Starting phenix.real_space_refine
on Wed Sep 17 14:43:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xss_38627/09_2025/8xss_38627.map"
  }
  resolution = 3.33
  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=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    5781      2.51       5
     N    1612      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 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: 9119
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4348
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 19, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4743
          Classifications: {'peptide': 619}
          Link IDs: {'PTRANS': 18, 'TRANS': 600}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.21
  Number of scatterers: 9119
  At special positions: 0
  Unit cell: (69.888, 91.52, 148.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      33     16.00
     P       2     15.00
     Mg      1     11.99
     O    1690      8.00
     N    1612      7.00
     C    5781      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: 0.87
  Conformation dependent library (CDL) restraints added in 349.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 4 sheets defined
      64.7% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid -1 through 10
      removed outlier: 4.271A  pdb=" N   TRP A   3 " --> pdb=" O   SER A  -1 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR A   9 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 30
      removed outlier: 3.645A  pdb=" N   ILE A  26 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 45
      removed outlier: 3.861A  pdb=" N   THR A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A  40 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 71
      removed outlier: 3.963A  pdb=" N   ILE A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL A  55 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   VAL A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 99
      removed outlier: 3.673A  pdb=" N   ARG A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A  82 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   THR A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   GLY A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   HIS A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   LEU A  90 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A  96 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
      removed outlier: 3.563A  pdb=" N   ARG A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 3.513A  pdb=" N   HIS A 124 " --> pdb=" O   ASN A 120 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN A 130 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 153
    Processing helix  chain 'A' and resid 154 through 156
      No H-bonds generated for 'chain 'A' and resid 154 through 156'
    Processing helix  chain 'A' and resid 157 through 203
      removed outlier: 4.385A  pdb=" N   LEU A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.780A  pdb=" N   ASN A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 176 " --> pdb=" O   ASN A 172 " (cutoff:3.500A)
      Proline residue:  A 181  - end of helix
      removed outlier: 3.567A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 183 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 196 " --> pdb=" O   GLY A 192 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY A 203 " --> pdb=" O   ASP A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 210
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.514A  pdb=" N   GLN A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   THR A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.675A  pdb=" N   TRP A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 265
      removed outlier: 3.619A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TRP A 258 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ARG A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 293
      removed outlier: 4.050A  pdb=" N   LEU A 274 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 313
      removed outlier: 3.861A  pdb=" N   VAL A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   CYS A 304 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 382
      removed outlier: 3.678A  pdb=" N   LEU A 377 " --> pdb=" O   GLY A 373 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 402
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.701A  pdb=" N   ALA A 410 " --> pdb=" O   GLN A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 430 through 433
    Processing helix  chain 'A' and resid 437 through 448
      removed outlier: 3.570A  pdb=" N   TRP A 442 " --> pdb=" O   ASP A 438 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A 444 " --> pdb=" O   GLU A 440 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 445 " --> pdb=" O   MET A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.779A  pdb=" N   VAL A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 552 through 558
      removed outlier: 4.225A  pdb=" N   ALA A 558 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 569
      removed outlier: 3.742A  pdb=" N   SER A 569 " --> pdb=" O   GLU A 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 27
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 31 through 45
      removed outlier: 3.626A  pdb=" N   VAL B  38 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU B  41 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 68
      removed outlier: 3.968A  pdb=" N   ARG B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 88
    Processing helix  chain 'B' and resid 90 through 99
    Processing helix  chain 'B' and resid 109 through 158
      removed outlier: 3.672A  pdb=" N   VAL B 113 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLN B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ALA B 148 " --> pdb=" O   ARG B 144 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 154 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 167
      removed outlier: 3.840A  pdb=" N   PHE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.632A  pdb=" N   ARG B 176 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 190
    Processing helix  chain 'B' and resid 195 through 213
      removed outlier: 3.949A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   VAL B 205 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE B 212 " --> pdb=" O   MET B 208 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 3.689A  pdb=" N   LEU B 218 " --> pdb=" O   PRO B 214 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   THR B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 238
      removed outlier: 3.766A  pdb=" N   VAL B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   THR B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 262
      removed outlier: 3.664A  pdb=" N   TRP B 246 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLU B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY B 262 " --> pdb=" O   GLU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 268
    Processing helix  chain 'B' and resid 271 through 299
      removed outlier: 4.637A  pdb=" N   GLU B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLN B 288 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER B 289 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLY B 292 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 309 through 325
      removed outlier: 3.663A  pdb=" N   ALA B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 345
      removed outlier: 3.554A  pdb=" N   ALA B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN B 345 " --> pdb=" O   ARG B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 363
      removed outlier: 3.912A  pdb=" N   THR B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER B 359 " --> pdb=" O   ASN B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 372
      removed outlier: 3.900A  pdb=" N   PHE B 368 " --> pdb=" O   ALA B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 438
    Processing helix  chain 'B' and resid 459 through 468
      removed outlier: 4.033A  pdb=" N   GLY B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 487
    Processing helix  chain 'B' and resid 493 through 503
      removed outlier: 3.574A  pdb=" N   GLU B 499 " --> pdb=" O   ASP B 495 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA B 503 " --> pdb=" O   GLU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 511
    Processing helix  chain 'B' and resid 529 through 545
      removed outlier: 3.830A  pdb=" N   THR B 537 " --> pdb=" O   LYS B 533 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 544 " --> pdb=" O   ARG B 540 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG B 545 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 570
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 608 through 614
    Processing helix  chain 'B' and resid 617 through 627
    Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 341
      removed outlier: 5.123A  pdb=" N   HIS A 337 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   PHE A 356 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   PHE A 341 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   GLN A 352 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414
      removed outlier: 6.445A  pdb=" N   GLY A 412 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   ASP A 496 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL A 414 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   THR A 363 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   VAL A 540 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ALA A 365 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   ILE A 542 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 549 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424
      removed outlier: 4.152A  pdb=" N   GLY A 423 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 469 through 470
      removed outlier: 6.582A  pdb=" N   VAL B 470 " --> pdb=" O   ASP B 552 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLU B 605 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1326 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: 1.28

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3076
        1.34 -     1.46: 1905
        1.46 -     1.58: 4228
        1.58 -     1.70: 4
        1.70 -     1.81: 61
  Bond restraints: 9274
  Sorted by residual:
  bond pdb=" CB  PRO B 416 "
       pdb=" CG  PRO B 416 "
    ideal  model  delta    sigma   weight residual
    1.492  1.607 -0.115 5.00e-02 4.00e+02 5.32e+00
  bond pdb=" C   VAL A 165 "
       pdb=" N   PRO A 166 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.23e-02 6.61e+03 4.53e+00
  bond pdb=" CA  ASP B 522 "
       pdb=" CB  ASP B 522 "
    ideal  model  delta    sigma   weight residual
    1.530  1.558 -0.027 1.69e-02 3.50e+03 2.64e+00
  bond pdb=" CB  ASN B 355 "
       pdb=" CG  ASN B 355 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.30e+00
  bond pdb=" N   ARG A 217 "
       pdb=" CA  ARG A 217 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.12e+00
  ... (remaining 9269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 12369
        2.39 -     4.78: 212
        4.78 -     7.17: 33
        7.17 -     9.56: 12
        9.56 -    11.95: 2
  Bond angle restraints: 12628
  Sorted by residual:
  angle pdb=" C   VAL A 165 "
        pdb=" N   PRO A 166 "
        pdb=" CA  PRO A 166 "
      ideal   model   delta    sigma   weight residual
     119.19  112.59    6.60 1.06e+00 8.90e-01 3.88e+01
  angle pdb=" N   VAL A  19 "
        pdb=" CA  VAL A  19 "
        pdb=" C   VAL A  19 "
      ideal   model   delta    sigma   weight residual
     113.43  106.83    6.60 1.09e+00 8.42e-01 3.67e+01
  angle pdb=" N   ILE B  48 "
        pdb=" CA  ILE B  48 "
        pdb=" C   ILE B  48 "
      ideal   model   delta    sigma   weight residual
     112.96  107.36    5.60 1.00e+00 1.00e+00 3.14e+01
  angle pdb=" N   ILE B 192 "
        pdb=" CA  ILE B 192 "
        pdb=" C   ILE B 192 "
      ideal   model   delta    sigma   weight residual
     113.71  108.44    5.27 9.50e-01 1.11e+00 3.08e+01
  angle pdb=" CA  PRO B 416 "
        pdb=" N   PRO B 416 "
        pdb=" CD  PRO B 416 "
      ideal   model   delta    sigma   weight residual
     112.00  105.04    6.96 1.40e+00 5.10e-01 2.47e+01
  ... (remaining 12623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.29: 5366
       34.29 -    68.58: 129
       68.58 -   102.88: 13
      102.88 -   137.17: 2
      137.17 -   171.46: 1
  Dihedral angle restraints: 5511
    sinusoidal: 2102
      harmonic: 3409
  Sorted by residual:
  dihedral pdb=" O2A ADP B 701 "
           pdb=" O3A ADP B 701 "
           pdb=" PA  ADP B 701 "
           pdb=" PB  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  111.46 -171.46     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" O1B ADP B 701 "
           pdb=" O3A ADP B 701 "
           pdb=" PB  ADP B 701 "
           pdb=" PA  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   71.34 -131.35     1      2.00e+01 2.50e-03 3.99e+01
  dihedral pdb=" C5' ADP B 701 "
           pdb=" O5' ADP B 701 "
           pdb=" PA  ADP B 701 "
           pdb=" O2A ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   43.74 -103.73     1      2.00e+01 2.50e-03 2.97e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1118
       0.046 -    0.091: 331
       0.091 -    0.136: 65
       0.136 -    0.182: 4
       0.182 -    0.227: 2
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CB  ILE B 448 "
            pdb=" CA  ILE B 448 "
            pdb=" CG1 ILE B 448 "
            pdb=" CG2 ILE B 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE A 487 "
            pdb=" CA  ILE A 487 "
            pdb=" CG1 ILE A 487 "
            pdb=" CG2 ILE A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality pdb=" CA  ASP A 154 "
            pdb=" N   ASP A 154 "
            pdb=" C   ASP A 154 "
            pdb=" CB  ASP A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1517 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 415 "   -0.072 5.00e-02 4.00e+02   1.05e-01 1.78e+01
        pdb=" N   PRO B 416 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO B 416 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO B 416 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 213 "    0.044 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO A 214 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 594 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.92e+00
        pdb=" C   LEU B 594 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LEU B 594 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE B 595 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 106
        2.62 -     3.19: 8270
        3.19 -     3.76: 14240
        3.76 -     4.33: 19567
        4.33 -     4.90: 32276
  Nonbonded interactions: 74459
  Sorted by model distance:
  nonbonded pdb=" O3B ADP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" OG1 THR B 431 "
            pdb="MG    MG B 702 "
     model   vdw
     2.141 2.170
  nonbonded pdb=" OG1 THR A  36 "
            pdb=" OH  TYR A 280 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD2 ASP B 166 "
            pdb=" OH  TYR B 441 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   LEU B 321 "
            pdb=" OG1 THR B 325 "
     model   vdw
     2.238 3.040
  ... (remaining 74454 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:             2.240
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.010
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.115   9274  Z= 0.161
  Angle     :  0.812  11.950  12628  Z= 0.463
  Chirality :  0.044   0.227   1520
  Planarity :  0.005   0.105   1617
  Dihedral  : 15.457 171.460   3317
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.23 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.60 %
    Favored  : 80.36 %
  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: -3.15 (0.22), residues: 1189
  helix: -1.78 (0.18), residues: 734
  sheet: -1.90 (0.63), residues: 47
  loop : -2.42 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 561 
 TYR   0.012   0.001   TYR B 482 
 PHE   0.024   0.001   PHE A 453 
 TRP   0.013   0.001   TRP B 229 
 HIS   0.010   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9274)
  covalent geometry    : angle       0.81164 (12628)
  hydrogen bonds       : bond        0.19950 (  449)
  hydrogen bonds       : angle       7.57104 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8051 (m-30)
REVERT: A  214 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7801 (Cg_endo)
REVERT: A  478 GLN cc_start: 0.7778 (tp40) cc_final: 0.7163 (mt0)
REVERT: B   31 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6303 (mm-40)
REVERT: B  180 ASP cc_start: 0.8416 (t0) cc_final: 0.8134 (t0)
REVERT: B  281 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7244 (mt-10)
REVERT: B  345 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7055 (tt0)
REVERT: B  353 MET cc_start: 0.7975 (ttm) cc_final: 0.7482 (mtm)
REVERT: B  438 MET cc_start: 0.8898 (mmm) cc_final: 0.8606 (tpp)
REVERT: B  472 GLN cc_start: 0.8196 (tt0) cc_final: 0.7976 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 162
  average time/residue: 0.0709
  time to fit residues: 16.9128
Evaluate side-chains
  148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain B residue  345 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.162799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.118721 restraints weight = 10920.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.27
r_work: 0.3264 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9274  Z= 0.152
  Angle     :  0.692  11.756  12628  Z= 0.344
  Chirality :  0.043   0.205   1520
  Planarity :  0.005   0.059   1617
  Dihedral  :  8.296 156.103   1330
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 15.88 %
    Favored  : 80.15 %
  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: -2.49 (0.23), residues: 1189
  helix: -1.28 (0.18), residues: 756
  sheet: -1.70 (0.63), residues: 52
  loop : -2.12 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.017   0.001   TYR B 482 
 PHE   0.015   0.001   PHE A 453 
 TRP   0.010   0.001   TRP B 229 
 HIS   0.009   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9274)
  covalent geometry    : angle       0.69164 (12628)
  hydrogen bonds       : bond        0.03903 (  449)
  hydrogen bonds       : angle       4.62407 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (m-30)
REVERT: A  195 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7131 (tpt170)
REVERT: B  180 ASP cc_start: 0.8354 (t0) cc_final: 0.8028 (t0)
REVERT: B  213 SER cc_start: 0.8723 (t) cc_final: 0.7963 (p)
REVERT: B  301 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8380 (t)
REVERT: B  345 GLN cc_start: 0.7839 (tt0) cc_final: 0.7624 (tm-30)
REVERT: B  353 MET cc_start: 0.7998 (ttm) cc_final: 0.7400 (mtm)
REVERT: B  392 GLU cc_start: 0.7824 (tt0) cc_final: 0.7586 (pt0)
REVERT: B  472 GLN cc_start: 0.8382 (tt0) cc_final: 0.8147 (tt0)
REVERT: B  613 LEU cc_start: 0.8943 (tp) cc_final: 0.8714 (tp)
REVERT: B  621 GLU cc_start: 0.8565 (tt0) cc_final: 0.7361 (tm-30)
  outliers start: 38
  outliers final: 20
  residues processed: 175
  average time/residue: 0.0723
  time to fit residues: 18.6186
Evaluate side-chains
  159 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   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  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.164106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119911 restraints weight = 10793.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.32
r_work: 0.3248 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9274  Z= 0.132
  Angle     :  0.663  12.628  12628  Z= 0.324
  Chirality :  0.043   0.206   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  7.096 131.073   1321
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.72 %
    Favored  : 79.21 %
  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: -2.07 (0.24), residues: 1189
  helix: -0.88 (0.19), residues: 762
  sheet: -2.10 (0.60), residues: 64
  loop : -1.98 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 460 
 TYR   0.013   0.001   TYR B 482 
 PHE   0.008   0.001   PHE B 295 
 TRP   0.008   0.001   TRP B 229 
 HIS   0.008   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9274)
  covalent geometry    : angle       0.66311 (12628)
  hydrogen bonds       : bond        0.03430 (  449)
  hydrogen bonds       : angle       4.24351 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7578 (tp40)
REVERT: A  183 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8637 (t80)
REVERT: A  195 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7049 (tpt170)
REVERT: A  300 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6447 (ttp80)
REVERT: A  326 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.7065 (mmt-90)
REVERT: A  352 GLN cc_start: 0.7353 (tm-30) cc_final: 0.7080 (tm-30)
REVERT: A  535 GLU cc_start: 0.8399 (tp30) cc_final: 0.7967 (tp30)
REVERT: B  180 ASP cc_start: 0.8408 (t0) cc_final: 0.8021 (t0)
REVERT: B  213 SER cc_start: 0.8694 (t) cc_final: 0.7950 (p)
REVERT: B  257 GLU cc_start: 0.8559 (tp30) cc_final: 0.8288 (tp30)
REVERT: B  345 GLN cc_start: 0.7734 (tt0) cc_final: 0.7507 (tm-30)
REVERT: B  353 MET cc_start: 0.7905 (ttm) cc_final: 0.7284 (mtm)
REVERT: B  472 GLN cc_start: 0.8369 (tt0) cc_final: 0.8113 (tt0)
REVERT: B  613 LEU cc_start: 0.8907 (tp) cc_final: 0.8692 (tp)
REVERT: B  621 GLU cc_start: 0.8546 (tt0) cc_final: 0.7418 (tm-30)
  outliers start: 39
  outliers final: 25
  residues processed: 171
  average time/residue: 0.0846
  time to fit residues: 21.2404
Evaluate side-chains
  162 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.161649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.119488 restraints weight = 10963.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.21
r_work: 0.3204 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9274  Z= 0.156
  Angle     :  0.675  15.056  12628  Z= 0.329
  Chirality :  0.043   0.208   1520
  Planarity :  0.004   0.060   1617
  Dihedral  :  6.660 117.582   1319
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 16.51 %
    Favored  : 78.58 %
  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: -1.85 (0.24), residues: 1189
  helix: -0.73 (0.19), residues: 759
  sheet: -2.02 (0.61), residues: 64
  loop : -1.87 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 488 
 TYR   0.011   0.001   TYR A   9 
 PHE   0.016   0.001   PHE A 453 
 TRP   0.009   0.001   TRP B 229 
 HIS   0.008   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9274)
  covalent geometry    : angle       0.67494 (12628)
  hydrogen bonds       : bond        0.03494 (  449)
  hydrogen bonds       : angle       4.21428 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7583 (tp40)
REVERT: A  136 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7940 (mp)
REVERT: A  183 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8696 (t80)
REVERT: A  195 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7105 (tpt170)
REVERT: A  217 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7696 (ptt180)
REVERT: A  300 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6394 (ttp80)
REVERT: A  326 ARG cc_start: 0.7549 (mmt-90) cc_final: 0.7148 (mmt-90)
REVERT: A  463 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6267 (ttp)
REVERT: A  535 GLU cc_start: 0.8404 (tp30) cc_final: 0.7999 (tp30)
REVERT: B  180 ASP cc_start: 0.8404 (t0) cc_final: 0.8000 (t0)
REVERT: B  472 GLN cc_start: 0.8344 (tt0) cc_final: 0.8091 (tt0)
REVERT: B  496 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: B  613 LEU cc_start: 0.8907 (tp) cc_final: 0.8706 (tp)
REVERT: B  621 GLU cc_start: 0.8559 (tt0) cc_final: 0.7454 (tm-30)
  outliers start: 47
  outliers final: 34
  residues processed: 173
  average time/residue: 0.0869
  time to fit residues: 21.7256
Evaluate side-chains
  172 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  463 MET
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.162270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120893 restraints weight = 11007.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.06
r_work: 0.3264 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9274  Z= 0.143
  Angle     :  0.665  14.904  12628  Z= 0.324
  Chirality :  0.043   0.188   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  6.419 109.376   1319
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 17.03 %
    Favored  : 77.74 %
  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: -1.67 (0.24), residues: 1189
  helix: -0.53 (0.19), residues: 755
  sheet: -1.91 (0.63), residues: 64
  loop : -1.91 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.014   0.001   TYR A   9 
 PHE   0.010   0.001   PHE A 453 
 TRP   0.008   0.001   TRP A  15 
 HIS   0.007   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9274)
  covalent geometry    : angle       0.66508 (12628)
  hydrogen bonds       : bond        0.03347 (  449)
  hydrogen bonds       : angle       4.11733 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7608 (tp40)
REVERT: A  136 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: A  183 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8707 (t80)
REVERT: A  195 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7127 (tpt170)
REVERT: A  217 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7592 (ptt-90)
REVERT: A  300 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6460 (ttp80)
REVERT: A  326 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7026 (mpt180)
REVERT: A  352 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7107 (tm-30)
REVERT: A  535 GLU cc_start: 0.8414 (tp30) cc_final: 0.8011 (tp30)
REVERT: B  180 ASP cc_start: 0.8353 (t0) cc_final: 0.7950 (t0)
REVERT: B  190 MET cc_start: 0.7954 (tmm) cc_final: 0.7752 (tmm)
REVERT: B  472 GLN cc_start: 0.8331 (tt0) cc_final: 0.8067 (tt0)
REVERT: B  496 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7548 (mm-30)
REVERT: B  605 GLU cc_start: 0.8205 (pm20) cc_final: 0.7577 (pm20)
REVERT: B  613 LEU cc_start: 0.8912 (tp) cc_final: 0.8712 (tp)
REVERT: B  621 GLU cc_start: 0.8578 (tt0) cc_final: 0.7488 (tm-30)
  outliers start: 50
  outliers final: 31
  residues processed: 172
  average time/residue: 0.0893
  time to fit residues: 21.9178
Evaluate side-chains
  164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.163057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.118433 restraints weight = 11013.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.37
r_work: 0.3212 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9274  Z= 0.133
  Angle     :  0.666  15.939  12628  Z= 0.320
  Chirality :  0.042   0.184   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  6.167 100.300   1319
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.66 %
    Favored  : 77.74 %
  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: -1.51 (0.25), residues: 1189
  helix: -0.39 (0.19), residues: 755
  sheet: -2.00 (0.61), residues: 63
  loop : -1.89 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 488 
 TYR   0.012   0.001   TYR A   9 
 PHE   0.010   0.001   PHE A 453 
 TRP   0.007   0.001   TRP A  15 
 HIS   0.007   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9274)
  covalent geometry    : angle       0.66648 (12628)
  hydrogen bonds       : bond        0.03232 (  449)
  hydrogen bonds       : angle       4.06120 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 137
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7560 (tp40)
REVERT: A  136 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7867 (mp)
REVERT: A  183 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8651 (t80)
REVERT: A  195 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7012 (tpt170)
REVERT: A  217 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7547 (ptt-90)
REVERT: A  300 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6279 (ttp80)
REVERT: A  326 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.6944 (mpt180)
REVERT: A  352 GLN cc_start: 0.7294 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: A  535 GLU cc_start: 0.8428 (tp30) cc_final: 0.8016 (tp30)
REVERT: B  180 ASP cc_start: 0.8307 (t0) cc_final: 0.7870 (t0)
REVERT: B  257 GLU cc_start: 0.8591 (tp30) cc_final: 0.8345 (tp30)
REVERT: B  281 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7659 (mt-10)
REVERT: B  496 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: B  605 GLU cc_start: 0.8209 (pm20) cc_final: 0.7610 (pm20)
REVERT: B  621 GLU cc_start: 0.8596 (tt0) cc_final: 0.7493 (tm-30)
  outliers start: 44
  outliers final: 32
  residues processed: 169
  average time/residue: 0.0888
  time to fit residues: 21.7290
Evaluate side-chains
  164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.163427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.118981 restraints weight = 10925.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.31
r_work: 0.3227 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9274  Z= 0.125
  Angle     :  0.658  15.233  12628  Z= 0.315
  Chirality :  0.042   0.172   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  5.929  90.157   1319
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.39 %
    Favored  : 76.91 %
  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: -1.41 (0.25), residues: 1189
  helix: -0.31 (0.19), residues: 759
  sheet: -1.89 (0.62), residues: 63
  loop : -1.85 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.012   0.001   TYR A   9 
 PHE   0.009   0.001   PHE A 453 
 TRP   0.008   0.001   TRP A  15 
 HIS   0.006   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9274)
  covalent geometry    : angle       0.65843 (12628)
  hydrogen bonds       : bond        0.03155 (  449)
  hydrogen bonds       : angle       3.98503 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7488 (tp40)
REVERT: A   43 ASP cc_start: 0.8184 (t0) cc_final: 0.7871 (m-30)
REVERT: A  183 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8642 (t80)
REVERT: A  195 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7000 (tpt170)
REVERT: A  217 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7527 (ptt-90)
REVERT: A  253 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7542 (m)
REVERT: A  300 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6314 (ttp80)
REVERT: A  326 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7251 (mmt90)
REVERT: A  352 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6960 (tm-30)
REVERT: B   31 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6271 (mm-40)
REVERT: B  180 ASP cc_start: 0.8314 (t0) cc_final: 0.7870 (t0)
REVERT: B  257 GLU cc_start: 0.8627 (tp30) cc_final: 0.8405 (tp30)
REVERT: B  281 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7647 (mt-10)
REVERT: B  496 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: B  605 GLU cc_start: 0.8213 (pm20) cc_final: 0.7612 (pm20)
REVERT: B  621 GLU cc_start: 0.8598 (tt0) cc_final: 0.7523 (tm-30)
  outliers start: 45
  outliers final: 30
  residues processed: 177
  average time/residue: 0.0879
  time to fit residues: 22.6612
Evaluate side-chains
  171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0970
   chunk 106 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN
B 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.164497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120444 restraints weight = 10812.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.30
r_work: 0.3245 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9274  Z= 0.118
  Angle     :  0.668  17.599  12628  Z= 0.316
  Chirality :  0.042   0.171   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  5.762  81.698   1319
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.44 %
    Favored  : 76.18 %
  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: -1.28 (0.25), residues: 1189
  helix: -0.22 (0.19), residues: 759
  sheet: -1.77 (0.63), residues: 63
  loop : -1.81 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.011   0.001   TYR A   9 
 PHE   0.011   0.001   PHE A 453 
 TRP   0.006   0.001   TRP A  15 
 HIS   0.006   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9274)
  covalent geometry    : angle       0.66792 (12628)
  hydrogen bonds       : bond        0.03059 (  449)
  hydrogen bonds       : angle       3.95150 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7518 (tp40)
REVERT: A   43 ASP cc_start: 0.8152 (t0) cc_final: 0.7906 (m-30)
REVERT: A  183 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8650 (t80)
REVERT: A  217 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7585 (ptt-90)
REVERT: A  253 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7575 (m)
REVERT: A  300 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6409 (ttp80)
REVERT: A  326 ARG cc_start: 0.7439 (mmt-90) cc_final: 0.7200 (mmt90)
REVERT: A  352 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  568 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8574 (mm-30)
REVERT: B  180 ASP cc_start: 0.8336 (t0) cc_final: 0.7880 (t0)
REVERT: B  257 GLU cc_start: 0.8634 (tp30) cc_final: 0.8382 (tp30)
REVERT: B  496 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: B  605 GLU cc_start: 0.8216 (pm20) cc_final: 0.7598 (pm20)
REVERT: B  621 GLU cc_start: 0.8611 (tt0) cc_final: 0.7538 (tm-30)
  outliers start: 42
  outliers final: 33
  residues processed: 168
  average time/residue: 0.0881
  time to fit residues: 21.7672
Evaluate side-chains
  173 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117711 restraints weight = 11012.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.01
r_work: 0.3167 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9274  Z= 0.181
  Angle     :  0.723  17.299  12628  Z= 0.343
  Chirality :  0.044   0.195   1520
  Planarity :  0.004   0.060   1617
  Dihedral  :  5.852  76.283   1319
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.91 %
    Favored  : 76.28 %
  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: -1.46 (0.24), residues: 1189
  helix: -0.40 (0.19), residues: 760
  sheet: -1.82 (0.62), residues: 63
  loop : -1.77 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 307 
 TYR   0.013   0.001   TYR A   9 
 PHE   0.012   0.001   PHE B 295 
 TRP   0.007   0.001   TRP B 229 
 HIS   0.006   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 9274)
  covalent geometry    : angle       0.72314 (12628)
  hydrogen bonds       : bond        0.03540 (  449)
  hydrogen bonds       : angle       4.13283 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 135
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7454 (tp40)
REVERT: A   43 ASP cc_start: 0.8230 (t0) cc_final: 0.7902 (m-30)
REVERT: A  183 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8720 (t80)
REVERT: A  195 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7032 (tpt170)
REVERT: A  217 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7550 (ptt180)
REVERT: A  300 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6450 (ttp80)
REVERT: A  326 ARG cc_start: 0.7469 (mmt-90) cc_final: 0.7126 (mmt-90)
REVERT: A  352 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6952 (tm-30)
REVERT: B   18 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7255 (mptt)
REVERT: B  106 GLN cc_start: 0.8090 (mt0) cc_final: 0.7859 (mt0)
REVERT: B  281 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: B  496 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: B  605 GLU cc_start: 0.8246 (pm20) cc_final: 0.7597 (pm20)
REVERT: B  621 GLU cc_start: 0.8622 (tt0) cc_final: 0.7532 (tm-30)
  outliers start: 46
  outliers final: 37
  residues processed: 168
  average time/residue: 0.0838
  time to fit residues: 20.5965
Evaluate side-chains
  170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.162763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120968 restraints weight = 11028.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.32
r_work: 0.3202 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9274  Z= 0.133
  Angle     :  0.692  17.137  12628  Z= 0.328
  Chirality :  0.043   0.172   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  5.633  62.936   1319
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 20.06 %
    Favored  : 75.76 %
  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: -1.32 (0.25), residues: 1189
  helix: -0.28 (0.19), residues: 760
  sheet: -1.71 (0.63), residues: 63
  loop : -1.76 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.012   0.001   TYR A   9 
 PHE   0.022   0.001   PHE A 293 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.006   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9274)
  covalent geometry    : angle       0.69162 (12628)
  hydrogen bonds       : bond        0.03222 (  449)
  hydrogen bonds       : angle       4.00482 ( 1326)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7429 (tp40)
REVERT: A   43 ASP cc_start: 0.8186 (t0) cc_final: 0.7886 (m-30)
REVERT: A  183 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8695 (t80)
REVERT: A  195 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7015 (tpt170)
REVERT: A  217 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7589 (ptt-90)
REVERT: A  253 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7529 (m)
REVERT: A  300 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6349 (ttp80)
REVERT: A  326 ARG cc_start: 0.7404 (mmt-90) cc_final: 0.7045 (mmt-90)
REVERT: A  352 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: A  568 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8544 (mm-30)
REVERT: B   18 LYS cc_start: 0.7570 (mmtt) cc_final: 0.7267 (mptt)
REVERT: B   31 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6021 (mm-40)
REVERT: B  106 GLN cc_start: 0.8010 (mt0) cc_final: 0.7795 (mt0)
REVERT: B  180 ASP cc_start: 0.8388 (t0) cc_final: 0.7900 (t0)
REVERT: B  257 GLU cc_start: 0.8526 (tp30) cc_final: 0.8291 (tp30)
REVERT: B  281 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7956 (mt-10)
REVERT: B  415 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7033 (tm-30)
REVERT: B  496 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7512 (mm-30)
REVERT: B  605 GLU cc_start: 0.8239 (pm20) cc_final: 0.7627 (pm20)
REVERT: B  621 GLU cc_start: 0.8656 (tt0) cc_final: 0.7586 (tm-30)
  outliers start: 40
  outliers final: 33
  residues processed: 171
  average time/residue: 0.0833
  time to fit residues: 21.0469
Evaluate side-chains
  177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   41 ILE
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  169 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  434 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  558 VAL
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  578 THR
Chi-restraints excluded: chain B residue  604 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.164030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119429 restraints weight = 10847.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.36
r_work: 0.3219 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9274  Z= 0.128
  Angle     :  0.691  17.008  12628  Z= 0.326
  Chirality :  0.042   0.172   1520
  Planarity :  0.004   0.059   1617
  Dihedral  :  5.539  55.357   1319
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.96 %
    Favored  : 75.76 %
  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: -1.26 (0.25), residues: 1189
  helix: -0.22 (0.19), residues: 759
  sheet: -1.63 (0.64), residues: 63
  loop : -1.80 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  32 
 TYR   0.012   0.001   TYR A   9 
 PHE   0.013   0.001   PHE B  93 
 TRP   0.009   0.001   TRP A  15 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9274)
  covalent geometry    : angle       0.69142 (12628)
  hydrogen bonds       : bond        0.03184 (  449)
  hydrogen bonds       : angle       4.00555 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2478.51 seconds
wall clock time: 43 minutes 6.10 seconds (2586.10 seconds total)