Starting phenix.real_space_refine
on Sat Oct 11 08:29:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j5s_35992/10_2025/8j5s_35992.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.070
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: 7
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    8402      2.51       5
     N    2368      2.21       5
     O    2452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13275
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4003
          Classifications: {'peptide': 527}
          Link IDs: {'PTRANS': 28, 'TRANS': 498}
    Chain: "B"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2475
          Classifications: {'peptide': 325}
          Link IDs: {'PTRANS': 11, 'TRANS': 313}
    Chain: "C"
      Number of atoms: 2130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2130
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 13, 'TRANS': 268}
    Chain: "D"
      Number of atoms: 4555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 608, 4555
          Classifications: {'peptide': 608}
          Link IDs: {'PTRANS': 35, 'TRANS': 572}
    Chain: "E"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 40
          Classifications: {'peptide': 8}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'UNK:plan-1': 8}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 72
          Unusual residues: {' MG': 2, 'ANP': 2, 'SF4': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10814  SG  CYS D 299      20.668  26.978  21.695  1.00 42.55           S
  ATOM  10947  SG  CYS D 317      26.841  25.253  20.106  1.00 37.75           S
  ATOM  10714  SG  CYS D 286      25.527  27.181  26.537  1.00 34.10           S
  ATOM  10761  SG  CYS D 292      25.576  31.656  21.276  1.00 32.40           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLU A 510 " occ=0.94
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 510 " occ=0.94
  Time building chain proxies: 3.24, per 1000 atoms: 0.24
  Number of scatterers: 13275
  At special positions: 0
  Unit cell: (86.528, 95.68, 168.064, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     S      41     16.00
     P       6     15.00
     Mg      2     11.99
     O    2452      8.00
     N    2368      7.00
     C    8402      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 619.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 D 705 "
        pdb="FE4  SF4 D 705 " - pdb=" SG  CYS D 292 "
        pdb="FE3  SF4 D 705 " - pdb=" SG  CYS D 286 "
        pdb="FE1  SF4 D 705 " - pdb=" SG  CYS D 299 "
        pdb="FE2  SF4 D 705 " - pdb=" SG  CYS D 317 "
      Number of angles added : 12


  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3190

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 12 sheets defined
      50.1% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 111 through 119
      removed outlier: 5.243A  pdb=" N   MET A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 182
      removed outlier: 3.593A  pdb=" N   ILE A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLN A 178 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 3.884A  pdb=" N   GLY A 225 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   MET A 226 " --> pdb=" O   TRP A 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 226'
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 296 through 299
      removed outlier: 3.523A  pdb=" N   ALA A 299 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 296 through 299'
    Processing helix  chain 'A' and resid 300 through 306
    Processing helix  chain 'A' and resid 316 through 325
      removed outlier: 3.837A  pdb=" N   ALA A 323 " --> pdb=" O   GLN A 319 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 363
      removed outlier: 3.749A  pdb=" N   LYS A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 375
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.633A  pdb=" N   ALA A 405 " --> pdb=" O   GLY A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 417
    Processing helix  chain 'A' and resid 445 through 459
      removed outlier: 3.980A  pdb=" N   PHE A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLN A 459 " --> pdb=" O   HIS A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 499 through 505
      removed outlier: 3.967A  pdb=" N   GLN A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 530
    Processing helix  chain 'A' and resid 533 through 550
      removed outlier: 3.577A  pdb=" N   ALA A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 30
      removed outlier: 3.956A  pdb=" N   ASN B  11 " --> pdb=" O   ARG B   7 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B  14 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 45 through 55
    Processing helix  chain 'B' and resid 61 through 74
      removed outlier: 3.781A  pdb=" N   ASN B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   HIS B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 123
      removed outlier: 3.925A  pdb=" N   GLY B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ARG B  93 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLY B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL B  97 " --> pdb=" O   ARG B  93 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 101 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 141
      removed outlier: 3.777A  pdb=" N   MET B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 163
      removed outlier: 4.829A  pdb=" N   ARG B 157 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL B 158 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 221
      removed outlier: 3.768A  pdb=" N   ARG B 188 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU B 194 " --> pdb=" O   GLN B 190 " (cutoff:3.500A)
      Proline residue:  B 195  - end of helix
      removed outlier: 3.626A  pdb=" N   ALA B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ARG B 209 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   TYR B 210 " --> pdb=" O   GLY B 206 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN B 213 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 229
      removed outlier: 3.888A  pdb=" N   THR B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 241
      removed outlier: 3.653A  pdb=" N   LEU B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 248 through 252
    Processing helix  chain 'B' and resid 253 through 273
      removed outlier: 3.776A  pdb=" N   VAL B 266 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 287
    Processing helix  chain 'B' and resid 289 through 319
      removed outlier: 3.576A  pdb=" N   VAL B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL B 298 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 17
      removed outlier: 4.186A  pdb=" N   ARG C  13 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG C  14 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 38
      removed outlier: 4.062A  pdb=" N   TYR C  36 " --> pdb=" O   PHE C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 42
    Processing helix  chain 'C' and resid 72 through 110
      removed outlier: 3.532A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE C 105 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 125
      removed outlier: 3.591A  pdb=" N   ASP C 114 " --> pdb=" O   GLY C 110 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL C 121 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 137
      removed outlier: 3.714A  pdb=" N   VAL C 136 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 155
    Processing helix  chain 'C' and resid 158 through 174
      removed outlier: 3.738A  pdb=" N   SER C 171 " --> pdb=" O   GLY C 167 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU C 174 " --> pdb=" O   MET C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 202 through 225
      removed outlier: 3.994A  pdb=" N   ALA C 209 " --> pdb=" O   ILE C 205 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LEU C 210 " --> pdb=" O   ILE C 206 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   VAL C 212 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ALA C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU C 225 " --> pdb=" O   GLY C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 244
    Processing helix  chain 'C' and resid 245 through 247
      No H-bonds generated for 'chain 'C' and resid 245 through 247'
    Processing helix  chain 'C' and resid 251 through 280
      removed outlier: 3.808A  pdb=" N   PHE C 256 " --> pdb=" O   TRP C 252 " (cutoff:3.500A)
      Proline residue:  C 257  - end of helix
    Processing helix  chain 'D' and resid 47 through 52
    Processing helix  chain 'D' and resid 82 through 87
    Processing helix  chain 'D' and resid 108 through 120
      removed outlier: 3.685A  pdb=" N   GLU D 114 " --> pdb=" O   ASP D 110 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE D 116 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   HIS D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 140
      removed outlier: 3.709A  pdb=" N   ASP D 137 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU D 138 " --> pdb=" O   GLU D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 148
    Processing helix  chain 'D' and resid 149 through 150
      No H-bonds generated for 'chain 'D' and resid 149 through 150'
    Processing helix  chain 'D' and resid 151 through 155
    Processing helix  chain 'D' and resid 159 through 170
      removed outlier: 3.685A  pdb=" N   VAL D 164 " --> pdb=" O   ARG D 160 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE D 165 " --> pdb=" O   GLN D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 204
    Processing helix  chain 'D' and resid 214 through 222
      removed outlier: 4.102A  pdb=" N   VAL D 218 " --> pdb=" O   ASP D 214 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA D 219 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU D 220 " --> pdb=" O   GLY D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 243
    Processing helix  chain 'D' and resid 248 through 256
    Processing helix  chain 'D' and resid 327 through 332
    Processing helix  chain 'D' and resid 399 through 409
    Processing helix  chain 'D' and resid 419 through 423
    Processing helix  chain 'D' and resid 429 through 436
      removed outlier: 3.739A  pdb=" N   SER D 435 " --> pdb=" O   ALA D 431 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU D 436 " --> pdb=" O   GLU D 432 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 446 through 451
      removed outlier: 3.672A  pdb=" N   SER D 450 " --> pdb=" O   ASP D 446 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU D 451 " --> pdb=" O   PRO D 447 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 446 through 451'
    Processing helix  chain 'D' and resid 456 through 462
    Processing helix  chain 'D' and resid 462 through 467
    Processing helix  chain 'D' and resid 472 through 486
      removed outlier: 3.848A  pdb=" N   ALA D 477 " --> pdb=" O   ASN D 473 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL D 486 " --> pdb=" O   LEU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 495
    Processing helix  chain 'D' and resid 496 through 500
    Processing helix  chain 'D' and resid 501 through 514
      removed outlier: 3.626A  pdb=" N   ARG D 507 " --> pdb=" O   GLY D 503 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE D 508 " --> pdb=" O   GLN D 504 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY D 509 " --> pdb=" O   LYS D 505 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 531 through 550
      removed outlier: 3.591A  pdb=" N   ALA D 536 " --> pdb=" O   VAL D 532 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 559 through 567
      removed outlier: 4.222A  pdb=" N   VAL D 563 " --> pdb=" O   ASP D 559 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS D 565 " --> pdb=" O   SER D 561 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 593 through 602
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95
      removed outlier: 6.524A  pdb=" N   ARG A 271 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LEU A 265 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL A 273 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 146
      removed outlier: 3.759A  pdb=" N   SER A 143 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU A 145 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER A 202 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313
    Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 469
      removed outlier: 4.578A  pdb=" N   TYR A 441 " --> pdb=" O   GLN A 488 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   GLY A 490 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A 489 " --> pdb=" O   HIS A 341 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER A 338 " --> pdb=" O   GLN A 559 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   GLN A 559 " --> pdb=" O   SER A 338 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   TYR A 340 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 469
      removed outlier: 4.578A  pdb=" N   TYR A 441 " --> pdb=" O   GLN A 488 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   GLY A 490 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 428 through 429
    Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571
      removed outlier: 3.609A  pdb=" N   GLY A 587 " --> pdb=" O   ALA A 571 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 29
      removed outlier: 6.826A  pdb=" N   ALA D  23 " --> pdb=" O   PHE D  14 " (cutoff:3.500A)
      removed outlier: 8.474A  pdb=" N   PHE D  14 " --> pdb=" O   ALA D  23 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ARG D  25 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D  25 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR D  29 " --> pdb=" O   THR D   8 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   THR D   8 " --> pdb=" O   TYR D  29 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 94
      removed outlier: 6.062A  pdb=" N   GLY D  92 " --> pdb=" O   ILE D 177 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASP D 179 " --> pdb=" O   GLY D  92 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL D  94 " --> pdb=" O   ASP D 179 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   LEU D 176 " --> pdb=" O   LEU D 209 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   ILE D 211 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   CYS D 178 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL D  36 " --> pdb=" O   ARG D 224 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   LEU D 226 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ALA D  38 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   MET D 228 " --> pdb=" O   ALA D  38 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL D  40 " --> pdb=" O   MET D 228 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA D 225 " --> pdb=" O   SER D 236 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   SER D 236 " --> pdb=" O   ALA D 225 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL D 227 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   HIS D 313 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU D 307 " --> pdb=" O   ALA D 315 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 355 through 359
      removed outlier: 4.712A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 379 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS D 357 " --> pdb=" O   VAL D 377 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   TYR D 359 " --> pdb=" O   ARG D 375 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   ARG D 375 " --> pdb=" O   TYR D 359 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 440 through 443
      removed outlier: 6.464A  pdb=" N   THR D 389 " --> pdb=" O   GLN D 569 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   ALA D 571 " --> pdb=" O   THR D 389 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLY D 391 " --> pdb=" O   ALA D 571 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   MET D 573 " --> pdb=" O   GLY D 391 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   VAL D 393 " --> pdb=" O   MET D 573 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL D 570 " --> pdb=" O   GLN D 581 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   GLN D 581 " --> pdb=" O   VAL D 570 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL D 572 " --> pdb=" O   VAL D 579 " (cutoff:3.500A)

    593 hydrogen bonds defined for protein.
    1716 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.19 -     1.41: 5394
        1.41 -     1.63: 8051
        1.63 -     1.85: 70
        1.85 -     2.07: 0
        2.07 -     2.29: 12
  Bond restraints: 13527
  Sorted by residual:
  bond pdb=" N3B ANP D 703 "
       pdb=" PG  ANP D 703 "
    ideal  model  delta    sigma   weight residual
    1.795  1.633  0.162 2.00e-02 2.50e+03 6.55e+01
  bond pdb=" N3B ANP D 701 "
       pdb=" PG  ANP D 701 "
    ideal  model  delta    sigma   weight residual
    1.795  1.633  0.162 2.00e-02 2.50e+03 6.55e+01
  bond pdb=" O3A ANP D 701 "
       pdb=" PB  ANP D 701 "
    ideal  model  delta    sigma   weight residual
    1.700  1.602  0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" O3A ANP D 703 "
       pdb=" PB  ANP D 703 "
    ideal  model  delta    sigma   weight residual
    1.700  1.602  0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" C   HIS D 476 "
       pdb=" O   HIS D 476 "
    ideal  model  delta    sigma   weight residual
    1.236  1.295 -0.058 1.25e-02 6.40e+03 2.19e+01
  ... (remaining 13522 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 17818
        2.08 -     4.15: 526
        4.15 -     6.23: 68
        6.23 -     8.30: 22
        8.30 -    10.38: 7
  Bond angle restraints: 18441
  Sorted by residual:
  angle pdb=" N   ARG D  85 "
        pdb=" CA  ARG D  85 "
        pdb=" C   ARG D  85 "
      ideal   model   delta    sigma   weight residual
     114.62  106.39    8.23 1.14e+00 7.69e-01 5.21e+01
  angle pdb=" N   VAL D 479 "
        pdb=" CA  VAL D 479 "
        pdb=" C   VAL D 479 "
      ideal   model   delta    sigma   weight residual
     111.05  104.26    6.79 1.25e+00 6.40e-01 2.95e+01
  angle pdb=" N   ARG B  40 "
        pdb=" CA  ARG B  40 "
        pdb=" C   ARG B  40 "
      ideal   model   delta    sigma   weight residual
     109.59  101.43    8.16 1.61e+00 3.86e-01 2.57e+01
  angle pdb=" C   MET A 589 "
        pdb=" N   ARG A 590 "
        pdb=" CA  ARG A 590 "
      ideal   model   delta    sigma   weight residual
     122.41  115.60    6.81 1.41e+00 5.03e-01 2.34e+01
  angle pdb=" CA  TRP A 281 "
        pdb=" CB  TRP A 281 "
        pdb=" CG  TRP A 281 "
      ideal   model   delta    sigma   weight residual
     113.60  122.37   -8.77 1.90e+00 2.77e-01 2.13e+01
  ... (remaining 18436 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 7080
       17.97 -    35.95: 801
       35.95 -    53.92: 178
       53.92 -    71.90: 36
       71.90 -    89.87: 18
  Dihedral angle restraints: 8113
    sinusoidal: 3140
      harmonic: 4973
  Sorted by residual:
  dihedral pdb=" CA  ARG B 123 "
           pdb=" C   ARG B 123 "
           pdb=" N   GLN B 124 "
           pdb=" CA  GLN B 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.17  -22.83     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ALA A 150 "
           pdb=" C   ALA A 150 "
           pdb=" N   PRO A 151 "
           pdb=" CA  PRO A 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.44   22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ILE A 322 "
           pdb=" C   ILE A 322 "
           pdb=" N   ALA A 323 "
           pdb=" CA  ALA A 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 8110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1768
       0.067 -    0.134: 372
       0.134 -    0.201: 29
       0.201 -    0.268: 4
       0.268 -    0.335: 2
  Chirality restraints: 2175
  Sorted by residual:
  chirality pdb=" C3' ANP D 703 "
            pdb=" C2' ANP D 703 "
            pdb=" C4' ANP D 703 "
            pdb=" O3' ANP D 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" C3' ANP D 701 "
            pdb=" C2' ANP D 701 "
            pdb=" C4' ANP D 701 "
            pdb=" O3' ANP D 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  CYS D 292 "
            pdb=" N   CYS D 292 "
            pdb=" C   CYS D 292 "
            pdb=" CB  CYS D 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 2172 not shown)

  Planarity restraints: 2379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  43 "   -0.585 9.50e-02 1.11e+02   2.62e-01 4.20e+01
        pdb=" NE  ARG B  43 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  43 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  43 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  43 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  40 "   -0.347 9.50e-02 1.11e+02   1.56e-01 1.48e+01
        pdb=" NE  ARG B  40 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  40 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  40 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  40 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "    0.024 2.00e-02 2.50e+03   1.75e-02 7.64e+00
        pdb=" CG  TRP A 281 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2376 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1603
        2.74 -     3.28: 13093
        3.28 -     3.82: 21405
        3.82 -     4.36: 26803
        4.36 -     4.90: 45953
  Nonbonded interactions: 108857
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 423 "
            pdb=" OE1 GLU A 428 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD1 ASP A 416 "
            pdb=" NH2 ARG A 427 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG1 THR A 147 "
            pdb=" O   VAL A 153 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH1 ARG D 375 "
            pdb=" OD1 ASP D 378 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OD1 ASP A 208 "
            pdb=" OD1 ASP A 209 "
     model   vdw
     2.232 3.040
  ... (remaining 108852 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=0.94 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:             2.100
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.070
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
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      :  0.010   0.313  13531  Z= 0.438
  Angle     :  0.874  12.504  18453  Z= 0.491
  Chirality :  0.054   0.335   2175
  Planarity :  0.008   0.262   2379
  Dihedral  : 16.458  89.871   4923
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.80 %
    Favored  : 98.83 %
  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: -2.34 (0.19), residues: 1734
  helix: -0.61 (0.18), residues: 816
  sheet: -2.16 (0.40), residues: 148
  loop : -2.45 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 173 
 TYR   0.017   0.002   TYR A 340 
 PHE   0.028   0.002   PHE C 224 
 TRP   0.048   0.002   TRP A 281 
 HIS   0.010   0.002   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00880 (13527)
  covalent geometry    : angle       0.85183 (18441)
  hydrogen bonds       : bond        0.17159 (  584)
  hydrogen bonds       : angle       6.91426 ( 1716)
  metal coordination   : bond        0.23931 (    4)
  metal coordination   : angle       7.65712 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.531 
Fit side-chains
REVERT: C  273 ASP cc_start: 0.7986 (m-30) cc_final: 0.7786 (m-30)
REVERT: C  280 ASP cc_start: 0.7127 (m-30) cc_final: 0.6893 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 175
  average time/residue: 0.6504
  time to fit residues: 123.7407
Evaluate side-chains
  140 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain B residue   40 ARG
Chi-restraints excluded: chain B residue   43 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.2980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 467 GLN
B 275 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.116147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.099697 restraints weight = 19464.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.98
r_work: 0.3071 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13531  Z= 0.132
  Angle     :  0.640  12.225  18453  Z= 0.322
  Chirality :  0.044   0.155   2175
  Planarity :  0.005   0.064   2379
  Dihedral  :  8.006  54.943   1989
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.14 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.72 (0.19), residues: 1734
  helix: -0.05 (0.19), residues: 804
  sheet: -1.94 (0.40), residues: 151
  loop : -2.16 (0.20), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  68 
 TYR   0.017   0.001   TYR A 340 
 PHE   0.012   0.001   PHE C 256 
 TRP   0.012   0.001   TRP A 172 
 HIS   0.006   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (13527)
  covalent geometry    : angle       0.62473 (18441)
  hydrogen bonds       : bond        0.04406 (  584)
  hydrogen bonds       : angle       5.22262 ( 1716)
  metal coordination   : bond        0.01382 (    4)
  metal coordination   : angle       5.55010 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A  238 MET cc_start: 0.8459 (mmm) cc_final: 0.8196 (mmm)
REVERT: A  293 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8256 (pt)
REVERT: A  589 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5481 (pmm)
REVERT: B   40 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7914 (mpt-90)
REVERT: B  279 GLU cc_start: 0.8538 (tt0) cc_final: 0.8293 (tt0)
REVERT: C   46 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5616 (t80)
REVERT: C  280 ASP cc_start: 0.7136 (m-30) cc_final: 0.6834 (m-30)
REVERT: D  161 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.8345 (tp40)
  outliers start: 28
  outliers final: 5
  residues processed: 163
  average time/residue: 0.6044
  time to fit residues: 107.8153
Evaluate side-chains
  145 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   40 ARG
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  161 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 163 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 158 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 166 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.114638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.098006 restraints weight = 19811.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.02
r_work: 0.3046 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  13531  Z= 0.149
  Angle     :  0.609   8.347  18453  Z= 0.309
  Chirality :  0.043   0.159   2175
  Planarity :  0.005   0.064   2379
  Dihedral  :  6.504  54.283   1983
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.64 %
    Favored  : 82.52 %
  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: -1.55 (0.20), residues: 1734
  helix:  0.11 (0.19), residues: 803
  sheet: -2.16 (0.38), residues: 165
  loop : -1.99 (0.20), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG D 319 
 TYR   0.014   0.001   TYR A 340 
 PHE   0.010   0.001   PHE A 449 
 TRP   0.018   0.001   TRP A 172 
 HIS   0.006   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13527)
  covalent geometry    : angle       0.60225 (18441)
  hydrogen bonds       : bond        0.04221 (  584)
  hydrogen bonds       : angle       4.88523 ( 1716)
  metal coordination   : bond        0.00376 (    4)
  metal coordination   : angle       3.50488 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A  238 MET cc_start: 0.8504 (mmm) cc_final: 0.8200 (mmm)
REVERT: A  293 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8149 (pt)
REVERT: A  589 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6056 (pmm)
REVERT: B  283 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8283 (tmt-80)
REVERT: C   46 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5518 (t80)
REVERT: C  280 ASP cc_start: 0.7111 (m-30) cc_final: 0.6475 (t0)
REVERT: D  161 GLN cc_start: 0.9479 (OUTLIER) cc_final: 0.8331 (tp40)
REVERT: D  483 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8194 (pt)
REVERT: D  551 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8603 (mp)
  outliers start: 39
  outliers final: 13
  residues processed: 173
  average time/residue: 0.5846
  time to fit residues: 110.7403
Evaluate side-chains
  153 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  551 LEU
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 146 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0370
   chunk 88 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 167 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 150 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.100341 restraints weight = 19798.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.66
r_work: 0.3075 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13531  Z= 0.114
  Angle     :  0.586  13.743  18453  Z= 0.293
  Chirality :  0.042   0.164   2175
  Planarity :  0.004   0.063   2379
  Dihedral  :  5.487  54.555   1979
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.61 %
    Favored  : 80.48 %
  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: -1.31 (0.20), residues: 1734
  helix:  0.28 (0.19), residues: 804
  sheet: -1.99 (0.39), residues: 163
  loop : -1.84 (0.21), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 283 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.009   0.001   PHE C 177 
 TRP   0.014   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (13527)
  covalent geometry    : angle       0.57842 (18441)
  hydrogen bonds       : bond        0.03638 (  584)
  hydrogen bonds       : angle       4.68295 ( 1716)
  metal coordination   : bond        0.00189 (    4)
  metal coordination   : angle       3.61854 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  238 MET cc_start: 0.8555 (mmm) cc_final: 0.8277 (mmm)
REVERT: A  293 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8317 (pt)
REVERT: B  138 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8798 (pp)
REVERT: C   46 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5571 (t80)
REVERT: C  280 ASP cc_start: 0.7173 (m-30) cc_final: 0.6603 (t0)
REVERT: D  161 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8250 (tp40)
REVERT: D  483 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8435 (pt)
  outliers start: 40
  outliers final: 17
  residues processed: 175
  average time/residue: 0.5728
  time to fit residues: 110.1975
Evaluate side-chains
  152 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 170 optimal weight:    6.9990
   chunk 171 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 136 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.115745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.098967 restraints weight = 19735.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.04
r_work: 0.3064 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13531  Z= 0.119
  Angle     :  0.573  11.014  18453  Z= 0.288
  Chirality :  0.042   0.163   2175
  Planarity :  0.004   0.063   2379
  Dihedral  :  5.165  56.899   1979
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.92 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.20), residues: 1734
  helix:  0.34 (0.19), residues: 813
  sheet: -1.96 (0.39), residues: 165
  loop : -1.74 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.010   0.001   PHE B 145 
 TRP   0.016   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (13527)
  covalent geometry    : angle       0.56569 (18441)
  hydrogen bonds       : bond        0.03619 (  584)
  hydrogen bonds       : angle       4.57938 ( 1716)
  metal coordination   : bond        0.00198 (    4)
  metal coordination   : angle       3.50375 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 134
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8076 (pt)
REVERT: B  138 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8722 (pp)
REVERT: C   46 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.5415 (t80)
REVERT: D  161 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8316 (tp40)
REVERT: D  483 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8299 (pt)
  outliers start: 41
  outliers final: 20
  residues processed: 167
  average time/residue: 0.5139
  time to fit residues: 94.8657
Evaluate side-chains
  151 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 156 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 139 optimal weight:    0.0970
   chunk 100 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
C  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.100016 restraints weight = 19478.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.96
r_work: 0.3079 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13531  Z= 0.111
  Angle     :  0.564   9.481  18453  Z= 0.284
  Chirality :  0.042   0.158   2175
  Planarity :  0.004   0.063   2379
  Dihedral  :  5.030  57.115   1979
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.43 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.20), residues: 1734
  helix:  0.52 (0.19), residues: 806
  sheet: -1.79 (0.40), residues: 161
  loop : -1.67 (0.21), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 325 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.009   0.001   PHE B 145 
 TRP   0.021   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (13527)
  covalent geometry    : angle       0.55651 (18441)
  hydrogen bonds       : bond        0.03456 (  584)
  hydrogen bonds       : angle       4.49230 ( 1716)
  metal coordination   : bond        0.00194 (    4)
  metal coordination   : angle       3.70771 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 136
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8071 (pt)
REVERT: B   35 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7431 (tp30)
REVERT: B  129 ASP cc_start: 0.7877 (t0) cc_final: 0.7558 (t0)
REVERT: B  138 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8685 (pp)
REVERT: C   46 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5382 (t80)
REVERT: D  161 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.8320 (tp40)
  outliers start: 45
  outliers final: 23
  residues processed: 170
  average time/residue: 0.5570
  time to fit residues: 104.1849
Evaluate side-chains
  158 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 127 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 116 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
C  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.110727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.094000 restraints weight = 19948.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.01
r_work: 0.2984 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  13531  Z= 0.259
  Angle     :  0.695  15.440  18453  Z= 0.347
  Chirality :  0.047   0.160   2175
  Planarity :  0.005   0.065   2379
  Dihedral  :  5.538  60.995   1979
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.45 %
    Favored  : 76.98 %
  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: -1.37 (0.20), residues: 1734
  helix:  0.23 (0.19), residues: 809
  sheet: -1.86 (0.39), residues: 163
  loop : -1.93 (0.20), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  68 
 TYR   0.015   0.002   TYR A 156 
 PHE   0.013   0.002   PHE B 145 
 TRP   0.031   0.002   TRP A 172 
 HIS   0.005   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 (13527)
  covalent geometry    : angle       0.68526 (18441)
  hydrogen bonds       : bond        0.04918 (  584)
  hydrogen bonds       : angle       4.77206 ( 1716)
  metal coordination   : bond        0.01071 (    4)
  metal coordination   : angle       4.61216 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (pt)
REVERT: A  296 ASP cc_start: 0.8487 (p0) cc_final: 0.7767 (p0)
REVERT: B   35 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7618 (tp30)
REVERT: B  129 ASP cc_start: 0.8107 (t0) cc_final: 0.7789 (t0)
REVERT: B  138 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (pp)
REVERT: C   46 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5580 (t80)
REVERT: C  168 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7660 (ttt)
REVERT: C  280 ASP cc_start: 0.7382 (m-30) cc_final: 0.6638 (t0)
REVERT: D   97 ASP cc_start: 0.8256 (t70) cc_final: 0.7688 (p0)
REVERT: D  133 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8197 (t)
REVERT: D  161 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.8455 (tp40)
  outliers start: 49
  outliers final: 27
  residues processed: 168
  average time/residue: 0.5157
  time to fit residues: 95.6779
Evaluate side-chains
  154 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   10 LEU
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 79 optimal weight:    0.5980
   chunk 114 optimal weight:    0.0970
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 167 optimal weight:    0.8980
   chunk 126 optimal weight:    4.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.115791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.099660 restraints weight = 19545.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.96
r_work: 0.3063 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13531  Z= 0.111
  Angle     :  0.590  14.618  18453  Z= 0.294
  Chirality :  0.042   0.183   2175
  Planarity :  0.004   0.063   2379
  Dihedral  :  5.198  57.761   1979
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.32 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.02 (0.20), residues: 1734
  helix:  0.50 (0.19), residues: 815
  sheet: -1.73 (0.40), residues: 161
  loop : -1.74 (0.21), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  68 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.010   0.001   PHE A 342 
 TRP   0.028   0.001   TRP A 172 
 HIS   0.003   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (13527)
  covalent geometry    : angle       0.58011 (18441)
  hydrogen bonds       : bond        0.03550 (  584)
  hydrogen bonds       : angle       4.54050 ( 1716)
  metal coordination   : bond        0.00217 (    4)
  metal coordination   : angle       4.17477 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8154 (pt)
REVERT: A  296 ASP cc_start: 0.8408 (p0) cc_final: 0.7675 (p0)
REVERT: B   35 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7503 (tp30)
REVERT: B  129 ASP cc_start: 0.7763 (t0) cc_final: 0.7550 (t0)
REVERT: C   46 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5519 (t80)
REVERT: C  280 ASP cc_start: 0.7136 (m-30) cc_final: 0.6427 (t0)
REVERT: D   97 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7664 (p0)
REVERT: D  161 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.8313 (tp40)
  outliers start: 39
  outliers final: 23
  residues processed: 161
  average time/residue: 0.5695
  time to fit residues: 100.8511
Evaluate side-chains
  154 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  161 GLN
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 144 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9980
   chunk 147 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
C  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.096855 restraints weight = 19881.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.03
r_work: 0.3028 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13531  Z= 0.160
  Angle     :  0.625  14.259  18453  Z= 0.312
  Chirality :  0.044   0.171   2175
  Planarity :  0.005   0.064   2379
  Dihedral  :  5.234  59.394   1979
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.98 %
    Favored  : 76.77 %
  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: -1.01 (0.20), residues: 1734
  helix:  0.52 (0.19), residues: 814
  sheet: -1.69 (0.40), residues: 161
  loop : -1.76 (0.21), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  68 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.011   0.001   PHE B 145 
 TRP   0.034   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (13527)
  covalent geometry    : angle       0.61521 (18441)
  hydrogen bonds       : bond        0.03980 (  584)
  hydrogen bonds       : angle       4.56954 ( 1716)
  metal coordination   : bond        0.00532 (    4)
  metal coordination   : angle       4.30414 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (pt)
REVERT: A  296 ASP cc_start: 0.8377 (p0) cc_final: 0.7673 (p0)
REVERT: B   35 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7511 (tp30)
REVERT: C   46 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5580 (t80)
REVERT: C  280 ASP cc_start: 0.7278 (m-30) cc_final: 0.6541 (t0)
REVERT: D   97 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7701 (p0)
  outliers start: 31
  outliers final: 24
  residues processed: 155
  average time/residue: 0.5430
  time to fit residues: 92.6405
Evaluate side-chains
  156 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
C  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.113062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.096298 restraints weight = 19759.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.02
r_work: 0.3024 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13531  Z= 0.172
  Angle     :  0.641  14.220  18453  Z= 0.320
  Chirality :  0.044   0.170   2175
  Planarity :  0.005   0.064   2379
  Dihedral  :  5.301  59.699   1979
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.56 %
    Favored  : 76.11 %
  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: -1.06 (0.20), residues: 1734
  helix:  0.49 (0.19), residues: 814
  sheet: -1.70 (0.40), residues: 161
  loop : -1.80 (0.21), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 325 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.011   0.001   PHE B 145 
 TRP   0.038   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (13527)
  covalent geometry    : angle       0.63061 (18441)
  hydrogen bonds       : bond        0.04111 (  584)
  hydrogen bonds       : angle       4.60285 ( 1716)
  metal coordination   : bond        0.00646 (    4)
  metal coordination   : angle       4.45766 (   12)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  293 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8292 (pt)
REVERT: A  296 ASP cc_start: 0.8395 (p0) cc_final: 0.7664 (p0)
REVERT: B   35 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (tp30)
REVERT: C   46 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5652 (t80)
REVERT: C  280 ASP cc_start: 0.7356 (m-30) cc_final: 0.6618 (t0)
REVERT: D   97 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7674 (p0)
  outliers start: 32
  outliers final: 26
  residues processed: 153
  average time/residue: 0.5550
  time to fit residues: 93.5775
Evaluate side-chains
  158 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  280 TRP
Chi-restraints excluded: chain C residue   45 SER
Chi-restraints excluded: chain C residue   46 TYR
Chi-restraints excluded: chain C residue  114 ASP
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   85 ARG
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  139 VAL
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  408 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  557 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 161 optimal weight:    0.8980
   chunk 115 optimal weight:    3.9990
   chunk 142 optimal weight:    0.0970
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 148 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 165 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
C  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.098005 restraints weight = 19814.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.71
r_work: 0.3048 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13531  Z= 0.128
  Angle     :  0.621  14.150  18453  Z= 0.309
  Chirality :  0.043   0.166   2175
  Planarity :  0.005   0.066   2379
  Dihedral  :  5.233  58.773   1979
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.49 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.20), residues: 1734
  helix:  0.58 (0.19), residues: 816
  sheet: -1.67 (0.40), residues: 161
  loop : -1.70 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 325 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.010   0.001   PHE B 145 
 TRP   0.038   0.001   TRP A 172 
 HIS   0.004   0.001   HIS D 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13527)
  covalent geometry    : angle       0.61088 (18441)
  hydrogen bonds       : bond        0.03807 (  584)
  hydrogen bonds       : angle       4.55483 ( 1716)
  metal coordination   : bond        0.00327 (    4)
  metal coordination   : angle       4.47538 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4347.83 seconds
wall clock time: 74 minutes 45.47 seconds (4485.47 seconds total)