Starting phenix.real_space_refine
on Wed Sep 17 16:16:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g7f_51121/09_2025/9g7f_51121.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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      54      5.16       5
     C    6193      2.51       5
     N    1624      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  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: 9647
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 4359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4359
          Classifications: {'peptide': 543}
          Link IDs: {'PTRANS': 30, 'TRANS': 512}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3607
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 23, 'TRANS': 424}
    Chain: "C"
      Number of atoms: 1681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1681
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 10, 'TRANS': 196}
  Time building chain proxies: 2.40, per 1000 atoms: 0.25
  Number of scatterers: 9647
  At special positions: 0
  Unit cell: (104.784, 117.528, 97.704, 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      54     16.00
     O    1776      8.00
     N    1624      7.00
     C    6193      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: 0.89
  Conformation dependent library (CDL) restraints added in 372.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 14 sheets defined
      39.7% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 24
    Processing helix  chain 'B' and resid 26 through 33
      removed outlier: 3.678A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 40
    Processing helix  chain 'B' and resid 43 through 55
      removed outlier: 4.894A  pdb=" N   ARG B  51 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   HIS B  52 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 59
      removed outlier: 4.480A  pdb=" N   ASN B  59 " --> pdb=" O   PHE B  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 59'
    Processing helix  chain 'B' and resid 76 through 95
      removed outlier: 3.634A  pdb=" N   ASN B  95 " --> pdb=" O   ARG B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 122
      removed outlier: 3.762A  pdb=" N   TYR B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 146
      removed outlier: 3.558A  pdb=" N   VAL B 138 " --> pdb=" O   MET B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 5.126A  pdb=" N   GLU B 158 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE B 160 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 194
      removed outlier: 3.568A  pdb=" N   GLU B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 4.009A  pdb=" N   GLN B 233 " --> pdb=" O   GLU B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.532A  pdb=" N   TYR B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 272
      removed outlier: 3.644A  pdb=" N   TRP B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
    Processing helix  chain 'B' and resid 303 through 314
      removed outlier: 3.549A  pdb=" N   GLY B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 320
      removed outlier: 3.692A  pdb=" N   ALA B 318 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 422 through 429
    Processing helix  chain 'B' and resid 468 through 478
      removed outlier: 4.077A  pdb=" N   VAL B 472 " --> pdb=" O   GLY B 468 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU B 478 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 527
      removed outlier: 3.651A  pdb=" N   LYS B 516 " --> pdb=" O   SER B 512 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU B 517 " --> pdb=" O   ASP B 513 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B 518 " --> pdb=" O   LYS B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 559
    Processing helix  chain 'A' and resid 17 through 24
    Processing helix  chain 'A' and resid 26 through 32
      removed outlier: 3.846A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.738A  pdb=" N   GLU A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 95
    Processing helix  chain 'A' and resid 109 through 122
      removed outlier: 3.539A  pdb=" N   TYR A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.600A  pdb=" N   VAL A 138 " --> pdb=" O   MET A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
      removed outlier: 4.366A  pdb=" N   GLU A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 160
      No H-bonds generated for 'chain 'A' and resid 159 through 160'
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 187 through 192
      removed outlier: 3.771A  pdb=" N   LYS A 192 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 241
      removed outlier: 3.815A  pdb=" N   GLN A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 264
    Processing helix  chain 'A' and resid 266 through 272
      removed outlier: 3.526A  pdb=" N   ASN A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 4.028A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 422 through 429
      removed outlier: 3.582A  pdb=" N   TYR A 429 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 32
      removed outlier: 3.569A  pdb=" N   LEU C  30 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 58
    Processing helix  chain 'C' and resid 85 through 89
    Processing helix  chain 'C' and resid 111 through 122
    Processing helix  chain 'C' and resid 123 through 127
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 148 through 161
    Processing helix  chain 'C' and resid 162 through 164
      No H-bonds generated for 'chain 'C' and resid 162 through 164'
    Processing helix  chain 'C' and resid 174 through 178
      removed outlier: 3.591A  pdb=" N   SER C 177 " --> pdb=" O   GLU C 174 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   HIS C 178 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 174 through 178'
    Processing helix  chain 'C' and resid 192 through 204
    Processing helix  chain 'C' and resid 206 through 210
      removed outlier: 3.935A  pdb=" N   MET C 209 " --> pdb=" O   HIS C 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 75
      removed outlier: 5.909A  pdb=" N   ALA B  62 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ILE B 278 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   TYR B  64 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   CYS B 252 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL B 279 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   TYR B 301 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   TRP B 251 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL B 329 " --> pdb=" O   HIS B 353 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   THR B 355 " --> pdb=" O   VAL B 329 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   SER B 331 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 366 " --> pdb=" O   TRP B 356 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 129
      removed outlier: 3.707A  pdb=" N   VAL B 149 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL B 171 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 214
      removed outlier: 3.652A  pdb=" N   LEU B 210 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS B 222 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLY B 223 " --> pdb=" O   ILE B 419 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ILE B 419 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 225 " --> pdb=" O   HIS B 417 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 391
      removed outlier: 7.732A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER B 438 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 435 " --> pdb=" O   MET B 431 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 444
    Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 492
      removed outlier: 4.170A  pdb=" N   GLU B 484 " --> pdb=" O   ALA B 504 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 73 through 75
      removed outlier: 5.920A  pdb=" N   ALA A  62 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ILE A 278 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   TYR A  64 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS A 252 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   VAL A 279 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TYR A 301 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TRP A 251 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 355 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.493A  pdb=" N   VAL A 102 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 129 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE A 104 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL A 149 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A 150 " --> pdb=" O   PHE A 172 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   VAL A 171 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.811A  pdb=" N   HIS A 226 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LEU A 211 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TYR A 213 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LYS A 222 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY A 223 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   ILE A 419 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 225 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AB2, first strand: chain 'A' and resid 388 through 391
      removed outlier: 7.415A  pdb=" N   GLY A 404 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP A 440 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TRP A 435 " --> pdb=" O   MET A 431 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 388 through 391
      removed outlier: 7.415A  pdb=" N   GLY A 404 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP A 440 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 14
      removed outlier: 7.010A  pdb=" N   ILE C  63 " --> pdb=" O   PRO C  24 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ASP C  68 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ILE C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 95 through 97
      removed outlier: 6.462A  pdb=" N   ILE C  96 " --> pdb=" O   MET C 132 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   THR C 134 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU C 183 " --> pdb=" O   PHE C 168 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA C 185 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    975 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: 1.77

  Time building geometry restraints manager: 1.18 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: 3018
        1.34 -     1.45: 1624
        1.45 -     1.57: 5182
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 9924
  Sorted by residual:
  bond pdb=" C   MET A 431 "
       pdb=" N   PRO A 432 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 1.27e-02 6.20e+03 8.31e+00
  bond pdb=" C   TRP B 412 "
       pdb=" N   PRO B 413 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.28e-02 6.10e+03 4.42e+00
  bond pdb=" CG  LEU B 244 "
       pdb=" CD1 LEU B 244 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.08e+00
  bond pdb=" C   PRO A 399 "
       pdb=" N   PRO A 400 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.48e+00
  bond pdb=" N   TRP A 258 "
       pdb=" CA  TRP A 258 "
    ideal  model  delta    sigma   weight residual
    1.454  1.471 -0.017 1.15e-02 7.56e+03 2.16e+00
  ... (remaining 9919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 13214
        2.39 -     4.78: 188
        4.78 -     7.17: 36
        7.17 -     9.56: 5
        9.56 -    11.95: 3
  Bond angle restraints: 13446
  Sorted by residual:
  angle pdb=" CB  MET C 156 "
        pdb=" CG  MET C 156 "
        pdb=" SD  MET C 156 "
      ideal   model   delta    sigma   weight residual
     112.70  100.75   11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C   MET A 431 "
        pdb=" N   PRO A 432 "
        pdb=" CA  PRO A 432 "
      ideal   model   delta    sigma   weight residual
     119.90  115.87    4.03 1.02e+00 9.61e-01 1.56e+01
  angle pdb=" C   TRP B 412 "
        pdb=" CA  TRP B 412 "
        pdb=" CB  TRP B 412 "
      ideal   model   delta    sigma   weight residual
     109.11  114.77   -5.66 1.50e+00 4.44e-01 1.42e+01
  angle pdb=" C   GLY C  23 "
        pdb=" N   PRO C  24 "
        pdb=" CA  PRO C  24 "
      ideal   model   delta    sigma   weight residual
     119.83  115.79    4.04 1.08e+00 8.57e-01 1.40e+01
  angle pdb=" C   MET A 134 "
        pdb=" CA  MET A 134 "
        pdb=" CB  MET A 134 "
      ideal   model   delta    sigma   weight residual
     110.51  117.45   -6.94 1.89e+00 2.80e-01 1.35e+01
  ... (remaining 13441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4998
       17.96 -    35.92: 612
       35.92 -    53.88: 173
       53.88 -    71.84: 33
       71.84 -    89.80: 18
  Dihedral angle restraints: 5834
    sinusoidal: 2389
      harmonic: 3445
  Sorted by residual:
  dihedral pdb=" CA  SER C 120 "
           pdb=" C   SER C 120 "
           pdb=" N   MET C 121 "
           pdb=" CA  MET C 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  THR B 418 "
           pdb=" C   THR B 418 "
           pdb=" N   ILE B 419 "
           pdb=" CA  ILE B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.39   23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  VAL A 332 "
           pdb=" C   VAL A 332 "
           pdb=" N   GLY A 333 "
           pdb=" CA  GLY A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.48   23.52     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 5831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1070
       0.053 -    0.106: 244
       0.106 -    0.159: 51
       0.159 -    0.212: 11
       0.212 -    0.265: 2
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  TYR A 401 "
            pdb=" N   TYR A 401 "
            pdb=" C   TYR A 401 "
            pdb=" CB  TYR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  TRP B 412 "
            pdb=" N   TRP B 412 "
            pdb=" C   TRP B 412 "
            pdb=" CB  TRP B 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  MET C 156 "
            pdb=" N   MET C 156 "
            pdb=" C   MET C 156 "
            pdb=" CB  MET C 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1375 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 412 "   -0.056 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        pdb=" N   PRO A 413 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 414 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   SER A 414 "    0.036 2.00e-02 2.50e+03
        pdb=" O   SER A 414 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 415 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  44 "   -0.034 5.00e-02 4.00e+02   5.22e-02 4.37e+00
        pdb=" N   PRO C  45 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C  45 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C  45 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1854
        2.77 -     3.30: 9492
        3.30 -     3.83: 16981
        3.83 -     4.37: 20220
        4.37 -     4.90: 33724
  Nonbonded interactions: 82271
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 368 "
            pdb=" O   SER B 378 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OH  TYR B  18 "
            pdb=" O   PRO B 382 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR B 301 "
            pdb=" OG1 THR B 355 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 109 "
            pdb=" OE1 GLU A 111 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" NZ  LYS C  13 "
            pdb=" O   THR C  14 "
     model   vdw
     2.289 3.120
  ... (remaining 82266 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:             3.000
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9924  Z= 0.172
  Angle     :  0.742  11.952  13446  Z= 0.397
  Chirality :  0.050   0.265   1378
  Planarity :  0.005   0.085   1732
  Dihedral  : 17.485  89.798   3642
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 30.02 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.38 (0.24), residues: 1190
  helix: -0.14 (0.25), residues: 381
  sheet: -0.64 (0.37), residues: 210
  loop :  0.01 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 186 
 TYR   0.025   0.002   TYR B 443 
 PHE   0.010   0.001   PHE B 267 
 TRP   0.020   0.002   TRP A 240 
 HIS   0.009   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9924)
  covalent geometry    : angle       0.74244 (13446)
  hydrogen bonds       : bond        0.17621 (  340)
  hydrogen bonds       : angle       8.62519 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  431 MET cc_start: 0.5207 (ttm) cc_final: 0.4809 (tmm)
REVERT: C  142 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7873 (pt)
  outliers start: 8
  outliers final: 2
  residues processed: 154
  average time/residue: 0.5900
  time to fit residues: 97.4827
Evaluate side-chains
  128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  181 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:   40.0000
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   20.0000
   chunk 117 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B  88 ASN
B 144 ASN
B 186 ASN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 HIS
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
B 364 GLN
A  13 HIS
A  14 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 GLN
A 294 GLN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 ASN
C 198 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.174925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.131668 restraints weight = 14140.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.89
r_work: 0.3734 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9924  Z= 0.187
  Angle     :  0.648   9.370  13446  Z= 0.332
  Chirality :  0.047   0.177   1378
  Planarity :  0.004   0.059   1732
  Dihedral  :  5.145  46.082   1314
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.84 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.24), residues: 1190
  helix:  0.09 (0.25), residues: 393
  sheet: -0.84 (0.36), residues: 221
  loop :  0.13 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 282 
 TYR   0.033   0.002   TYR B 426 
 PHE   0.016   0.002   PHE B 267 
 TRP   0.014   0.002   TRP A 240 
 HIS   0.013   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 9924)
  covalent geometry    : angle       0.64760 (13446)
  hydrogen bonds       : bond        0.04381 (  340)
  hydrogen bonds       : angle       6.62133 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 142
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7582 (ttmt)
REVERT: B   97 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5824 (pp20)
REVERT: B  134 MET cc_start: 0.7023 (tpt) cc_final: 0.6781 (mpp)
REVERT: B  258 TRP cc_start: 0.6579 (OUTLIER) cc_final: 0.4866 (t-100)
REVERT: B  403 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.4129 (ttm)
REVERT: A   49 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7344 (mp)
REVERT: A  169 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7511 (mp10)
REVERT: A  286 GLU cc_start: 0.7943 (pm20) cc_final: 0.7628 (pm20)
REVERT: A  294 GLN cc_start: 0.7646 (tt0) cc_final: 0.7276 (tp-100)
REVERT: A  352 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5310 (pp)
REVERT: A  431 MET cc_start: 0.5129 (ttm) cc_final: 0.4514 (tmm)
REVERT: C   29 ASP cc_start: 0.6783 (p0) cc_final: 0.6554 (p0)
  outliers start: 55
  outliers final: 19
  residues processed: 173
  average time/residue: 0.5205
  time to fit residues: 97.4951
Evaluate side-chains
  150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 43 optimal weight:    0.0270
   chunk 107 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 116 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 114 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 108 optimal weight:    0.4980
   overall best weight:    1.4842

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.172672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.129222 restraints weight = 14237.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.89
r_work: 0.3689 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   9924  Z= 0.213
  Angle     :  0.662   7.947  13446  Z= 0.336
  Chirality :  0.048   0.149   1378
  Planarity :  0.005   0.056   1732
  Dihedral  :  5.081  37.088   1312
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 24.55 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.33 (0.25), residues: 1190
  helix:  0.06 (0.25), residues: 398
  sheet: -0.89 (0.36), residues: 226
  loop :  0.08 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 282 
 TYR   0.028   0.002   TYR B 187 
 PHE   0.017   0.002   PHE B 267 
 TRP   0.018   0.002   TRP A 270 
 HIS   0.015   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 9924)
  covalent geometry    : angle       0.66215 (13446)
  hydrogen bonds       : bond        0.04031 (  340)
  hydrogen bonds       : angle       6.27164 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 138
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6002 (pp20)
REVERT: B  134 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6960 (mpp)
REVERT: B  258 TRP cc_start: 0.6575 (OUTLIER) cc_final: 0.4916 (t-100)
REVERT: B  352 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5770 (mt)
REVERT: B  444 MET cc_start: 0.5848 (ptt) cc_final: 0.5580 (pmm)
REVERT: A  169 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7547 (mp10)
REVERT: A  231 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7262 (ptt)
REVERT: A  286 GLU cc_start: 0.7969 (pm20) cc_final: 0.7658 (pm20)
REVERT: A  294 GLN cc_start: 0.7809 (tt0) cc_final: 0.7422 (tp-100)
REVERT: A  346 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7512 (mmtm)
REVERT: A  414 SER cc_start: 0.7762 (t) cc_final: 0.7547 (t)
REVERT: A  415 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6806 (mmm)
REVERT: A  431 MET cc_start: 0.5282 (ttm) cc_final: 0.4615 (tmm)
REVERT: C   12 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8265 (mp)
REVERT: C   49 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7294 (m-70)
REVERT: C  201 ARG cc_start: 0.6403 (tmt90) cc_final: 0.6135 (tpp-160)
  outliers start: 71
  outliers final: 29
  residues processed: 182
  average time/residue: 0.4894
  time to fit residues: 97.1114
Evaluate side-chains
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  352 ILE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 78 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 112 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.175664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.132974 restraints weight = 14331.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 2.87
r_work: 0.3758 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9924  Z= 0.135
  Angle     :  0.603   7.958  13446  Z= 0.304
  Chirality :  0.046   0.173   1378
  Planarity :  0.004   0.053   1732
  Dihedral  :  4.877  29.500   1312
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 24.75 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.11 (0.25), residues: 1190
  helix:  0.35 (0.26), residues: 394
  sheet: -0.96 (0.36), residues: 228
  loop :  0.22 (0.28), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 186 
 TYR   0.027   0.002   TYR B 187 
 PHE   0.010   0.001   PHE B 267 
 TRP   0.019   0.001   TRP A 270 
 HIS   0.008   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9924)
  covalent geometry    : angle       0.60301 (13446)
  hydrogen bonds       : bond        0.03266 (  340)
  hydrogen bonds       : angle       5.98890 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 140
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7772 (ttmm)
REVERT: B   97 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5761 (pp20)
REVERT: B  134 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6716 (mpp)
REVERT: B  403 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.3911 (mtp)
REVERT: B  444 MET cc_start: 0.5842 (ptt) cc_final: 0.5615 (pmm)
REVERT: B  503 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8422 (pp)
REVERT: B  515 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8904 (pp)
REVERT: A  169 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7588 (mp10)
REVERT: A  231 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7203 (ptt)
REVERT: A  286 GLU cc_start: 0.7875 (pm20) cc_final: 0.7568 (pm20)
REVERT: A  294 GLN cc_start: 0.7807 (tt0) cc_final: 0.7393 (tp-100)
REVERT: A  346 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7553 (mmtm)
REVERT: A  352 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5018 (pp)
REVERT: A  431 MET cc_start: 0.5342 (ttm) cc_final: 0.4701 (tmm)
REVERT: C   29 ASP cc_start: 0.6637 (p0) cc_final: 0.6375 (p0)
REVERT: C   49 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7272 (m-70)
REVERT: C  156 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5821 (mpt)
REVERT: C  201 ARG cc_start: 0.6168 (tmt90) cc_final: 0.5885 (tpt170)
  outliers start: 64
  outliers final: 24
  residues processed: 176
  average time/residue: 0.5602
  time to fit residues: 106.2330
Evaluate side-chains
  166 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0770
   chunk 45 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.176154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.133876 restraints weight = 14269.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 2.85
r_work: 0.3764 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9924  Z= 0.139
  Angle     :  0.603   9.573  13446  Z= 0.302
  Chirality :  0.045   0.148   1378
  Planarity :  0.004   0.052   1732
  Dihedral  :  4.771  30.965   1310
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 25.84 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.07 (0.25), residues: 1190
  helix:  0.43 (0.26), residues: 395
  sheet: -0.83 (0.37), residues: 220
  loop :  0.13 (0.28), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 282 
 TYR   0.026   0.002   TYR C  33 
 PHE   0.012   0.001   PHE B 267 
 TRP   0.015   0.001   TRP A 240 
 HIS   0.009   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9924)
  covalent geometry    : angle       0.60294 (13446)
  hydrogen bonds       : bond        0.03124 (  340)
  hydrogen bonds       : angle       5.84498 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 139
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8557 (m-40) cc_final: 0.8348 (m110)
REVERT: B   97 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5727 (pp20)
REVERT: B  205 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8581 (mttp)
REVERT: B  403 MET cc_start: 0.5206 (OUTLIER) cc_final: 0.4030 (mtp)
REVERT: B  503 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8427 (pp)
REVERT: B  515 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8895 (pp)
REVERT: A  169 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7614 (mp10)
REVERT: A  231 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7065 (ptt)
REVERT: A  286 GLU cc_start: 0.7882 (pm20) cc_final: 0.7678 (mp0)
REVERT: A  294 GLN cc_start: 0.7808 (tt0) cc_final: 0.7450 (tp-100)
REVERT: A  346 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7692 (mmtm)
REVERT: A  352 ILE cc_start: 0.5291 (OUTLIER) cc_final: 0.4939 (pp)
REVERT: A  398 LEU cc_start: 0.7043 (mp) cc_final: 0.6750 (mp)
REVERT: A  431 MET cc_start: 0.5389 (ttm) cc_final: 0.4740 (tmm)
REVERT: C  148 ASP cc_start: 0.8552 (t0) cc_final: 0.8341 (p0)
REVERT: C  156 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5437 (mpt)
REVERT: C  201 ARG cc_start: 0.6257 (tmt90) cc_final: 0.5923 (tpt170)
  outliers start: 61
  outliers final: 27
  residues processed: 174
  average time/residue: 0.5621
  time to fit residues: 105.4819
Evaluate side-chains
  162 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 90 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 20 optimal weight:    0.1980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  11 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.176882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.134414 restraints weight = 14168.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 2.88
r_work: 0.3813 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9924  Z= 0.129
  Angle     :  0.615   9.747  13446  Z= 0.305
  Chirality :  0.045   0.192   1378
  Planarity :  0.004   0.054   1732
  Dihedral  :  4.668  30.461   1310
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 27.04 %
    Favored  : 67.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.02 (0.25), residues: 1190
  helix:  0.52 (0.26), residues: 396
  sheet: -0.78 (0.37), residues: 220
  loop :  0.16 (0.28), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 282 
 TYR   0.027   0.002   TYR C  33 
 PHE   0.010   0.001   PHE B 267 
 TRP   0.019   0.001   TRP A 270 
 HIS   0.007   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9924)
  covalent geometry    : angle       0.61549 (13446)
  hydrogen bonds       : bond        0.02986 (  340)
  hydrogen bonds       : angle       5.74355 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 137
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7317 (mtm-85)
REVERT: B   88 ASN cc_start: 0.8511 (m-40) cc_final: 0.8307 (m-40)
REVERT: B   97 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5669 (pp20)
REVERT: B  403 MET cc_start: 0.5082 (OUTLIER) cc_final: 0.3800 (mtp)
REVERT: B  444 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5995 (pmm)
REVERT: B  503 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8414 (pp)
REVERT: A  169 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7618 (mp10)
REVERT: A  286 GLU cc_start: 0.7860 (pm20) cc_final: 0.7613 (mp0)
REVERT: A  294 GLN cc_start: 0.7840 (tt0) cc_final: 0.7474 (tp-100)
REVERT: A  398 LEU cc_start: 0.7115 (mp) cc_final: 0.6843 (mp)
REVERT: A  431 MET cc_start: 0.5336 (ttm) cc_final: 0.4732 (tmm)
REVERT: C  201 ARG cc_start: 0.6214 (tmt90) cc_final: 0.5906 (tpt170)
  outliers start: 58
  outliers final: 29
  residues processed: 173
  average time/residue: 0.5575
  time to fit residues: 103.9146
Evaluate side-chains
  160 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  444 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 36 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0370
   chunk 104 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5862

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.177775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.135631 restraints weight = 14162.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.86
r_work: 0.3783 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9924  Z= 0.134
  Angle     :  0.621   9.939  13446  Z= 0.310
  Chirality :  0.045   0.189   1378
  Planarity :  0.004   0.057   1732
  Dihedral  :  4.682  29.859   1310
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.63 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.04 (0.25), residues: 1190
  helix:  0.53 (0.26), residues: 396
  sheet: -0.78 (0.37), residues: 217
  loop :  0.19 (0.28), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 282 
 TYR   0.027   0.002   TYR C  33 
 PHE   0.011   0.001   PHE A 267 
 TRP   0.027   0.001   TRP A 270 
 HIS   0.007   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9924)
  covalent geometry    : angle       0.62097 (13446)
  hydrogen bonds       : bond        0.03079 (  340)
  hydrogen bonds       : angle       5.72438 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7297 (mtm-85)
REVERT: B   88 ASN cc_start: 0.8520 (m-40) cc_final: 0.8316 (m-40)
REVERT: B   97 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5644 (pp20)
REVERT: B  403 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.3826 (mtp)
REVERT: B  503 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8400 (pp)
REVERT: B  515 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8868 (pp)
REVERT: A  169 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7617 (mp10)
REVERT: A  286 GLU cc_start: 0.7879 (pm20) cc_final: 0.7646 (mp0)
REVERT: A  294 GLN cc_start: 0.7850 (tt0) cc_final: 0.7490 (tp-100)
REVERT: A  308 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8363 (mmm160)
REVERT: A  398 LEU cc_start: 0.7099 (mp) cc_final: 0.6847 (mp)
REVERT: A  431 MET cc_start: 0.5386 (ttm) cc_final: 0.4934 (tmm)
REVERT: C   29 ASP cc_start: 0.6435 (p0) cc_final: 0.6141 (p0)
REVERT: C  156 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6021 (mpt)
REVERT: C  184 MET cc_start: 0.5764 (mmm) cc_final: 0.5495 (mmm)
REVERT: C  201 ARG cc_start: 0.6203 (tmt90) cc_final: 0.5907 (tpt170)
  outliers start: 49
  outliers final: 31
  residues processed: 161
  average time/residue: 0.5154
  time to fit residues: 89.7225
Evaluate side-chains
  164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0970
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7978

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.177171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.134332 restraints weight = 14179.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.93
r_work: 0.3796 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9924  Z= 0.149
  Angle     :  0.641   8.862  13446  Z= 0.317
  Chirality :  0.046   0.169   1378
  Planarity :  0.004   0.059   1732
  Dihedral  :  4.720  31.253   1310
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.44 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.02 (0.25), residues: 1190
  helix:  0.55 (0.26), residues: 395
  sheet: -0.81 (0.37), residues: 217
  loop :  0.15 (0.28), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 282 
 TYR   0.026   0.002   TYR C  33 
 PHE   0.013   0.001   PHE B 267 
 TRP   0.031   0.001   TRP A 270 
 HIS   0.006   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9924)
  covalent geometry    : angle       0.64075 (13446)
  hydrogen bonds       : bond        0.03156 (  340)
  hydrogen bonds       : angle       5.72372 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 131
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7303 (mtm-85)
REVERT: B   88 ASN cc_start: 0.8508 (m-40) cc_final: 0.8276 (m-40)
REVERT: B   97 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5705 (pp20)
REVERT: B  403 MET cc_start: 0.4986 (OUTLIER) cc_final: 0.3440 (mtp)
REVERT: B  443 TYR cc_start: 0.5614 (p90) cc_final: 0.4924 (p90)
REVERT: B  503 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8393 (pp)
REVERT: B  515 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8856 (pp)
REVERT: A  169 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7617 (mp10)
REVERT: A  286 GLU cc_start: 0.7892 (pm20) cc_final: 0.7653 (mp0)
REVERT: A  294 GLN cc_start: 0.7908 (tt0) cc_final: 0.7532 (tp-100)
REVERT: A  308 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8382 (mmm160)
REVERT: A  398 LEU cc_start: 0.7147 (mp) cc_final: 0.6893 (mp)
REVERT: A  431 MET cc_start: 0.5293 (ttm) cc_final: 0.4874 (tmm)
REVERT: C  156 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5900 (mpt)
REVERT: C  201 ARG cc_start: 0.6213 (tmt90) cc_final: 0.5918 (tpt170)
  outliers start: 52
  outliers final: 35
  residues processed: 164
  average time/residue: 0.5103
  time to fit residues: 90.7281
Evaluate side-chains
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.173514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.130202 restraints weight = 14111.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.92
r_work: 0.3734 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   9924  Z= 0.202
  Angle     :  0.693  11.475  13446  Z= 0.346
  Chirality :  0.047   0.174   1378
  Planarity :  0.005   0.058   1732
  Dihedral  :  4.973  33.499   1310
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 27.83 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.05 (0.25), residues: 1190
  helix:  0.46 (0.26), residues: 393
  sheet: -0.84 (0.37), residues: 206
  loop :  0.10 (0.28), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 282 
 TYR   0.029   0.002   TYR C  33 
 PHE   0.019   0.002   PHE B 267 
 TRP   0.038   0.002   TRP A 270 
 HIS   0.009   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 9924)
  covalent geometry    : angle       0.69327 (13446)
  hydrogen bonds       : bond        0.03623 (  340)
  hydrogen bonds       : angle       5.92166 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 125
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LYS cc_start: 0.7723 (tptp) cc_final: 0.7522 (ttpp)
REVERT: B   97 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6012 (pp20)
REVERT: B  403 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4720 (mmp)
REVERT: B  443 TYR cc_start: 0.5702 (p90) cc_final: 0.4995 (p90)
REVERT: B  515 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8888 (pp)
REVERT: A  286 GLU cc_start: 0.7987 (pm20) cc_final: 0.7736 (mp0)
REVERT: A  294 GLN cc_start: 0.8022 (tt0) cc_final: 0.7567 (tp-100)
REVERT: A  308 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8384 (mmm160)
REVERT: A  431 MET cc_start: 0.5281 (ttm) cc_final: 0.5037 (tmt)
REVERT: C   29 ASP cc_start: 0.6456 (p0) cc_final: 0.6208 (p0)
REVERT: C  156 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5385 (mpt)
REVERT: C  201 ARG cc_start: 0.6316 (tmt90) cc_final: 0.5985 (tpt170)
  outliers start: 48
  outliers final: 31
  residues processed: 157
  average time/residue: 0.4906
  time to fit residues: 83.8489
Evaluate side-chains
  150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 114 optimal weight:    0.3980
   chunk 54 optimal weight:    8.9990
   chunk 42 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.175622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.133250 restraints weight = 14040.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 2.88
r_work: 0.3754 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9924  Z= 0.149
  Angle     :  0.696  13.669  13446  Z= 0.340
  Chirality :  0.046   0.172   1378
  Planarity :  0.005   0.057   1732
  Dihedral  :  4.922  29.870   1310
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 29.13 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.04 (0.25), residues: 1190
  helix:  0.54 (0.26), residues: 394
  sheet: -1.03 (0.35), residues: 226
  loop :  0.20 (0.28), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 282 
 TYR   0.031   0.002   TYR C  33 
 PHE   0.011   0.001   PHE B  25 
 TRP   0.035   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9924)
  covalent geometry    : angle       0.69579 (13446)
  hydrogen bonds       : bond        0.03262 (  340)
  hydrogen bonds       : angle       5.78723 (  975)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8544 (m-40) cc_final: 0.8276 (m-40)
REVERT: B   97 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5782 (pp20)
REVERT: B  403 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4430 (mmp)
REVERT: B  443 TYR cc_start: 0.5627 (p90) cc_final: 0.4959 (p90)
REVERT: B  515 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8828 (pp)
REVERT: A  286 GLU cc_start: 0.7944 (pm20) cc_final: 0.7710 (mp0)
REVERT: A  294 GLN cc_start: 0.7976 (tt0) cc_final: 0.7555 (tp-100)
REVERT: A  308 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8411 (mmm160)
REVERT: A  431 MET cc_start: 0.5294 (ttm) cc_final: 0.5030 (tmt)
REVERT: C  122 MET cc_start: 0.3290 (pp-130) cc_final: 0.2986 (tmm)
REVERT: C  156 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5687 (mpt)
REVERT: C  201 ARG cc_start: 0.6268 (tmt90) cc_final: 0.5964 (tpt170)
  outliers start: 38
  outliers final: 27
  residues processed: 145
  average time/residue: 0.5288
  time to fit residues: 83.5327
Evaluate side-chains
  148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 88 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.176270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.132579 restraints weight = 14316.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 3.00
r_work: 0.3748 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9924  Z= 0.150
  Angle     :  0.689  12.924  13446  Z= 0.336
  Chirality :  0.046   0.163   1378
  Planarity :  0.004   0.057   1732
  Dihedral  :  4.888  30.854   1310
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.22 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.06 (0.25), residues: 1190
  helix:  0.53 (0.26), residues: 394
  sheet: -1.05 (0.36), residues: 218
  loop :  0.16 (0.28), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 282 
 TYR   0.030   0.002   TYR B 426 
 PHE   0.012   0.001   PHE B  25 
 TRP   0.043   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9924)
  covalent geometry    : angle       0.68869 (13446)
  hydrogen bonds       : bond        0.03207 (  340)
  hydrogen bonds       : angle       5.74442 (  975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4147.25 seconds
wall clock time: 71 minutes 26.27 seconds (4286.27 seconds total)