Starting phenix.real_space_refine
on Wed Mar 12 16:57:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ydm_33753/03_2025/7ydm_33753.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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      55      5.16       5
     C    5170      2.51       5
     N    1410      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8131
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1928
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2194
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
  Time building chain proxies: 4.85, per 1000 atoms: 0.60
  Number of scatterers: 8131
  At special positions: 0
  Unit cell: (79.2, 104.5, 136.4, 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      55     16.00
     O    1496      8.00
     N    1410      7.00
     C    5170      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " distance=2.03

  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: 1.76
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1924

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      39.5% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 3.637A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.525A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.530A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.601A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.615A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.575A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.731A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.847A  pdb=" N   ARG A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.628A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.699A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'R' and resid 532 through 537
      removed outlier: 3.708A  pdb=" N   LEU R 536 " --> pdb=" O   PHE R 533 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 544 through 572
      removed outlier: 3.657A  pdb=" N   THR R 548 " --> pdb=" O   ASP R 544 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU R 549 " --> pdb=" O   TRP R 545 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ILE R 550 " --> pdb=" O   LYS R 546 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 577 through 601
      removed outlier: 3.530A  pdb=" N   ILE R 601 " --> pdb=" O   PHE R 597 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 609 through 642
      removed outlier: 3.546A  pdb=" N   ARG R 613 " --> pdb=" O   GLY R 609 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 651 through 674
      removed outlier: 3.576A  pdb=" N   TYR R 660 " --> pdb=" O   CYS R 656 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL R 662 " --> pdb=" O   ILE R 658 " (cutoff:3.500A)
      Proline residue:  R 663  - end of helix
    Processing helix  chain 'R' and resid 688 through 692
    Processing helix  chain 'R' and resid 693 through 720
      Proline residue:  R 699  - end of helix
      removed outlier: 3.530A  pdb=" N   PHE R 702 " --> pdb=" O   GLY R 698 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ILE R 703 " --> pdb=" O   PRO R 699 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   VAL R 709 " --> pdb=" O   LEU R 705 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL R 712 " --> pdb=" O   ALA R 708 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 721 through 726
    Processing helix  chain 'R' and resid 733 through 747
      removed outlier: 4.032A  pdb=" N   ALA R 737 " --> pdb=" O   LYS R 733 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU R 738 " --> pdb=" O   LYS R 734 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   THR R 739 " --> pdb=" O   ALA R 735 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 751 through 759
      removed outlier: 4.017A  pdb=" N   PHE R 755 " --> pdb=" O   THR R 752 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   PHE R 758 " --> pdb=" O   PHE R 755 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE R 759 " --> pdb=" O   GLY R 756 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 765 through 776
    Processing helix  chain 'R' and resid 777 through 787
    Processing helix  chain 'R' and resid 790 through 804
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.424A  pdb=" N   LEU A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.763A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.364A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.662A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.866A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.019A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.801A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.017A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.022A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.989A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.549A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.049A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG N  38 " --> pdb=" O   GLU N  46 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 2.12 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: 2541
        1.34 -     1.45: 1217
        1.45 -     1.57: 4464
        1.57 -     1.69: 0
        1.69 -     1.81: 73
  Bond restraints: 8295
  Sorted by residual:
  bond pdb=" CA  ASP R 541 "
       pdb=" CB  ASP R 541 "
    ideal  model  delta    sigma   weight residual
    1.527  1.549 -0.022 1.61e-02 3.86e+03 1.81e+00
  bond pdb=" C   ILE B  93 "
       pdb=" N   PRO B  94 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.23e-02 6.61e+03 1.74e+00
  bond pdb=" CG  LEU A  46 "
       pdb=" CD1 LEU A  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.52e+00
  bond pdb=" CB  GLN A 385 "
       pdb=" CG  GLN A 385 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" C   GLN A  31 "
       pdb=" O   GLN A  31 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.013 1.15e-02 7.56e+03 1.27e+00
  ... (remaining 8290 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 10896
        1.81 -     3.62: 284
        3.62 -     5.42: 40
        5.42 -     7.23: 6
        7.23 -     9.04: 2
  Bond angle restraints: 11228
  Sorted by residual:
  angle pdb=" N   CYS R 751 "
        pdb=" CA  CYS R 751 "
        pdb=" C   CYS R 751 "
      ideal   model   delta    sigma   weight residual
     114.62  109.86    4.76 1.14e+00 7.69e-01 1.74e+01
  angle pdb=" N   ARG A 389 "
        pdb=" CA  ARG A 389 "
        pdb=" C   ARG A 389 "
      ideal   model   delta    sigma   weight residual
     114.04  109.28    4.76 1.24e+00 6.50e-01 1.47e+01
  angle pdb=" N   GLY R 600 "
        pdb=" CA  GLY R 600 "
        pdb=" C   GLY R 600 "
      ideal   model   delta    sigma   weight residual
     113.18  121.60   -8.42 2.37e+00 1.78e-01 1.26e+01
  angle pdb=" C   VAL R 641 "
        pdb=" N   VAL R 642 "
        pdb=" CA  VAL R 642 "
      ideal   model   delta    sigma   weight residual
     122.97  119.76    3.21 9.80e-01 1.04e+00 1.07e+01
  angle pdb=" C   VAL N  48 "
        pdb=" N   SER N  49 "
        pdb=" CA  SER N  49 "
      ideal   model   delta    sigma   weight residual
     121.75  116.18    5.57 1.73e+00 3.34e-01 1.04e+01
  ... (remaining 11223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 4459
       16.71 -    33.43: 375
       33.43 -    50.14: 65
       50.14 -    66.85: 16
       66.85 -    83.56: 8
  Dihedral angle restraints: 4923
    sinusoidal: 1940
      harmonic: 2983
  Sorted by residual:
  dihedral pdb=" CA  ALA B 203 "
           pdb=" C   ALA B 203 "
           pdb=" N   CYS B 204 "
           pdb=" CA  CYS B 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.18   32.82     0      5.00e+00 4.00e-02 4.31e+01
  dihedral pdb=" CA  LEU R 705 "
           pdb=" C   LEU R 705 "
           pdb=" N   CYS R 706 "
           pdb=" CA  CYS R 706 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CB  CYS R 612 "
           pdb=" SG  CYS R 612 "
           pdb=" SG  CYS R 684 "
           pdb=" CB  CYS R 684 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.61   44.61     1      1.00e+01 1.00e-02 2.77e+01
  ... (remaining 4920 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 848
       0.045 -    0.089: 324
       0.089 -    0.134: 86
       0.134 -    0.178: 9
       0.178 -    0.223: 2
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  ASP R 541 "
            pdb=" N   ASP R 541 "
            pdb=" C   ASP R 541 "
            pdb=" CB  ASP R 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  ILE R 759 "
            pdb=" CA  ILE R 759 "
            pdb=" CG1 ILE R 759 "
            pdb=" CG2 ILE R 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.27e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 1266 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 726 "    0.083 5.00e-02 4.00e+02   1.24e-01 2.46e+01
        pdb=" N   PRO R 727 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO R 727 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO R 727 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 680 "    0.042 5.00e-02 4.00e+02   6.29e-02 6.33e+00
        pdb=" N   PRO R 681 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO R 681 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 681 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  52 "   -0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO G  53 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 111
        2.67 -     3.23: 7169
        3.23 -     3.79: 11172
        3.79 -     4.34: 14860
        4.34 -     4.90: 25710
  Nonbonded interactions: 59022
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   ALA A  48 "
            pdb=" OG  SER A  51 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR R 674 "
            pdb=" NZ  LYS R 676 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.298 3.040
  ... (remaining 59017 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.150
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
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      :  0.007   0.048   8295  Z= 0.446
  Angle     :  0.725   9.039  11228  Z= 0.426
  Chirality :  0.049   0.223   1269
  Planarity :  0.006   0.124   1424
  Dihedral  : 13.257  83.565   2996
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1019
  helix:  0.98 (0.27), residues: 366
  sheet:  0.77 (0.34), residues: 238
  loop : -1.58 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 234 
 HIS   0.014   0.002   HIS A 357 
 PHE   0.025   0.003   PHE N 108 
 TYR   0.013   0.002   TYR N  95 
 ARG   0.007   0.000   ARG A 336 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  221 MET cc_start: 0.8534 (ttm) cc_final: 0.8169 (ttp)
REVERT: A  251 SER cc_start: 0.8728 (p) cc_final: 0.8329 (t)
REVERT: A  309 GLU cc_start: 0.7299 (pm20) cc_final: 0.7027 (pm20)
REVERT: A  390 GLU cc_start: 0.7313 (tp30) cc_final: 0.7060 (tp30)
REVERT: B  189 SER cc_start: 0.7771 (m) cc_final: 0.7529 (m)
REVERT: B  262 MET cc_start: 0.6975 (tpp) cc_final: 0.6444 (tpp)
REVERT: B  281 SER cc_start: 0.8507 (p) cc_final: 0.8267 (p)
REVERT: G   21 MET cc_start: 0.7616 (tpp) cc_final: 0.7241 (tpp)
REVERT: R  733 LYS cc_start: 0.8240 (mmpt) cc_final: 0.8017 (mmpt)
REVERT: R  775 ASN cc_start: 0.8445 (m-40) cc_final: 0.8046 (m-40)
  outliers start: 0
  outliers final: 1
  residues processed: 179
  average time/residue: 1.2993
  time to fit residues: 245.3860
Evaluate side-chains
  160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  759 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 292 ASN
A 385 GLN
B  75 GLN
B 155 ASN
B 268 ASN
R 745 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.121007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102582 restraints weight = 11544.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.13
r_work: 0.3198 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8295  Z= 0.231
  Angle     :  0.570   7.615  11228  Z= 0.317
  Chirality :  0.044   0.184   1269
  Planarity :  0.005   0.073   1424
  Dihedral  :  4.689  29.836   1125
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  8.50 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 1019
  helix:  1.64 (0.28), residues: 369
  sheet:  0.85 (0.33), residues: 246
  loop : -1.54 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.018   0.002   PHE B 199 
 TYR   0.035   0.002   TYR R 540 
 ARG   0.011   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  221 MET cc_start: 0.8865 (ttm) cc_final: 0.8552 (ttp)
REVERT: A  309 GLU cc_start: 0.7852 (pm20) cc_final: 0.7528 (pm20)
REVERT: A  356 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7520 (mtm110)
REVERT: G   21 MET cc_start: 0.8050 (tpp) cc_final: 0.7618 (tpp)
REVERT: R  673 ILE cc_start: 0.8655 (mm) cc_final: 0.8319 (tt)
REVERT: R  733 LYS cc_start: 0.8389 (mmpt) cc_final: 0.8089 (mmpt)
REVERT: R  775 ASN cc_start: 0.8691 (m-40) cc_final: 0.8368 (m-40)
  outliers start: 18
  outliers final: 7
  residues processed: 170
  average time/residue: 1.3163
  time to fit residues: 235.9287
Evaluate side-chains
  162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  557 LEU
Chi-restraints excluded: chain R residue  675 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 292 ASN
R 720 GLN
R 745 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.121285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.102786 restraints weight = 11674.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.15
r_work: 0.3212 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8295  Z= 0.199
  Angle     :  0.522   7.074  11228  Z= 0.290
  Chirality :  0.043   0.172   1269
  Planarity :  0.005   0.061   1424
  Dihedral  :  4.366  28.679   1123
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.15 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 1019
  helix:  2.01 (0.28), residues: 369
  sheet:  0.85 (0.33), residues: 242
  loop : -1.42 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.012   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7857 (pm20) cc_final: 0.7516 (pm20)
REVERT: A  342 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8411 (ttp-170)
REVERT: B   19 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7456 (ttm170)
REVERT: G   21 MET cc_start: 0.8037 (tpp) cc_final: 0.7615 (tpp)
REVERT: R  673 ILE cc_start: 0.8658 (mm) cc_final: 0.8335 (tt)
REVERT: R  775 ASN cc_start: 0.8641 (m-40) cc_final: 0.8393 (m-40)
  outliers start: 14
  outliers final: 6
  residues processed: 166
  average time/residue: 1.2655
  time to fit residues: 221.8208
Evaluate side-chains
  154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  682 ARG
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0370
   chunk 86 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
A 387 ASN
R 720 GLN
R 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.104467 restraints weight = 11561.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.13
r_work: 0.3233 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8295  Z= 0.167
  Angle     :  0.488   6.523  11228  Z= 0.272
  Chirality :  0.042   0.176   1269
  Planarity :  0.005   0.059   1424
  Dihedral  :  4.083  27.205   1123
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.63 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 1019
  helix:  2.15 (0.28), residues: 372
  sheet:  1.00 (0.34), residues: 230
  loop : -1.27 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.012   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7837 (pm20) cc_final: 0.7495 (pm20)
REVERT: A  342 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8366 (ttp-170)
REVERT: A  356 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7546 (mtm110)
REVERT: B   19 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7472 (ttm170)
REVERT: G   21 MET cc_start: 0.8016 (tpp) cc_final: 0.7607 (tpp)
REVERT: R  533 PHE cc_start: 0.8404 (t80) cc_final: 0.8150 (t80)
REVERT: R  673 ILE cc_start: 0.8648 (mm) cc_final: 0.8331 (tt)
REVERT: R  775 ASN cc_start: 0.8623 (m-40) cc_final: 0.8373 (m110)
  outliers start: 21
  outliers final: 10
  residues processed: 164
  average time/residue: 1.2080
  time to fit residues: 209.7104
Evaluate side-chains
  156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain R residue  759 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 2 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 387 ASN
R 745 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.103592 restraints weight = 11616.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.15
r_work: 0.3222 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8295  Z= 0.184
  Angle     :  0.492   6.516  11228  Z= 0.273
  Chirality :  0.042   0.174   1269
  Planarity :  0.005   0.062   1424
  Dihedral  :  4.068  27.022   1123
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.87 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.27), residues: 1019
  helix:  2.28 (0.28), residues: 368
  sheet:  1.03 (0.34), residues: 230
  loop : -1.21 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.013   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7854 (pm20) cc_final: 0.7519 (pm20)
REVERT: A  342 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8385 (ttp-170)
REVERT: A  356 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7576 (mtm110)
REVERT: B   19 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7512 (ttm170)
REVERT: G   21 MET cc_start: 0.8011 (tpp) cc_final: 0.7588 (tpp)
REVERT: N   34 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7884 (mmm)
REVERT: R  673 ILE cc_start: 0.8652 (mm) cc_final: 0.8334 (tt)
REVERT: R  682 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7703 (ttt-90)
REVERT: R  775 ASN cc_start: 0.8624 (m-40) cc_final: 0.8362 (m110)
  outliers start: 21
  outliers final: 14
  residues processed: 158
  average time/residue: 1.3081
  time to fit residues: 218.3109
Evaluate side-chains
  160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain R residue  759 ILE
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 91 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 387 ASN
B  75 GLN
R 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102511 restraints weight = 11655.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.14
r_work: 0.3196 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8295  Z= 0.252
  Angle     :  0.528   7.222  11228  Z= 0.294
  Chirality :  0.043   0.176   1269
  Planarity :  0.005   0.056   1424
  Dihedral  :  4.208  27.610   1123
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.78 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1019
  helix:  2.21 (0.28), residues: 367
  sheet:  0.93 (0.34), residues: 232
  loop : -1.21 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.018   0.002   PHE B 199 
 TYR   0.011   0.001   TYR N  60 
 ARG   0.008   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  251 SER cc_start: 0.8805 (p) cc_final: 0.8524 (t)
REVERT: A  274 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7734 (ttmt)
REVERT: A  275 SER cc_start: 0.8715 (t) cc_final: 0.8305 (m)
REVERT: A  309 GLU cc_start: 0.7813 (pm20) cc_final: 0.7510 (pm20)
REVERT: A  342 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8399 (ttp-170)
REVERT: A  349 SER cc_start: 0.8466 (p) cc_final: 0.8075 (p)
REVERT: A  356 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7612 (mtm110)
REVERT: B   19 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7536 (ttm170)
REVERT: G   21 MET cc_start: 0.8036 (tpp) cc_final: 0.7599 (tpp)
REVERT: R  643 ARG cc_start: 0.7838 (tmm160) cc_final: 0.7636 (ttp-170)
REVERT: R  673 ILE cc_start: 0.8656 (mm) cc_final: 0.8336 (tt)
REVERT: R  717 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7239 (mptt)
REVERT: R  775 ASN cc_start: 0.8685 (m-40) cc_final: 0.8375 (m-40)
  outliers start: 21
  outliers final: 13
  residues processed: 158
  average time/residue: 1.3226
  time to fit residues: 220.4672
Evaluate side-chains
  164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  717 LYS
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 745 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.121749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.103157 restraints weight = 11691.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.16
r_work: 0.3211 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8295  Z= 0.205
  Angle     :  0.508   7.643  11228  Z= 0.282
  Chirality :  0.042   0.169   1269
  Planarity :  0.005   0.081   1424
  Dihedral  :  4.112  26.815   1123
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.12 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1019
  helix:  2.27 (0.28), residues: 368
  sheet:  0.95 (0.34), residues: 232
  loop : -1.18 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.016   0.001   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7740 (ttmt)
REVERT: A  309 GLU cc_start: 0.7845 (pm20) cc_final: 0.7528 (pm20)
REVERT: A  342 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8388 (ttp-170)
REVERT: A  356 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7573 (mtm110)
REVERT: B   19 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7518 (ttm170)
REVERT: G   21 MET cc_start: 0.8009 (tpp) cc_final: 0.7574 (tpp)
REVERT: N   34 MET cc_start: 0.8297 (mmt) cc_final: 0.7608 (mmm)
REVERT: R  533 PHE cc_start: 0.8441 (t80) cc_final: 0.8155 (t80)
REVERT: R  643 ARG cc_start: 0.7757 (tmm160) cc_final: 0.7540 (ttp-170)
REVERT: R  673 ILE cc_start: 0.8624 (mm) cc_final: 0.8312 (tt)
REVERT: R  717 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7260 (mptt)
REVERT: R  775 ASN cc_start: 0.8643 (m-40) cc_final: 0.8359 (m110)
  outliers start: 22
  outliers final: 14
  residues processed: 154
  average time/residue: 1.4029
  time to fit residues: 228.0108
Evaluate side-chains
  159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  717 LYS
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  75 GLN
R 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.101908 restraints weight = 11816.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.17
r_work: 0.3189 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8295  Z= 0.254
  Angle     :  0.536   8.324  11228  Z= 0.298
  Chirality :  0.043   0.170   1269
  Planarity :  0.005   0.055   1424
  Dihedral  :  4.200  27.726   1123
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.57 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1019
  helix:  2.18 (0.28), residues: 369
  sheet:  0.94 (0.34), residues: 232
  loop : -1.21 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.009   0.000   ARG A  38 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A  251 SER cc_start: 0.8822 (p) cc_final: 0.8512 (t)
REVERT: A  274 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7785 (ttmt)
REVERT: A  275 SER cc_start: 0.8675 (t) cc_final: 0.8283 (m)
REVERT: A  309 GLU cc_start: 0.7831 (pm20) cc_final: 0.7521 (pm20)
REVERT: A  349 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8051 (p)
REVERT: A  356 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7609 (mtm110)
REVERT: B   19 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7508 (ttm170)
REVERT: B  214 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8482 (ttm170)
REVERT: B  234 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8128 (m-80)
REVERT: G   21 MET cc_start: 0.8018 (tpp) cc_final: 0.7570 (tpp)
REVERT: N   34 MET cc_start: 0.8275 (mmt) cc_final: 0.7702 (mmm)
REVERT: R  673 ILE cc_start: 0.8658 (mm) cc_final: 0.8353 (tt)
REVERT: R  717 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7249 (mptt)
REVERT: R  775 ASN cc_start: 0.8684 (m-40) cc_final: 0.8348 (m110)
  outliers start: 21
  outliers final: 13
  residues processed: 156
  average time/residue: 1.6127
  time to fit residues: 266.6847
Evaluate side-chains
  165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  604 GLU
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  717 LYS
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0270
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 745 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.103552 restraints weight = 11809.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.17
r_work: 0.3219 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8295  Z= 0.186
  Angle     :  0.493   6.435  11228  Z= 0.277
  Chirality :  0.042   0.161   1269
  Planarity :  0.004   0.056   1424
  Dihedral  :  4.037  25.994   1123
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.80 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 1019
  helix:  2.36 (0.28), residues: 368
  sheet:  0.92 (0.34), residues: 232
  loop : -1.13 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  251 SER cc_start: 0.8821 (p) cc_final: 0.8525 (t)
REVERT: A  275 SER cc_start: 0.8633 (t) cc_final: 0.8228 (m)
REVERT: A  309 GLU cc_start: 0.7827 (pm20) cc_final: 0.7517 (pm20)
REVERT: A  342 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8378 (ttp-170)
REVERT: A  349 SER cc_start: 0.8400 (p) cc_final: 0.7970 (p)
REVERT: A  356 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7548 (mtm110)
REVERT: B   19 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7533 (ttm170)
REVERT: B  214 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8580 (ttm170)
REVERT: B  234 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8127 (m-80)
REVERT: G   21 MET cc_start: 0.8003 (tpp) cc_final: 0.7585 (tpp)
REVERT: N   34 MET cc_start: 0.8225 (mmt) cc_final: 0.7748 (mmm)
REVERT: R  533 PHE cc_start: 0.8429 (t80) cc_final: 0.8119 (t80)
REVERT: R  673 ILE cc_start: 0.8624 (mm) cc_final: 0.8381 (tp)
REVERT: R  683 TYR cc_start: 0.8224 (m-10) cc_final: 0.8000 (m-10)
REVERT: R  717 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7213 (mptt)
REVERT: R  775 ASN cc_start: 0.8626 (m-40) cc_final: 0.8351 (m110)
  outliers start: 20
  outliers final: 13
  residues processed: 156
  average time/residue: 1.5457
  time to fit residues: 255.7526
Evaluate side-chains
  164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  717 LYS
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 220 GLN
R 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.103294 restraints weight = 11632.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.14
r_work: 0.3218 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8295  Z= 0.192
  Angle     :  0.497   6.222  11228  Z= 0.279
  Chirality :  0.042   0.164   1269
  Planarity :  0.004   0.055   1424
  Dihedral  :  4.035  26.197   1123
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.37 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 1019
  helix:  2.38 (0.28), residues: 369
  sheet:  0.94 (0.34), residues: 232
  loop : -1.14 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.009   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 SER cc_start: 0.8798 (p) cc_final: 0.8515 (t)
REVERT: A  275 SER cc_start: 0.8605 (t) cc_final: 0.8198 (m)
REVERT: A  309 GLU cc_start: 0.7825 (pm20) cc_final: 0.7510 (pm20)
REVERT: A  342 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8372 (ttp-170)
REVERT: A  349 SER cc_start: 0.8403 (p) cc_final: 0.7966 (p)
REVERT: A  356 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7572 (mtm110)
REVERT: B   19 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7515 (ttm170)
REVERT: B  214 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8570 (ttm170)
REVERT: B  234 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8129 (m-80)
REVERT: B  262 MET cc_start: 0.7467 (tpp) cc_final: 0.7082 (tpp)
REVERT: G   21 MET cc_start: 0.8015 (tpp) cc_final: 0.7583 (tpp)
REVERT: R  673 ILE cc_start: 0.8626 (mm) cc_final: 0.8378 (tp)
REVERT: R  683 TYR cc_start: 0.8253 (m-10) cc_final: 0.8019 (m-10)
REVERT: R  717 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7182 (mptt)
REVERT: R  775 ASN cc_start: 0.8621 (m-40) cc_final: 0.8345 (m110)
  outliers start: 16
  outliers final: 14
  residues processed: 155
  average time/residue: 1.2892
  time to fit residues: 211.3924
Evaluate side-chains
  161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  542 VAL
Chi-restraints excluded: chain R residue  675 SER
Chi-restraints excluded: chain R residue  717 LYS
Chi-restraints excluded: chain R residue  759 ILE
Chi-restraints excluded: chain R residue  760 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 220 GLN
R 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102789 restraints weight = 11728.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.15
r_work: 0.3197 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8295  Z= 0.241
  Angle     :  0.524   6.415  11228  Z= 0.293
  Chirality :  0.043   0.168   1269
  Planarity :  0.005   0.055   1424
  Dihedral  :  4.161  26.696   1123
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.71 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.27), residues: 1019
  helix:  2.32 (0.28), residues: 368
  sheet:  0.94 (0.34), residues: 237
  loop : -1.17 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG A  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6464.73 seconds
wall clock time: 113 minutes 1.74 seconds (6781.74 seconds total)