Starting phenix.real_space_refine
on Thu Sep 18 16:04:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bf1_44486/09_2025/9bf1_44486.cif"
  }
  resolution = 3.1
  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=   0.002 sd=   0.034
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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C   11484      2.51       5
     N    3192      2.21       5
     O    3436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18158
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1122, 9079
          Classifications: {'peptide': 1122}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 9079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1122, 9079
          Classifications: {'peptide': 1122}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088}
          Chain breaks: 3
  Time building chain proxies: 3.87, per 1000 atoms: 0.21
  Number of scatterers: 18158
  At special positions: 0
  Unit cell: (121.9, 132.5, 136.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    3436      8.00
     N    3192      7.00
     C   11484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 796.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4284

  Finding SS restraints...
    Secondary structure from input PDB file:
      95 helices and 20 sheets defined
      54.5% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
      removed outlier: 3.718A  pdb=" N   THR A   9 " --> pdb=" O   GLU A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 37
      Proline residue:  A  29  - end of helix
    Processing helix  chain 'A' and resid 54 through 78
    Processing helix  chain 'A' and resid 79 through 81
      No H-bonds generated for 'chain 'A' and resid 79 through 81'
    Processing helix  chain 'A' and resid 96 through 112
      removed outlier: 3.511A  pdb=" N   SER A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LYS A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 137 through 145
    Processing helix  chain 'A' and resid 146 through 157
      removed outlier: 3.575A  pdb=" N   LEU A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 178
      removed outlier: 3.565A  pdb=" N   GLN A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 207
      removed outlier: 3.805A  pdb=" N   SER A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 227
    Processing helix  chain 'A' and resid 227 through 235
      removed outlier: 4.028A  pdb=" N   LYS A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A 232 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 250
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 276 through 286
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.577A  pdb=" N   ILE A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
      removed outlier: 3.544A  pdb=" N   GLU A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 435
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.699A  pdb=" N   THR A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLN A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   GLU A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 463
      No H-bonds generated for 'chain 'A' and resid 461 through 463'
    Processing helix  chain 'A' and resid 464 through 471
    Processing helix  chain 'A' and resid 475 through 479
      removed outlier: 3.965A  pdb=" N   GLN A 479 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 3.590A  pdb=" N   HIS A 496 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 536
      removed outlier: 3.530A  pdb=" N   GLY A 536 " --> pdb=" O   MET A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 565
    Processing helix  chain 'A' and resid 572 through 587
    Processing helix  chain 'A' and resid 604 through 616
    Processing helix  chain 'A' and resid 621 through 629
      removed outlier: 4.412A  pdb=" N   ILE A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 657
      removed outlier: 4.631A  pdb=" N   PHE A 639 " --> pdb=" O   SER A 635 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA A 649 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 691
      removed outlier: 3.755A  pdb=" N   ILE A 678 " --> pdb=" O   THR A 674 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 688 " --> pdb=" O   PHE A 684 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS A 691 " --> pdb=" O   ASP A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 808
      removed outlier: 3.750A  pdb=" N   ASN A 793 " --> pdb=" O   SER A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 825
    Processing helix  chain 'A' and resid 827 through 837
      removed outlier: 4.075A  pdb=" N   GLN A 837 " --> pdb=" O   GLN A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 855
      removed outlier: 3.878A  pdb=" N   GLN A 842 " --> pdb=" O   THR A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 880
    Processing helix  chain 'A' and resid 889 through 901
      removed outlier: 3.687A  pdb=" N   SER A 901 " --> pdb=" O   ASN A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 937
      removed outlier: 3.970A  pdb=" N   ARG A 913 " --> pdb=" O   ASP A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 943 through 960
    Processing helix  chain 'A' and resid 970 through 972
      No H-bonds generated for 'chain 'A' and resid 970 through 972'
    Processing helix  chain 'A' and resid 992 through 996
      removed outlier: 3.732A  pdb=" N   PHE A 996 " --> pdb=" O   PRO A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1000 through 1002
      No H-bonds generated for 'chain 'A' and resid 1000 through 1002'
    Processing helix  chain 'A' and resid 1014 through 1019
    Processing helix  chain 'A' and resid 1023 through 1032
      removed outlier: 3.708A  pdb=" N   TRP A1027 " --> pdb=" O   TYR A1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1068
    Processing helix  chain 'A' and resid 1110 through 1127
    Processing helix  chain 'A' and resid 1176 through 1189
    Processing helix  chain 'B' and resid 4 through 9
    Processing helix  chain 'B' and resid 20 through 37
      removed outlier: 3.700A  pdb=" N   ILE B  26 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      Proline residue:  B  29  - end of helix
    Processing helix  chain 'B' and resid 54 through 78
    Processing helix  chain 'B' and resid 79 through 81
      No H-bonds generated for 'chain 'B' and resid 79 through 81'
    Processing helix  chain 'B' and resid 95 through 98
    Processing helix  chain 'B' and resid 99 through 112
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 162 through 178
      removed outlier: 3.615A  pdb=" N   HIS B 178 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 207
      removed outlier: 3.632A  pdb=" N   SER B 187 " --> pdb=" O   GLU B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 227
    Processing helix  chain 'B' and resid 227 through 234
      removed outlier: 3.874A  pdb=" N   LYS B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE B 232 " --> pdb=" O   PRO B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 250
    Processing helix  chain 'B' and resid 273 through 286
      removed outlier: 3.694A  pdb=" N   GLN B 277 " --> pdb=" O   GLU B 273 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ASN B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLN B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 312 through 316
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 401 through 435
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.501A  pdb=" N   GLN B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU B 450 " --> pdb=" O   GLY B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 463
      No H-bonds generated for 'chain 'B' and resid 461 through 463'
    Processing helix  chain 'B' and resid 464 through 471
    Processing helix  chain 'B' and resid 493 through 497
    Processing helix  chain 'B' and resid 524 through 536
      removed outlier: 3.663A  pdb=" N   GLY B 536 " --> pdb=" O   MET B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 565
      removed outlier: 3.637A  pdb=" N   GLU B 562 " --> pdb=" O   LYS B 558 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 568
      No H-bonds generated for 'chain 'B' and resid 566 through 568'
    Processing helix  chain 'B' and resid 572 through 587
    Processing helix  chain 'B' and resid 604 through 616
      removed outlier: 3.859A  pdb=" N   LYS B 616 " --> pdb=" O   LEU B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 629
      removed outlier: 3.554A  pdb=" N   ILE B 625 " --> pdb=" O   SER B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 657
      removed outlier: 4.257A  pdb=" N   ALA B 638 " --> pdb=" O   GLU B 634 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   PHE B 639 " --> pdb=" O   SER B 635 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS B 646 " --> pdb=" O   SER B 642 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA B 649 " --> pdb=" O   SER B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 675 through 691
      removed outlier: 3.558A  pdb=" N   LYS B 691 " --> pdb=" O   ASP B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 808
      removed outlier: 3.643A  pdb=" N   ASN B 793 " --> pdb=" O   SER B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 824
    Processing helix  chain 'B' and resid 827 through 836
    Processing helix  chain 'B' and resid 838 through 856
      removed outlier: 4.048A  pdb=" N   GLN B 842 " --> pdb=" O   THR B 838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 879
      removed outlier: 4.450A  pdb=" N   ILE B 877 " --> pdb=" O   GLY B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 889 through 902
    Processing helix  chain 'B' and resid 909 through 938
      removed outlier: 4.362A  pdb=" N   ARG B 913 " --> pdb=" O   ASP B 909 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 943 through 960
    Processing helix  chain 'B' and resid 970 through 972
      No H-bonds generated for 'chain 'B' and resid 970 through 972'
    Processing helix  chain 'B' and resid 1000 through 1002
      No H-bonds generated for 'chain 'B' and resid 1000 through 1002'
    Processing helix  chain 'B' and resid 1009 through 1014
      removed outlier: 3.586A  pdb=" N   SER B1014 " --> pdb=" O   GLU B1010 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1014 through 1019
    Processing helix  chain 'B' and resid 1023 through 1032
    Processing helix  chain 'B' and resid 1045 through 1068
    Processing helix  chain 'B' and resid 1077 through 1081
      removed outlier: 3.826A  pdb=" N   ILE B1080 " --> pdb=" O   PRO B1077 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR B1081 " --> pdb=" O   ASN B1078 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1077 through 1081'
    Processing helix  chain 'B' and resid 1110 through 1127
    Processing helix  chain 'B' and resid 1176 through 1190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44
      removed outlier: 5.937A  pdb=" N   ALA A  43 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   GLY A 541 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA A 267 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   LEU A 540 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU A 269 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ILE A 542 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE A 271 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LEU A  88 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   LEU A 242 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   TYR A  90 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252
    Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292
    Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 344
      removed outlier: 6.916A  pdb=" N   ASN A 343 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601
      removed outlier: 3.704A  pdb=" N   VAL A 870 " --> pdb=" O   LYS A 599 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 974 through 975
    Processing sheet with id=AA8, first strand: chain 'A' and resid 997 through 998
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1072 through 1074
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1097 through 1099
      removed outlier: 6.542A  pdb=" N   PHE A1131 " --> pdb=" O   ILE A1162 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ILE A1164 " --> pdb=" O   PHE A1131 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   TYR A1133 " --> pdb=" O   ILE A1164 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ARG A1145 " --> pdb=" O   GLU A1163 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 47
      removed outlier: 5.875A  pdb=" N   ALA B  43 " --> pdb=" O   ILE B 539 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   GLY B 541 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU B  45 " --> pdb=" O   GLY B 541 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ALA B 267 " --> pdb=" O   VAL B 538 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU B 540 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU B 269 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   ILE B 542 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE B 271 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B  88 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   LEU B 242 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   TYR B  90 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   THR B 243 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   LEU B 135 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 114
    Processing sheet with id=AB4, first strand: chain 'B' and resid 251 through 252
    Processing sheet with id=AB5, first strand: chain 'B' and resid 291 through 292
    Processing sheet with id=AB6, first strand: chain 'B' and resid 342 through 344
    Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 601
      removed outlier: 6.754A  pdb=" N   LEU B 664 " --> pdb=" O   TYR B 775 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 974 through 975
    Processing sheet with id=AB9, first strand: chain 'B' and resid 997 through 998
    Processing sheet with id=AC1, first strand: chain 'B' and resid 1072 through 1074
      removed outlier: 4.256A  pdb=" N   ASN B1086 " --> pdb=" O   LEU B1099 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU B1099 " --> pdb=" O   ASN B1086 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE B1097 " --> pdb=" O   VAL B1088 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   TRP B1098 " --> pdb=" O   ILE B1132 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   VAL B1134 " --> pdb=" O   TRP B1098 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B1100 " --> pdb=" O   VAL B1134 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG B1145 " --> pdb=" O   GLU B1163 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 1137 through 1138
      removed outlier: 4.457A  pdb=" N   GLY B1138 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2

    934 hydrogen bonds defined for protein.
    2676 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: 3.43

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6079
        1.34 -     1.46: 3127
        1.46 -     1.57: 9242
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 18520
  Sorted by residual:
  bond pdb=" C   THR A1045 "
       pdb=" N   PRO A1046 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.38e-02 5.25e+03 2.53e+00
  bond pdb=" CG  LEU B 142 "
       pdb=" CD1 LEU B 142 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CA  ASP B1070 "
       pdb=" CB  ASP B1070 "
    ideal  model  delta    sigma   weight residual
    1.527  1.541 -0.014 1.61e-02 3.86e+03 7.90e-01
  bond pdb=" CA  ASN A1042 "
       pdb=" C   ASN A1042 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.63e-01
  bond pdb=" CB  VAL A 502 "
       pdb=" CG1 VAL A 502 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.49e-01
  ... (remaining 18515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 24810
        2.09 -     4.17: 185
        4.17 -     6.26: 23
        6.26 -     8.34: 1
        8.34 -    10.43: 1
  Bond angle restraints: 25020
  Sorted by residual:
  angle pdb=" C   PHE B 999 "
        pdb=" CA  PHE B 999 "
        pdb=" CB  PHE B 999 "
      ideal   model   delta    sigma   weight residual
     116.34  109.81    6.53 1.40e+00 5.10e-01 2.17e+01
  angle pdb=" N   PHE B 999 "
        pdb=" CA  PHE B 999 "
        pdb=" C   PHE B 999 "
      ideal   model   delta    sigma   weight residual
     108.00  113.24   -5.24 1.48e+00 4.57e-01 1.25e+01
  angle pdb=" CA  LEU A 135 "
        pdb=" CB  LEU A 135 "
        pdb=" CG  LEU A 135 "
      ideal   model   delta    sigma   weight residual
     116.30  126.73  -10.43 3.50e+00 8.16e-02 8.88e+00
  angle pdb=" C   PHE A1069 "
        pdb=" N   ASP A1070 "
        pdb=" CA  ASP A1070 "
      ideal   model   delta    sigma   weight residual
     122.82  126.76   -3.94 1.42e+00 4.96e-01 7.71e+00
  angle pdb=" C   PHE B1069 "
        pdb=" N   ASP B1070 "
        pdb=" CA  ASP B1070 "
      ideal   model   delta    sigma   weight residual
     122.82  126.63   -3.81 1.42e+00 4.96e-01 7.21e+00
  ... (remaining 25015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 10027
       17.65 -    35.30: 964
       35.30 -    52.96: 131
       52.96 -    70.61: 63
       70.61 -    88.26: 27
  Dihedral angle restraints: 11212
    sinusoidal: 4612
      harmonic: 6600
  Sorted by residual:
  dihedral pdb=" CA  VAL B  98 "
           pdb=" C   VAL B  98 "
           pdb=" N   VAL B  99 "
           pdb=" CA  VAL B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.30   27.70     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  VAL A  98 "
           pdb=" C   VAL A  98 "
           pdb=" N   VAL A  99 "
           pdb=" CA  VAL A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.35   26.65     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  ARG B 675 "
           pdb=" C   ARG B 675 "
           pdb=" N   GLN B 676 "
           pdb=" CA  GLN B 676 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 11209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1936
       0.037 -    0.074: 625
       0.074 -    0.111: 152
       0.111 -    0.148: 28
       0.148 -    0.185: 5
  Chirality restraints: 2746
  Sorted by residual:
  chirality pdb=" CG  LEU A 135 "
            pdb=" CB  LEU A 135 "
            pdb=" CD1 LEU A 135 "
            pdb=" CD2 LEU A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CA  ASP A1070 "
            pdb=" N   ASP A1070 "
            pdb=" C   ASP A1070 "
            pdb=" CB  ASP A1070 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  ASP B1070 "
            pdb=" N   ASP B1070 "
            pdb=" C   ASP B1070 "
            pdb=" CB  ASP B1070 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 2743 not shown)

  Planarity restraints: 3256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1049 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.48e+00
        pdb=" C   PHE A1049 "    0.044 2.00e-02 2.50e+03
        pdb=" O   PHE A1049 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR A1050 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B1049 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.92e+00
        pdb=" C   PHE B1049 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   PHE B1049 "    0.016 2.00e-02 2.50e+03
        pdb=" N   THR B1050 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1050 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   THR A1050 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR A1050 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A1051 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 3253 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 596
        2.72 -     3.26: 18403
        3.26 -     3.81: 29519
        3.81 -     4.35: 35368
        4.35 -     4.90: 60769
  Nonbonded interactions: 144655
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 121 "
            pdb=" OE1 GLN A 124 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG  SER A 311 "
            pdb=" O   LEU B 379 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OH  TYR A 494 "
            pdb=" ND1 HIS A 799 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OH  TYR B 427 "
            pdb=" OE2 GLU B 450 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OE1 GLU A  77 "
            pdb=" OG1 THR A  80 "
     model   vdw
     2.232 3.040
  ... (remaining 144650 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:                  0.010
  Normalize map: mean=0, sd=1:             5.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.600
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2759
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      :  0.003   0.042  18520  Z= 0.142
  Angle     :  0.482  10.429  25020  Z= 0.262
  Chirality :  0.040   0.185   2746
  Planarity :  0.004   0.048   3256
  Dihedral  : 14.853  88.261   6928
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.18), residues: 2228
  helix:  1.72 (0.16), residues: 1084
  sheet: -0.12 (0.31), residues: 302
  loop : -0.95 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  72 
 TYR   0.021   0.001   TYR A1115 
 PHE   0.009   0.001   PHE A 157 
 TRP   0.011   0.001   TRP B 336 
 HIS   0.006   0.001   HIS B 836 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (18520)
  covalent geometry    : angle       0.48202 (25020)
  hydrogen bonds       : bond        0.13903 (  934)
  hydrogen bonds       : angle       5.95578 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.631 
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: A  298 ARG cc_start: 0.3167 (mtp180) cc_final: 0.2653 (ttm-80)
REVERT: A  978 MET cc_start: 0.2048 (mmt) cc_final: 0.1783 (mmt)
REVERT: B  500 LYS cc_start: 0.2382 (ttpt) cc_final: 0.1674 (ttpt)
REVERT: B  613 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7348 (mt-10)
REVERT: B 1102 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6862 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1503
  time to fit residues: 35.6300
Evaluate side-chains
  130 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 216 optimal weight:   50.0000
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    0.9980
   chunk 200 optimal weight:    3.9990
   chunk 212 optimal weight:    4.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 125 GLN
A 131 GLN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 ASN
** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 253 ASN
A 495 HIS
A 679 ASN
A 794 GLN
A 799 HIS
A 800 GLN
A 805 GLN
A 834 GLN
A 920 GLN
A 935 HIS
A 938 HIS
A1060 GLN
A1188 HIS
B  65 GLN
B 131 GLN
B 141 GLN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 279 GLN
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 460 ASN
B 495 HIS
B 507 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 637 GLN
B 790 HIS
** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 935 HIS
B 994 ASN
B1060 GLN
B1078 ASN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.218306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.188031 restraints weight = 28248.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 2.53
r_work: 0.4184 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5835
moved from start:          0.8625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074  18520  Z= 0.343
  Angle     :  1.047  20.287  25020  Z= 0.547
  Chirality :  0.056   0.265   2746
  Planarity :  0.008   0.082   3256
  Dihedral  :  6.263  25.632   2460
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.33 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.97 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.16), residues: 2228
  helix: -0.25 (0.14), residues: 1122
  sheet: -0.78 (0.36), residues: 210
  loop : -1.75 (0.19), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 921 
 TYR   0.051   0.004   TYR A1115 
 PHE   0.036   0.004   PHE A 996 
 TRP   0.041   0.003   TRP B 336 
 HIS   0.021   0.003   HIS B 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00768 (18520)
  covalent geometry    : angle       1.04736 (25020)
  hydrogen bonds       : bond        0.06359 (  934)
  hydrogen bonds       : angle       5.98494 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 232
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 THR cc_start: 0.7561 (p) cc_final: 0.7030 (t)
REVERT: A  450 GLU cc_start: 0.7754 (tt0) cc_final: 0.6873 (tt0)
REVERT: A  463 GLU cc_start: 0.7359 (mp0) cc_final: 0.6745 (mp0)
REVERT: A  522 ASN cc_start: 0.6347 (m-40) cc_final: 0.5900 (m110)
REVERT: A 1028 PHE cc_start: 0.5628 (m-10) cc_final: 0.4750 (m-10)
REVERT: A 1047 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6805 (tp)
REVERT: B  118 PRO cc_start: 0.8059 (Cg_exo) cc_final: 0.7772 (Cg_endo)
REVERT: B  172 ILE cc_start: 0.6286 (mm) cc_final: 0.5518 (mm)
REVERT: B  273 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6829 (mt-10)
REVERT: B  315 TYR cc_start: 0.7924 (m-80) cc_final: 0.7688 (m-80)
REVERT: B  469 TYR cc_start: 0.7015 (m-10) cc_final: 0.6768 (m-10)
REVERT: B  613 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: B  646 LYS cc_start: 0.5526 (mttt) cc_final: 0.5141 (mptt)
REVERT: B  786 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6754 (t0)
REVERT: B  829 GLU cc_start: 0.6755 (mp0) cc_final: 0.6445 (mp0)
REVERT: B  983 TYR cc_start: 0.6848 (p90) cc_final: 0.5745 (p90)
REVERT: B  984 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5364 (mtm-85)
REVERT: B 1044 MET cc_start: 0.6387 (ptp) cc_final: 0.6132 (ptp)
REVERT: B 1059 GLU cc_start: 0.7109 (pt0) cc_final: 0.6853 (pt0)
  outliers start: 38
  outliers final: 14
  residues processed: 258
  average time/residue: 0.1302
  time to fit residues: 51.9309
Evaluate side-chains
  204 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  494 TYR
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  871 ASP
Chi-restraints excluded: chain A residue 1047 ILE
Chi-restraints excluded: chain A residue 1057 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  776 LEU
Chi-restraints excluded: chain B residue  786 ASP
Chi-restraints excluded: chain B residue  962 THR
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1023 TYR
Chi-restraints excluded: chain B residue 1045 THR
Chi-restraints excluded: chain B residue 1047 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 183 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 180 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 150 optimal weight:    0.4980
   chunk 136 optimal weight:    0.5980
   chunk 122 optimal weight:    1.9990
   chunk 198 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
A 112 GLN
A 160 ASN
A 350 ASN
A 460 ASN
A 495 HIS
A 676 GLN
A 799 HIS
A 800 GLN
A 920 GLN
A 939 ASN
A 956 GLN
B  65 GLN
B  70 GLN
B  97 ASN
B 131 GLN
B 144 GLN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 279 GLN
B 307 HIS
B 335 ASN
B 495 HIS
B 637 GLN
B 805 GLN
B 817 ASN
B 821 GLN
B1051 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.203001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.167417 restraints weight = 26467.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 2.52
r_work: 0.3944 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.9810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  18520  Z= 0.186
  Angle     :  0.622  13.082  25020  Z= 0.326
  Chirality :  0.043   0.362   2746
  Planarity :  0.005   0.068   3256
  Dihedral  :  4.533  28.274   2460
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.89 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.67 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.17), residues: 2228
  helix:  0.86 (0.15), residues: 1126
  sheet: -0.53 (0.32), residues: 262
  loop : -1.49 (0.20), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 478 
 TYR   0.028   0.002   TYR A1115 
 PHE   0.017   0.002   PHE A 798 
 TRP   0.012   0.001   TRP A1037 
 HIS   0.011   0.001   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (18520)
  covalent geometry    : angle       0.62205 (25020)
  hydrogen bonds       : bond        0.04346 (  934)
  hydrogen bonds       : angle       4.91592 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 209
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.6739 (mp10) cc_final: 0.5982 (mp10)
REVERT: A  230 GLU cc_start: 0.6223 (tp30) cc_final: 0.5651 (tp30)
REVERT: A  278 ASN cc_start: 0.7880 (t0) cc_final: 0.7366 (t0)
REVERT: A  379 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7854 (mm)
REVERT: A  814 SER cc_start: 0.8344 (t) cc_final: 0.7946 (m)
REVERT: A  928 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7301 (mp)
REVERT: A 1028 PHE cc_start: 0.6066 (m-10) cc_final: 0.5346 (m-10)
REVERT: A 1059 GLU cc_start: 0.4808 (pt0) cc_final: 0.4238 (pt0)
REVERT: B   14 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6369 (tm-30)
REVERT: B  105 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7078 (tp)
REVERT: B  172 ILE cc_start: 0.6588 (mm) cc_final: 0.6385 (mm)
REVERT: B  271 ILE cc_start: 0.8202 (mt) cc_final: 0.7543 (mp)
REVERT: B  273 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7018 (mt-10)
REVERT: B  366 SER cc_start: 0.8119 (p) cc_final: 0.7872 (m)
REVERT: B  469 TYR cc_start: 0.7589 (m-10) cc_final: 0.7383 (m-10)
REVERT: B  521 LEU cc_start: 0.8179 (tp) cc_final: 0.7960 (tt)
REVERT: B  549 ASP cc_start: 0.7855 (t0) cc_final: 0.7596 (t0)
REVERT: B  578 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6990 (mtt-85)
REVERT: B  613 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7715 (mt-10)
REVERT: B  807 ASN cc_start: 0.6765 (t0) cc_final: 0.6292 (t0)
REVERT: B  820 ARG cc_start: 0.6889 (ttp-170) cc_final: 0.6532 (ttp-170)
REVERT: B  824 MET cc_start: 0.6905 (mpp) cc_final: 0.6395 (mpp)
REVERT: B  980 LYS cc_start: 0.7356 (mttt) cc_final: 0.7106 (mttt)
REVERT: B  983 TYR cc_start: 0.6951 (p90) cc_final: 0.5741 (p90)
REVERT: B  984 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5373 (mtm-85)
REVERT: B  986 GLN cc_start: 0.7054 (tp40) cc_final: 0.6733 (tp40)
REVERT: B 1008 VAL cc_start: 0.6647 (t) cc_final: 0.6264 (t)
REVERT: B 1029 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7498 (mt-10)
  outliers start: 33
  outliers final: 17
  residues processed: 235
  average time/residue: 0.1475
  time to fit residues: 52.8635
Evaluate side-chains
  208 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  251 PHE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  928 LEU
Chi-restraints excluded: chain A residue  938 HIS
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1099 LEU
Chi-restraints excluded: chain A residue 1144 ILE
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  984 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 223 optimal weight:    6.9990
   chunk 215 optimal weight:   20.0000
   chunk 197 optimal weight:    0.5980
   chunk 180 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 219 optimal weight:    2.9990
   chunk 217 optimal weight:   10.0000
   chunk 189 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 131 GLN
A 506 HIS
A 581 ASN
A 821 GLN
A 834 GLN
B 131 GLN
B 141 GLN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 GLN
B 522 ASN
B 628 HIS
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.200663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163433 restraints weight = 26446.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 2.65
r_work: 0.3869 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          1.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  18520  Z= 0.187
  Angle     :  0.597   9.925  25020  Z= 0.312
  Chirality :  0.043   0.389   2746
  Planarity :  0.005   0.062   3256
  Dihedral  :  4.401  23.575   2460
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  5.70 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.38 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.18), residues: 2228
  helix:  1.12 (0.15), residues: 1126
  sheet: -0.39 (0.32), residues: 256
  loop : -1.34 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 262 
 TYR   0.033   0.002   TYR A1115 
 PHE   0.022   0.002   PHE B 970 
 TRP   0.016   0.001   TRP B 336 
 HIS   0.005   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (18520)
  covalent geometry    : angle       0.59747 (25020)
  hydrogen bonds       : bond        0.03998 (  934)
  hydrogen bonds       : angle       4.76108 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 242
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLN cc_start: 0.7758 (mp10) cc_final: 0.7018 (mp10)
REVERT: A  379 LEU cc_start: 0.8328 (mm) cc_final: 0.8119 (mm)
REVERT: A  990 ASP cc_start: 0.5730 (p0) cc_final: 0.5529 (p0)
REVERT: A 1028 PHE cc_start: 0.6480 (m-10) cc_final: 0.5507 (m-10)
REVERT: A 1044 MET cc_start: 0.5021 (tpp) cc_final: 0.4732 (ttm)
REVERT: A 1048 MET cc_start: 0.7510 (mmt) cc_final: 0.7202 (mmt)
REVERT: A 1059 GLU cc_start: 0.5656 (pt0) cc_final: 0.5295 (pt0)
REVERT: A 1074 GLU cc_start: 0.7127 (mp0) cc_final: 0.6706 (mp0)
REVERT: B    1 MET cc_start: -0.1614 (OUTLIER) cc_final: -0.2471 (ptm)
REVERT: B   14 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6976 (tm-30)
REVERT: B  218 SER cc_start: 0.7650 (m) cc_final: 0.7292 (p)
REVERT: B  232 ILE cc_start: 0.7628 (mt) cc_final: 0.7384 (tt)
REVERT: B  273 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7250 (mt-10)
REVERT: B  366 SER cc_start: 0.7863 (p) cc_final: 0.7605 (m)
REVERT: B  449 GLN cc_start: 0.6635 (tt0) cc_final: 0.6310 (tt0)
REVERT: B  469 TYR cc_start: 0.7827 (m-10) cc_final: 0.7040 (m-10)
REVERT: B  552 ILE cc_start: 0.8193 (mt) cc_final: 0.7506 (tt)
REVERT: B  578 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6937 (mtt-85)
REVERT: B  613 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7826 (mt-10)
REVERT: B  807 ASN cc_start: 0.7008 (t0) cc_final: 0.6477 (t0)
REVERT: B  980 LYS cc_start: 0.7414 (mttt) cc_final: 0.7133 (mttt)
REVERT: B  983 TYR cc_start: 0.6940 (p90) cc_final: 0.5582 (p90)
REVERT: B  986 GLN cc_start: 0.7279 (tp40) cc_final: 0.6955 (tp40)
REVERT: B 1008 VAL cc_start: 0.6767 (t) cc_final: 0.6365 (t)
REVERT: B 1029 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: B 1044 MET cc_start: 0.7226 (ptp) cc_final: 0.6807 (ptm)
  outliers start: 36
  outliers final: 18
  residues processed: 265
  average time/residue: 0.1437
  time to fit residues: 57.2124
Evaluate side-chains
  246 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 227
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  733 TYR
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  522 ASN
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  893 VAL
Chi-restraints excluded: chain B residue  934 VAL
Chi-restraints excluded: chain B residue 1023 TYR
Chi-restraints excluded: chain B residue 1057 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 201 optimal weight:    0.0060
   chunk 35 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 203 optimal weight:    5.9990
   chunk 199 optimal weight:    0.0060
   chunk 53 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 153 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.3812

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

Flipped N/Q/H residues before XYZ refinement:
A 566 ASN
A 917 ASN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
B 479 GLN
B 805 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.201784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.164131 restraints weight = 26319.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 2.66
r_work: 0.3880 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          1.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  18520  Z= 0.107
  Angle     :  0.490   7.265  25020  Z= 0.257
  Chirality :  0.040   0.212   2746
  Planarity :  0.004   0.047   3256
  Dihedral  :  3.960  24.072   2460
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.26 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.68 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.18), residues: 2228
  helix:  1.61 (0.15), residues: 1119
  sheet: -0.31 (0.32), residues: 256
  loop : -1.14 (0.21), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 255 
 TYR   0.028   0.001   TYR A1115 
 PHE   0.018   0.001   PHE B 970 
 TRP   0.010   0.001   TRP A 169 
 HIS   0.002   0.000   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (18520)
  covalent geometry    : angle       0.48951 (25020)
  hydrogen bonds       : bond        0.03327 (  934)
  hydrogen bonds       : angle       4.37801 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 247
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A   50 GLN cc_start: 0.7619 (mp10) cc_final: 0.6970 (mp10)
REVERT: A  262 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7769 (tpp80)
REVERT: A  278 ASN cc_start: 0.8173 (t0) cc_final: 0.7970 (t0)
REVERT: A  379 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8083 (mm)
REVERT: A  556 ASP cc_start: 0.7898 (t0) cc_final: 0.7681 (t0)
REVERT: A  568 LEU cc_start: 0.7762 (mp) cc_final: 0.7489 (mt)
REVERT: A  806 GLU cc_start: 0.6877 (mp0) cc_final: 0.6657 (mp0)
REVERT: A  814 SER cc_start: 0.8415 (t) cc_final: 0.8086 (m)
REVERT: A  970 PHE cc_start: 0.7888 (m-80) cc_final: 0.7610 (m-80)
REVERT: A 1028 PHE cc_start: 0.6409 (m-10) cc_final: 0.5481 (m-10)
REVERT: A 1059 GLU cc_start: 0.5592 (pt0) cc_final: 0.5301 (pt0)
REVERT: A 1074 GLU cc_start: 0.7126 (mp0) cc_final: 0.6721 (mp0)
REVERT: A 1075 GLU cc_start: 0.7727 (pt0) cc_final: 0.7525 (tt0)
REVERT: B   14 GLN cc_start: 0.7322 (tm-30) cc_final: 0.7065 (pp30)
REVERT: B   55 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6520 (mtmt)
REVERT: B  218 SER cc_start: 0.7553 (m) cc_final: 0.7232 (p)
REVERT: B  232 ILE cc_start: 0.7611 (mt) cc_final: 0.7404 (tt)
REVERT: B  273 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7179 (mt-10)
REVERT: B  366 SER cc_start: 0.7681 (p) cc_final: 0.7468 (m)
REVERT: B  420 MET cc_start: 0.8087 (tpp) cc_final: 0.7802 (mmt)
REVERT: B  449 GLN cc_start: 0.6583 (tt0) cc_final: 0.6355 (tt0)
REVERT: B  469 TYR cc_start: 0.7849 (m-10) cc_final: 0.7248 (m-10)
REVERT: B  521 LEU cc_start: 0.8264 (tp) cc_final: 0.8048 (tt)
REVERT: B  551 VAL cc_start: 0.7948 (p) cc_final: 0.7706 (p)
REVERT: B  552 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7574 (tt)
REVERT: B  578 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6861 (mtt-85)
REVERT: B  613 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7811 (mt-10)
REVERT: B  797 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7742 (mp10)
REVERT: B  807 ASN cc_start: 0.6964 (t0) cc_final: 0.6459 (t0)
REVERT: B  962 THR cc_start: 0.8500 (m) cc_final: 0.8158 (m)
REVERT: B  980 LYS cc_start: 0.7324 (mttt) cc_final: 0.7102 (mttt)
REVERT: B  986 GLN cc_start: 0.7319 (tp40) cc_final: 0.6993 (tp40)
REVERT: B 1029 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7574 (mt-10)
  outliers start: 27
  outliers final: 16
  residues processed: 261
  average time/residue: 0.1341
  time to fit residues: 52.9710
Evaluate side-chains
  252 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  733 TYR
Chi-restraints excluded: chain A residue  938 HIS
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain B residue   55 LYS
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  522 ASN
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  797 GLN
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue 1018 LEU
Chi-restraints excluded: chain B residue 1040 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 213 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 215 optimal weight:   20.0000
   chunk 26 optimal weight:    0.5980
   chunk 133 optimal weight:    7.9990
   chunk 115 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 507 ASN
A 566 ASN
A 821 GLN
B  97 ASN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 460 ASN
B 522 ASN
B 584 HIS
B 668 ASN
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 923 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.195153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.155650 restraints weight = 25339.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.52
r_work: 0.3793 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          1.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  18520  Z= 0.205
  Angle     :  0.611   9.003  25020  Z= 0.317
  Chirality :  0.043   0.234   2746
  Planarity :  0.005   0.068   3256
  Dihedral  :  4.360  19.577   2460
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.73 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.18), residues: 2228
  helix:  1.36 (0.15), residues: 1122
  sheet: -0.41 (0.31), residues: 264
  loop : -1.17 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 921 
 TYR   0.026   0.002   TYR A1115 
 PHE   0.026   0.002   PHE B 251 
 TRP   0.025   0.002   TRP B 336 
 HIS   0.011   0.001   HIS A 836 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (18520)
  covalent geometry    : angle       0.61063 (25020)
  hydrogen bonds       : bond        0.04253 (  934)
  hydrogen bonds       : angle       4.71811 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 237
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.7069 (tp30) cc_final: 0.6770 (tp30)
REVERT: A  212 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7029 (ttm-80)
REVERT: A  254 THR cc_start: 0.7765 (m) cc_final: 0.7085 (p)
REVERT: A  262 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7664 (tpp80)
REVERT: A  663 MET cc_start: 0.4466 (tmm) cc_final: 0.4180 (tmm)
REVERT: A  806 GLU cc_start: 0.6947 (mp0) cc_final: 0.6724 (mp0)
REVERT: A 1025 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6918 (mmm-85)
REVERT: A 1059 GLU cc_start: 0.6272 (pt0) cc_final: 0.5899 (pt0)
REVERT: B   74 GLU cc_start: 0.7970 (tp30) cc_final: 0.7734 (tp30)
REVERT: B  206 LYS cc_start: 0.7641 (ttmm) cc_final: 0.7235 (ttpp)
REVERT: B  218 SER cc_start: 0.7371 (m) cc_final: 0.7011 (p)
REVERT: B  255 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7865 (ttm-80)
REVERT: B  261 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8227 (tt)
REVERT: B  273 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: B  366 SER cc_start: 0.7911 (p) cc_final: 0.7575 (m)
REVERT: B  380 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7900 (ttm170)
REVERT: B  449 GLN cc_start: 0.6538 (tt0) cc_final: 0.6166 (tt0)
REVERT: B  469 TYR cc_start: 0.7992 (m-10) cc_final: 0.7071 (m-10)
REVERT: B  470 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6890 (mp0)
REVERT: B  552 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7628 (tt)
REVERT: B  613 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: B  797 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7766 (mp10)
REVERT: B  803 SER cc_start: 0.8444 (t) cc_final: 0.8091 (p)
REVERT: B  807 ASN cc_start: 0.7039 (t0) cc_final: 0.6579 (t0)
REVERT: B  983 TYR cc_start: 0.6979 (p90) cc_final: 0.5665 (p90)
REVERT: B  984 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5346 (mtm-85)
REVERT: B 1029 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7660 (mt-10)
REVERT: B 1048 MET cc_start: 0.6490 (mtp) cc_final: 0.6203 (mtt)
  outliers start: 45
  outliers final: 22
  residues processed: 265
  average time/residue: 0.1694
  time to fit residues: 64.8397
Evaluate side-chains
  245 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  797 GLN
Chi-restraints excluded: chain B residue  824 MET
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  973 LEU
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1018 LEU
Chi-restraints excluded: chain B residue 1040 GLU
Chi-restraints excluded: chain B residue 1047 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 120 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 131 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 194 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 206 optimal weight:    7.9990
   chunk 165 optimal weight:    0.8980
   chunk 186 optimal weight:    0.6980
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
A 566 ASN
A 797 GLN
A 920 GLN
B 144 GLN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.195249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.156125 restraints weight = 25472.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 2.53
r_work: 0.3800 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          1.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  18520  Z= 0.154
  Angle     :  0.528   7.881  25020  Z= 0.275
  Chirality :  0.041   0.182   2746
  Planarity :  0.004   0.047   3256
  Dihedral  :  4.047  24.205   2460
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.78 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.18), residues: 2228
  helix:  1.52 (0.15), residues: 1119
  sheet: -0.46 (0.31), residues: 275
  loop : -1.15 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 855 
 TYR   0.025   0.001   TYR A1115 
 PHE   0.019   0.001   PHE A 251 
 TRP   0.011   0.001   TRP A1186 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (18520)
  covalent geometry    : angle       0.52848 (25020)
  hydrogen bonds       : bond        0.03621 (  934)
  hydrogen bonds       : angle       4.42506 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  254 THR cc_start: 0.7648 (m) cc_final: 0.7145 (p)
REVERT: A  262 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7643 (tpp80)
REVERT: A  284 GLU cc_start: 0.7646 (tp30) cc_final: 0.7325 (tp30)
REVERT: B   74 GLU cc_start: 0.7943 (tp30) cc_final: 0.7680 (tp30)
REVERT: B   98 VAL cc_start: 0.7147 (m) cc_final: 0.6881 (p)
REVERT: B  138 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.6963 (mt0)
REVERT: B  206 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7511 (mtpt)
REVERT: B  207 GLN cc_start: 0.7850 (tp40) cc_final: 0.7383 (tp40)
REVERT: B  255 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7850 (ttm-80)
REVERT: B  273 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7256 (mt-10)
REVERT: B  366 SER cc_start: 0.7690 (p) cc_final: 0.7423 (m)
REVERT: B  445 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6863 (mm-30)
REVERT: B  552 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7704 (tt)
REVERT: B  613 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: B  807 ASN cc_start: 0.7101 (t0) cc_final: 0.6626 (t0)
REVERT: B  983 TYR cc_start: 0.6921 (p90) cc_final: 0.5483 (p90)
REVERT: B  984 ARG cc_start: 0.5985 (OUTLIER) cc_final: 0.5288 (mtm-85)
REVERT: B  986 GLN cc_start: 0.7307 (tp40) cc_final: 0.7098 (tp40)
  outliers start: 36
  outliers final: 17
  residues processed: 262
  average time/residue: 0.1511
  time to fit residues: 58.1509
Evaluate side-chains
  243 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 223
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  934 VAL
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1040 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 161 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 176 optimal weight:    3.9990
   chunk 198 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 148 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 938 HIS
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 797 GLN
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.193812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.155047 restraints weight = 25301.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.50
r_work: 0.3788 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          1.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18520  Z= 0.153
  Angle     :  0.557  12.668  25020  Z= 0.286
  Chirality :  0.041   0.212   2746
  Planarity :  0.004   0.047   3256
  Dihedral  :  4.066  21.994   2460
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.98 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.18), residues: 2228
  helix:  1.50 (0.15), residues: 1126
  sheet: -0.32 (0.32), residues: 265
  loop : -1.15 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 921 
 TYR   0.025   0.002   TYR A1115 
 PHE   0.036   0.001   PHE A 195 
 TRP   0.024   0.001   TRP B1027 
 HIS   0.004   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (18520)
  covalent geometry    : angle       0.55651 (25020)
  hydrogen bonds       : bond        0.03705 (  934)
  hydrogen bonds       : angle       4.50052 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 235
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.7739 (t0) cc_final: 0.7406 (t0)
REVERT: A  124 GLN cc_start: 0.7924 (mp10) cc_final: 0.7651 (mp10)
REVERT: A  195 PHE cc_start: 0.6380 (t80) cc_final: 0.6144 (t80)
REVERT: A  254 THR cc_start: 0.7621 (m) cc_final: 0.7089 (p)
REVERT: A  262 ARG cc_start: 0.7906 (tpp80) cc_final: 0.7587 (tpp80)
REVERT: A  284 GLU cc_start: 0.7629 (tp30) cc_final: 0.7329 (tp30)
REVERT: A  306 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7364 (m-30)
REVERT: A  954 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7517 (mtp85)
REVERT: B   74 GLU cc_start: 0.7945 (tp30) cc_final: 0.7696 (tp30)
REVERT: B  138 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7092 (mt0)
REVERT: B  207 GLN cc_start: 0.7827 (tp40) cc_final: 0.7406 (tp40)
REVERT: B  230 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6719 (tp30)
REVERT: B  255 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7824 (ttm-80)
REVERT: B  273 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7230 (mt-10)
REVERT: B  366 SER cc_start: 0.7736 (p) cc_final: 0.7444 (m)
REVERT: B  445 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6970 (mm-30)
REVERT: B  457 THR cc_start: 0.8032 (m) cc_final: 0.7538 (t)
REVERT: B  552 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7732 (tt)
REVERT: B  613 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: B  797 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7923 (mp10)
REVERT: B  807 ASN cc_start: 0.7057 (t0) cc_final: 0.6608 (t0)
REVERT: B  824 MET cc_start: 0.6462 (mpp) cc_final: 0.5729 (mpp)
REVERT: B  983 TYR cc_start: 0.6933 (p90) cc_final: 0.5553 (p90)
REVERT: B  984 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5338 (mtm-85)
REVERT: B  986 GLN cc_start: 0.7294 (tp40) cc_final: 0.7021 (tp40)
  outliers start: 37
  outliers final: 22
  residues processed: 255
  average time/residue: 0.1681
  time to fit residues: 62.8020
Evaluate side-chains
  258 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 230
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLN
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  989 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  522 ASN
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  797 GLN
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  934 VAL
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1018 LEU
Chi-restraints excluded: chain B residue 1040 GLU
Chi-restraints excluded: chain B residue 1115 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 39 optimal weight:   30.0000
   chunk 85 optimal weight:    2.9990
   chunk 180 optimal weight:    0.7980
   chunk 163 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 166 optimal weight:    0.8980
   chunk 146 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0070
   chunk 112 optimal weight:    3.9990
   chunk 189 optimal weight:    4.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
A 453 GLN
A 566 ASN
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1022 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 522 ASN
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.194570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.156079 restraints weight = 25195.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 2.50
r_work: 0.3797 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          1.4623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  18520  Z= 0.126
  Angle     :  0.527  10.306  25020  Z= 0.272
  Chirality :  0.040   0.189   2746
  Planarity :  0.004   0.046   3256
  Dihedral  :  3.968  24.356   2460
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.08 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.18), residues: 2228
  helix:  1.54 (0.15), residues: 1132
  sheet: -0.27 (0.32), residues: 265
  loop : -1.09 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 855 
 TYR   0.025   0.001   TYR A1115 
 PHE   0.029   0.001   PHE A1033 
 TRP   0.010   0.001   TRP B 336 
 HIS   0.003   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (18520)
  covalent geometry    : angle       0.52701 (25020)
  hydrogen bonds       : bond        0.03492 (  934)
  hydrogen bonds       : angle       4.39174 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 232
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.7779 (t0) cc_final: 0.7446 (t0)
REVERT: A  262 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7545 (tpp80)
REVERT: A  284 GLU cc_start: 0.7617 (tp30) cc_final: 0.7317 (tp30)
REVERT: A  306 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7344 (m-30)
REVERT: A  954 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7437 (mtp85)
REVERT: A 1020 GLN cc_start: 0.7742 (mt0) cc_final: 0.7526 (mt0)
REVERT: B  138 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7062 (mt0)
REVERT: B  207 GLN cc_start: 0.7770 (tp40) cc_final: 0.7390 (tp40)
REVERT: B  255 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7813 (ttm-80)
REVERT: B  284 GLU cc_start: 0.7378 (tp30) cc_final: 0.7136 (mm-30)
REVERT: B  289 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7484 (mt0)
REVERT: B  366 SER cc_start: 0.7631 (p) cc_final: 0.7366 (m)
REVERT: B  445 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7139 (mm-30)
REVERT: B  457 THR cc_start: 0.7990 (m) cc_final: 0.7700 (p)
REVERT: B  552 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7736 (tt)
REVERT: B  575 GLN cc_start: 0.7318 (mt0) cc_final: 0.7105 (mt0)
REVERT: B  613 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7838 (mt-10)
REVERT: B  807 ASN cc_start: 0.7081 (t0) cc_final: 0.6676 (t0)
REVERT: B  824 MET cc_start: 0.6421 (mpp) cc_final: 0.5738 (mpp)
REVERT: B  983 TYR cc_start: 0.6929 (p90) cc_final: 0.5512 (p90)
REVERT: B  984 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5305 (mtm-85)
REVERT: B  986 GLN cc_start: 0.7269 (tp40) cc_final: 0.7010 (tp40)
REVERT: B 1048 MET cc_start: 0.6409 (mtt) cc_final: 0.6177 (mtt)
  outliers start: 36
  outliers final: 27
  residues processed: 252
  average time/residue: 0.1596
  time to fit residues: 59.7738
Evaluate side-chains
  257 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 226
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLN
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1057 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  522 ASN
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  791 THR
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  934 VAL
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1018 LEU
Chi-restraints excluded: chain B residue 1040 GLU
Chi-restraints excluded: chain B residue 1115 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 116 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 214 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 208 optimal weight:    0.0060
   chunk 16 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 223 optimal weight:    0.9980
   chunk 153 optimal weight:    0.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
A 566 ASN
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.193702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.155278 restraints weight = 25272.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 2.47
r_work: 0.3788 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          1.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18520  Z= 0.136
  Angle     :  0.539  14.572  25020  Z= 0.277
  Chirality :  0.041   0.241   2746
  Planarity :  0.004   0.046   3256
  Dihedral  :  3.983  23.250   2460
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.43 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.18), residues: 2228
  helix:  1.56 (0.15), residues: 1136
  sheet: -0.26 (0.32), residues: 265
  loop : -1.03 (0.22), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 972 
 TYR   0.025   0.001   TYR A1115 
 PHE   0.032   0.001   PHE A1033 
 TRP   0.012   0.001   TRP B 336 
 HIS   0.003   0.001   HIS B 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (18520)
  covalent geometry    : angle       0.53906 (25020)
  hydrogen bonds       : bond        0.03545 (  934)
  hydrogen bonds       : angle       4.38093 ( 2676)

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

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

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4456 Ramachandran restraints generated.
    2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 231
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.7818 (t0) cc_final: 0.7484 (t0)
REVERT: A  194 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6814 (m-80)
REVERT: A  284 GLU cc_start: 0.7616 (tp30) cc_final: 0.7325 (tp30)
REVERT: A  306 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7339 (m-30)
REVERT: A  816 GLU cc_start: 0.6676 (tp30) cc_final: 0.6401 (tp30)
REVERT: A  925 ASP cc_start: 0.7668 (t0) cc_final: 0.7370 (t0)
REVERT: A  954 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7438 (mtp85)
REVERT: A 1020 GLN cc_start: 0.7765 (mt0) cc_final: 0.7539 (mt0)
REVERT: B  138 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7106 (mt0)
REVERT: B  207 GLN cc_start: 0.7787 (tp40) cc_final: 0.7419 (tp40)
REVERT: B  255 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7774 (ttm-80)
REVERT: B  284 GLU cc_start: 0.7366 (tp30) cc_final: 0.7118 (mm-30)
REVERT: B  366 SER cc_start: 0.7646 (p) cc_final: 0.7381 (m)
REVERT: B  445 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7196 (mm-30)
REVERT: B  457 THR cc_start: 0.7998 (m) cc_final: 0.7690 (p)
REVERT: B  552 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: B  613 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: B  824 MET cc_start: 0.6422 (mpp) cc_final: 0.5739 (mpp)
REVERT: B  983 TYR cc_start: 0.6857 (p90) cc_final: 0.5452 (p90)
REVERT: B  984 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5317 (mtm-85)
REVERT: B  986 GLN cc_start: 0.7273 (tp40) cc_final: 0.7003 (tp40)
  outliers start: 32
  outliers final: 24
  residues processed: 250
  average time/residue: 0.1611
  time to fit residues: 59.6193
Evaluate side-chains
  255 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLN
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue 1044 MET
Chi-restraints excluded: chain A residue 1057 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  552 ILE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  784 LEU
Chi-restraints excluded: chain B residue  874 LEU
Chi-restraints excluded: chain B residue  934 VAL
Chi-restraints excluded: chain B residue  984 ARG
Chi-restraints excluded: chain B residue 1040 GLU
Chi-restraints excluded: chain B residue 1115 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 186 optimal weight:    0.8980
   chunk 197 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 173 optimal weight:    0.0010
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
A 453 GLN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.194194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.155983 restraints weight = 25562.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.51
r_work: 0.3803 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          1.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18520  Z= 0.117
  Angle     :  0.522  13.614  25020  Z= 0.269
  Chirality :  0.040   0.252   2746
  Planarity :  0.003   0.045   3256
  Dihedral  :  3.907  24.381   2460
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.54 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.18), residues: 2228
  helix:  1.64 (0.15), residues: 1134
  sheet: -0.21 (0.32), residues: 264
  loop : -1.07 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 921 
 TYR   0.025   0.001   TYR A1115 
 PHE   0.030   0.001   PHE A1033 
 TRP   0.010   0.001   TRP A1186 
 HIS   0.002   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (18520)
  covalent geometry    : angle       0.52240 (25020)
  hydrogen bonds       : bond        0.03392 (  934)
  hydrogen bonds       : angle       4.31342 ( 2676)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5059.06 seconds
wall clock time: 87 minutes 25.69 seconds (5245.69 seconds total)