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  433 CYS
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  728 VAL
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  980 THR
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1121 LEU
Chi-restraints excluded: chain B residue 1167 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 223 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 198 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 197 optimal weight:    0.2980
   chunk 218 optimal weight:    2.9990
   chunk 219 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
A 527 ASN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.103363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.073207 restraints weight = 106735.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.90
r_work: 0.2972 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  19768  Z= 0.115
  Angle     :  0.535   6.845  26888  Z= 0.274
  Chirality :  0.043   0.413   3042
  Planarity :  0.005   0.087   3502
  Dihedral  :  6.358  65.363   2732
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.60 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.08 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.46 (0.17), residues: 2500
  helix:  2.08 (0.16), residues: 1024
  sheet:  0.74 (0.33), residues: 250
  loop : -1.43 (0.17), residues: 1226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1077 
 TYR   0.018   0.001   TYR B 468 
 PHE   0.015   0.001   PHE B 348 
 TRP   0.011   0.001   TRP B 393 
 HIS   0.004   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (19768)
  covalent geometry    : angle       0.53524 (26888)
  hydrogen bonds       : bond        0.03775 (  882)
  hydrogen bonds       : angle       4.29573 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 129
  time to evaluate  : 1.136 
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: A  167 ARG cc_start: 0.3021 (OUTLIER) cc_final: 0.1999 (tpp80)
REVERT: A  323 GLN cc_start: 0.4112 (OUTLIER) cc_final: 0.2715 (mp10)
REVERT: A  705 LYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5752 (mttm)
REVERT: A  723 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7339 (tt0)
REVERT: A 1121 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8500 (pp)
REVERT: B   43 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8363 (m)
REVERT: B  167 ARG cc_start: 0.3117 (OUTLIER) cc_final: 0.2165 (tpp80)
REVERT: B  574 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4997 (t80)
REVERT: B  723 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7378 (tt0)
REVERT: B 1121 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8512 (pp)
  outliers start: 64
  outliers final: 43
  residues processed: 185
  average time/residue: 1.6218
  time to fit residues: 337.1306
Evaluate side-chains
  174 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 123
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1167 ASP
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  574 TYR
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1121 LEU
Chi-restraints excluded: chain B residue 1167 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 229 optimal weight:    5.9990
   chunk 249 optimal weight:    0.9980
   chunk 237 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 182 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 204 optimal weight:    3.9990
   chunk 114 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 460 GLN
A 527 ASN
B 107 GLN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.101402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072023 restraints weight = 108503.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.84
r_work: 0.2931 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  19768  Z= 0.222
  Angle     :  0.583   6.708  26888  Z= 0.301
  Chirality :  0.046   0.410   3042
  Planarity :  0.005   0.074   3502
  Dihedral  :  6.418  61.939   2731
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.28 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.51 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 aren not related in a simple way.
  whole:  0.26 (0.17), residues: 2500
  helix:  1.77 (0.16), residues: 1046
  sheet:  0.64 (0.33), residues: 250
  loop : -1.46 (0.17), residues: 1204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1077 
 TYR   0.019   0.002   TYR B 468 
 PHE   0.019   0.001   PHE B 348 
 TRP   0.010   0.001   TRP B 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (19768)
  covalent geometry    : angle       0.58272 (26888)
  hydrogen bonds       : bond        0.04558 (  882)
  hydrogen bonds       : angle       4.45339 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 120
  time to evaluate  : 1.152 
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: A  167 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.2151 (tpp80)
REVERT: A  323 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.3026 (mp10)
REVERT: A  705 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5511 (mmtt)
REVERT: A  723 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7560 (tt0)
REVERT: A 1121 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8548 (pp)
REVERT: B   43 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8374 (m)
REVERT: B  354 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6711 (ttp-110)
REVERT: B  723 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7551 (tt0)
  outliers start: 68
  outliers final: 51
  residues processed: 177
  average time/residue: 1.5747
  time to fit residues: 313.5174
Evaluate side-chains
  174 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 118
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  433 CYS
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1167 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 203 optimal weight:    0.8980
   chunk 206 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 225 optimal weight:    2.9990
   chunk 162 optimal weight:    0.5980
   chunk 134 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 233 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 460 GLN
B 107 GLN
B 460 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.102710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.072497 restraints weight = 107174.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.91
r_work: 0.2957 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  19768  Z= 0.127
  Angle     :  0.544   7.704  26888  Z= 0.279
  Chirality :  0.043   0.416   3042
  Planarity :  0.005   0.093   3502
  Dihedral  :  6.281  63.899   2731
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.92 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.31 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 aren not related in a simple way.
  whole:  0.41 (0.17), residues: 2500
  helix:  1.92 (0.16), residues: 1042
  sheet:  0.69 (0.33), residues: 250
  loop : -1.38 (0.18), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1077 
 TYR   0.018   0.001   TYR B 468 
 PHE   0.014   0.001   PHE B 348 
 TRP   0.012   0.001   TRP B 393 
 HIS   0.006   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (19768)
  covalent geometry    : angle       0.54368 (26888)
  hydrogen bonds       : bond        0.03959 (  882)
  hydrogen bonds       : angle       4.31419 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 120
  time to evaluate  : 1.377 
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: A  167 ARG cc_start: 0.3057 (OUTLIER) cc_final: 0.2040 (tpp80)
REVERT: A  323 GLN cc_start: 0.4217 (OUTLIER) cc_final: 0.2889 (mp10)
REVERT: A  705 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5685 (mttp)
REVERT: A  723 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7418 (tt0)
REVERT: A 1121 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8493 (pp)
REVERT: B   43 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8364 (m)
REVERT: B  354 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6632 (ttp-110)
REVERT: B  723 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7444 (tt0)
REVERT: B 1033 MET cc_start: 0.9051 (mtp) cc_final: 0.8718 (mtt)
  outliers start: 55
  outliers final: 45
  residues processed: 167
  average time/residue: 1.6778
  time to fit residues: 315.0346
Evaluate side-chains
  168 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 118
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  725 VAL
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  910 SER
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  574 TYR
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1088 LEU
Chi-restraints excluded: chain B residue 1167 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 226 optimal weight:    2.9990
   chunk 84 optimal weight:    0.4980
   chunk 51 optimal weight:    9.9990
   chunk 145 optimal weight:    0.3980
   chunk 58 optimal weight:   30.0000
   chunk 88 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 122 optimal weight:    0.5980
   chunk 206 optimal weight:    2.9990
   chunk 215 optimal weight:    3.9990
   chunk 212 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
A 527 ASN
B 460 GLN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.104162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.074046 restraints weight = 106741.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.92
r_work: 0.2993 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  19768  Z= 0.102
  Angle     :  0.525  10.485  26888  Z= 0.266
  Chirality :  0.043   0.411   3042
  Planarity :  0.005   0.092   3502
  Dihedral  :  5.990  66.258   2728
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.72 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.83 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 aren not related in a simple way.
  whole:  0.69 (0.17), residues: 2500
  helix:  2.19 (0.16), residues: 1046
  sheet:  0.65 (0.31), residues: 286
  loop : -1.29 (0.18), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG B1077 
 TYR   0.016   0.001   TYR B 468 
 PHE   0.008   0.001   PHE B 348 
 TRP   0.011   0.001   TRP B 393 
 HIS   0.004   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (19768)
  covalent geometry    : angle       0.52455 (26888)
  hydrogen bonds       : bond        0.03451 (  882)
  hydrogen bonds       : angle       4.17008 ( 2508)

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

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

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5000 Ramachandran restraints generated.
    2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 124
  time to evaluate  : 1.117 
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: A  167 ARG cc_start: 0.2811 (OUTLIER) cc_final: 0.1829 (tpp80)
REVERT: A  323 GLN cc_start: 0.4137 (OUTLIER) cc_final: 0.2864 (mp10)
REVERT: A 1121 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8469 (pp)
REVERT: B  354 ARG cc_start: 0.7003 (ttm110) cc_final: 0.6585 (ttp-110)
REVERT: B  574 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4588 (t80)
REVERT: B 1033 MET cc_start: 0.9022 (mtp) cc_final: 0.8688 (mtt)
  outliers start: 48
  outliers final: 36
  residues processed: 163
  average time/residue: 1.7090
  time to fit residues: 312.0573
Evaluate side-chains
  161 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  673 SER
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  808 HIS
Chi-restraints excluded: chain A residue 1081 ASP
Chi-restraints excluded: chain A residue 1086 CYS
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  167 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  332 PHE
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  398 LYS
Chi-restraints excluded: chain B residue  556 SER
Chi-restraints excluded: chain B residue  574 TYR
Chi-restraints excluded: chain B residue  673 SER
Chi-restraints excluded: chain B residue  781 THR
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  988 VAL
Chi-restraints excluded: chain B residue 1086 CYS
Chi-restraints excluded: chain B residue 1088 LEU
Chi-restraints excluded: chain B residue 1167 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 170 optimal weight:    0.8980
   chunk 169 optimal weight:    0.8980
   chunk 166 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
B 460 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.103505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.073350 restraints weight = 106547.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.89
r_work: 0.2976 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  19768  Z= 0.127
  Angle     :  0.532   6.612  26888  Z= 0.272
  Chirality :  0.043   0.413   3042
  Planarity :  0.005   0.093   3502
  Dihedral  :  5.904  65.371   2724
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.00 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.21 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 aren not related in a simple way.
  whole:  0.65 (0.17), residues: 2500
  helix:  2.15 (0.16), residues: 1042
  sheet:  0.66 (0.31), residues: 286
  loop : -1.30 (0.18), residues: 1172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG A1077 
 TYR   0.018   0.001   TYR B 468 
 PHE   0.007   0.001   PHE B 348 
 TRP   0.011   0.001   TRP B 393 
 HIS   0.005   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (19768)
  covalent geometry    : angle       0.53229 (26888)
  hydrogen bonds       : bond        0.03698 (  882)
  hydrogen bonds       : angle       4.20554 ( 2508)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14512.68 seconds
wall clock time: 246 minutes 18.01 seconds (14778.01 seconds total)