Starting phenix.real_space_refine
on Fri Sep 11 15:42:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nq0_0477/09_2026/6nq0_0477.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      60      5.16       5
     C    6724      2.51       5
     N    1622      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10140
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5023
          Classifications: {'peptide': 621}
          Link IDs: {'PTRANS': 21, 'TRANS': 599}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 47
          Unusual residues: {'EUJ': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.72, per 1000 atoms: 0.37
  Number of scatterers: 10140
  At special positions: 0
  Unit cell: (116.63, 125.19, 103.79, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       6     15.00
     O    1728      8.00
     N    1622      7.00
     C    6724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 623 " - pdb=" SG  CYS B 623 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS B 180 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 347.8 milliseconds
  

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 0 sheets defined
      78.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 59
      removed outlier: 3.536A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A  58 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 78
      removed outlier: 3.721A  pdb=" N   ARG A  75 " --> pdb=" O   MET A  71 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 96
      removed outlier: 3.623A  pdb=" N   PHE A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   PHE A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  94 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.833A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 146
      removed outlier: 3.790A  pdb=" N   SER A 141 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 155
      removed outlier: 3.565A  pdb=" N   LYS A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 178
      removed outlier: 3.553A  pdb=" N   LEU A 159 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 176 " --> pdb=" O   TRP A 172 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU A 178 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 189
    Processing helix  chain 'A' and resid 190 through 191
      No H-bonds generated for 'chain 'A' and resid 190 through 191'
    Processing helix  chain 'A' and resid 192 through 199
      removed outlier: 3.639A  pdb=" N   ASN A 198 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 211
      removed outlier: 3.644A  pdb=" N   ARG A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TRP A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 216 through 238
      removed outlier: 3.882A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A 230 " --> pdb=" O   HIS A 226 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET A 232 " --> pdb=" O   CYS A 228 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 237 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 238 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 269
      removed outlier: 3.673A  pdb=" N   VAL A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 285 through 287
      No H-bonds generated for 'chain 'A' and resid 285 through 287'
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 4.118A  pdb=" N   PHE A 292 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 343
      removed outlier: 3.520A  pdb=" N   LEU A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   THR A 308 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ARG A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 334 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
      removed outlier: 4.006A  pdb=" N   LEU A 362 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLN A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 385
      removed outlier: 3.848A  pdb=" N   MET A 379 " --> pdb=" O   HIS A 375 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 400
      removed outlier: 3.722A  pdb=" N   PHE A 400 " --> pdb=" O   PHE A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.802A  pdb=" N   ASP A 404 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 430
      removed outlier: 3.779A  pdb=" N   SER A 424 " --> pdb=" O   PRO A 420 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA A 425 " --> pdb=" O   PHE A 421 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A 427 " --> pdb=" O   GLN A 423 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A 430 " --> pdb=" O   GLN A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 454
      removed outlier: 3.847A  pdb=" N   ASN A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 449 " --> pdb=" O   ASN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 492
      removed outlier: 4.356A  pdb=" N   VAL A 475 " --> pdb=" O   ILE A 471 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A 476 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 499 through 523
      removed outlier: 3.583A  pdb=" N   VAL A 503 " --> pdb=" O   TYR A 499 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 510 " --> pdb=" O   GLY A 506 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 517 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 555
      removed outlier: 3.578A  pdb=" N   LEU A 547 " --> pdb=" O   MET A 543 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 548 " --> pdb=" O   THR A 544 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 562
      removed outlier: 3.701A  pdb=" N   SER A 561 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 575
      removed outlier: 4.270A  pdb=" N   VAL A 567 " --> pdb=" O   LYS A 563 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL A 568 " --> pdb=" O   PRO A 564 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 572 " --> pdb=" O   VAL A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 583
      removed outlier: 5.578A  pdb=" N   ALA A 581 " --> pdb=" O   GLN A 577 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE A 582 " --> pdb=" O   ASN A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 599
      removed outlier: 3.958A  pdb=" N   VAL A 587 " --> pdb=" O   GLY A 583 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A 588 " --> pdb=" O   GLY A 584 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 595 " --> pdb=" O   TYR A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 4.459A  pdb=" N   ALA A 633 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 646
      removed outlier: 3.618A  pdb=" N   LEU A 643 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 644 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 651
    Processing helix  chain 'A' and resid 654 through 665
      removed outlier: 4.227A  pdb=" N   PHE A 658 " --> pdb=" O   ASN A 654 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 659 " --> pdb=" O   TRP A 655 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 669
      No H-bonds generated for 'chain 'A' and resid 667 through 669'
    Processing helix  chain 'A' and resid 670 through 681
      removed outlier: 3.767A  pdb=" N   PHE A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 700
      removed outlier: 3.525A  pdb=" N   LEU A 692 " --> pdb=" O   LEU A 688 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASN A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 698 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 59
      removed outlier: 3.537A  pdb=" N   LEU B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B  51 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE B  52 " --> pdb=" O   GLN B  48 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B  58 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 78
      removed outlier: 3.721A  pdb=" N   ARG B  75 " --> pdb=" O   MET B  71 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B  76 " --> pdb=" O   TRP B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 96
      removed outlier: 3.623A  pdb=" N   PHE B  88 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   PHE B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU B  94 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 3.832A  pdb=" N   VAL B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLU B 129 " --> pdb=" O   THR B 125 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 131 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 146
      removed outlier: 3.789A  pdb=" N   SER B 141 " --> pdb=" O   ALA B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 155
      removed outlier: 3.566A  pdb=" N   LYS B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 178
      removed outlier: 3.553A  pdb=" N   LEU B 159 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 165 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 176 " --> pdb=" O   TRP B 172 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 189
    Processing helix  chain 'B' and resid 190 through 191
      No H-bonds generated for 'chain 'B' and resid 190 through 191'
    Processing helix  chain 'B' and resid 192 through 199
      removed outlier: 3.640A  pdb=" N   ASN B 198 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 211
      removed outlier: 3.644A  pdb=" N   ARG B 210 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TRP B 211 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 215
    Processing helix  chain 'B' and resid 216 through 238
      removed outlier: 3.883A  pdb=" N   LEU B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE B 230 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET B 232 " --> pdb=" O   CYS B 228 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU B 237 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B 238 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 269
      removed outlier: 3.673A  pdb=" N   VAL B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 285 through 287
      No H-bonds generated for 'chain 'B' and resid 285 through 287'
    Processing helix  chain 'B' and resid 288 through 299
      removed outlier: 4.119A  pdb=" N   PHE B 292 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 343
      removed outlier: 3.520A  pdb=" N   LEU B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 308 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 329 " --> pdb=" O   THR B 325 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ARG B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG B 331 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 334 " --> pdb=" O   ARG B 330 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B 340 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
      removed outlier: 4.006A  pdb=" N   LEU B 362 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 363 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLN B 364 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU B 366 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 385
      removed outlier: 3.847A  pdb=" N   MET B 379 " --> pdb=" O   HIS B 375 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG B 384 " --> pdb=" O   MET B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 400
      removed outlier: 3.721A  pdb=" N   PHE B 400 " --> pdb=" O   PHE B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 405
      removed outlier: 3.802A  pdb=" N   ASP B 404 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 430
      removed outlier: 3.779A  pdb=" N   SER B 424 " --> pdb=" O   PRO B 420 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA B 425 " --> pdb=" O   PHE B 421 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN B 426 " --> pdb=" O   LEU B 422 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY B 430 " --> pdb=" O   GLN B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.847A  pdb=" N   ASN B 439 " --> pdb=" O   ASP B 435 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER B 448 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE B 449 " --> pdb=" O   ASN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 492
      removed outlier: 4.355A  pdb=" N   VAL B 475 " --> pdb=" O   ILE B 471 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE B 476 " --> pdb=" O   LEU B 472 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 497
    Processing helix  chain 'B' and resid 499 through 523
      removed outlier: 3.583A  pdb=" N   VAL B 503 " --> pdb=" O   TYR B 499 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B 508 " --> pdb=" O   PHE B 504 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 510 " --> pdb=" O   GLY B 506 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 517 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 555
      removed outlier: 3.578A  pdb=" N   LEU B 547 " --> pdb=" O   MET B 543 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASN B 548 " --> pdb=" O   THR B 544 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 551 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 562
      removed outlier: 3.702A  pdb=" N   SER B 561 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 575
      removed outlier: 4.270A  pdb=" N   VAL B 567 " --> pdb=" O   LYS B 563 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL B 568 " --> pdb=" O   PRO B 564 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 572 " --> pdb=" O   VAL B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 583
      removed outlier: 5.578A  pdb=" N   ALA B 581 " --> pdb=" O   GLN B 577 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE B 582 " --> pdb=" O   ASN B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 599
      removed outlier: 3.958A  pdb=" N   VAL B 587 " --> pdb=" O   GLY B 583 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B 588 " --> pdb=" O   GLY B 584 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 595 " --> pdb=" O   TYR B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 634
      removed outlier: 4.460A  pdb=" N   ALA B 633 " --> pdb=" O   GLU B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 646
      removed outlier: 3.618A  pdb=" N   LEU B 643 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL B 644 " --> pdb=" O   ALA B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 646 through 651
    Processing helix  chain 'B' and resid 654 through 665
      removed outlier: 4.226A  pdb=" N   PHE B 658 " --> pdb=" O   ASN B 654 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B 659 " --> pdb=" O   TRP B 655 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 669
      No H-bonds generated for 'chain 'B' and resid 667 through 669'
    Processing helix  chain 'B' and resid 670 through 681
      removed outlier: 3.766A  pdb=" N   PHE B 674 " --> pdb=" O   SER B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 700
      removed outlier: 3.525A  pdb=" N   LEU B 692 " --> pdb=" O   LEU B 688 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN B 696 " --> pdb=" O   LEU B 692 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU B 698 " --> pdb=" O   LEU B 694 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS B 700 " --> pdb=" O   ASN B 696 " (cutoff:3.500A)

    494 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1500
        1.31 -     1.44: 2994
        1.44 -     1.56: 5793
        1.56 -     1.69: 9
        1.69 -     1.81: 100
  Bond restraints: 10396
  Sorted by residual:
  bond pdb=" O3  EUJ A1000 "
       pdb=" P3  EUJ A1000 "
    ideal  model  delta    sigma   weight residual
    1.727  1.646  0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" O3  EUJ B1000 "
       pdb=" P3  EUJ B1000 "
    ideal  model  delta    sigma   weight residual
    1.727  1.646  0.081 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" C1B EUJ B1000 "
       pdb=" O3C EUJ B1000 "
    ideal  model  delta    sigma   weight residual
    1.330  1.399 -0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1B EUJ A1000 "
       pdb=" O3C EUJ A1000 "
    ideal  model  delta    sigma   weight residual
    1.330  1.399 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C1A EUJ A1000 "
       pdb=" O2C EUJ A1000 "
    ideal  model  delta    sigma   weight residual
    1.332  1.400 -0.068 2.00e-02 2.50e+03 1.15e+01
  ... (remaining 10391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.22: 14022
        4.22 -     8.45: 102
        8.45 -    12.67: 16
       12.67 -    16.89: 0
       16.89 -    21.12: 4
  Bond angle restraints: 14144
  Sorted by residual:
  angle pdb=" N   SER B 177 "
        pdb=" CA  SER B 177 "
        pdb=" C   SER B 177 "
      ideal   model   delta    sigma   weight residual
     111.28  119.33   -8.05 1.09e+00 8.42e-01 5.45e+01
  angle pdb=" N   SER A 177 "
        pdb=" CA  SER A 177 "
        pdb=" C   SER A 177 "
      ideal   model   delta    sigma   weight residual
     111.28  119.29   -8.01 1.09e+00 8.42e-01 5.40e+01
  angle pdb=" C1  EUJ B1000 "
        pdb=" C2  EUJ B1000 "
        pdb=" O2  EUJ B1000 "
      ideal   model   delta    sigma   weight residual
     109.53  130.65  -21.12 3.00e+00 1.11e-01 4.95e+01
  angle pdb=" C1  EUJ A1000 "
        pdb=" C2  EUJ A1000 "
        pdb=" O2  EUJ A1000 "
      ideal   model   delta    sigma   weight residual
     109.53  130.61  -21.08 3.00e+00 1.11e-01 4.94e+01
  angle pdb=" C3  EUJ A1000 "
        pdb=" C2  EUJ A1000 "
        pdb=" O2  EUJ A1000 "
      ideal   model   delta    sigma   weight residual
     110.74   92.02   18.72 3.00e+00 1.11e-01 3.89e+01
  ... (remaining 14139 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.12: 5927
       31.12 -    62.24: 202
       62.24 -    93.37: 20
       93.37 -   124.49: 6
      124.49 -   155.61: 4
  Dihedral angle restraints: 6159
    sinusoidal: 2491
      harmonic: 3668
  Sorted by residual:
  dihedral pdb=" CB  CYS A 623 "
           pdb=" SG  CYS A 623 "
           pdb=" SG  CYS B 623 "
           pdb=" CB  CYS B 623 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -26.95  -59.05     1      1.00e+01 1.00e-02 4.66e+01
  dihedral pdb=" C6  EUJ B1000 "
           pdb=" C1  EUJ B1000 "
           pdb=" O1  EUJ B1000 "
           pdb=" P1  EUJ B1000 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.83  -56.56 -155.61     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" C6  EUJ A1000 "
           pdb=" C1  EUJ A1000 "
           pdb=" O1  EUJ A1000 "
           pdb=" P1  EUJ A1000 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.83  -56.60 -155.57     1      3.00e+01 1.11e-03 2.04e+01
  ... (remaining 6156 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1385
       0.066 -    0.132: 205
       0.132 -    0.199: 50
       0.199 -    0.265: 2
       0.265 -    0.331: 6
  Chirality restraints: 1648
  Sorted by residual:
  chirality pdb=" C2C EUJ A1000 "
            pdb=" C1C EUJ A1000 "
            pdb=" C3C EUJ A1000 "
            pdb=" O2C EUJ A1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.16   -2.49    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C2C EUJ B1000 "
            pdb=" C1C EUJ B1000 "
            pdb=" C3C EUJ B1000 "
            pdb=" O2C EUJ B1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.16   -2.49    0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" C2  EUJ B1000 "
            pdb=" C1  EUJ B1000 "
            pdb=" C3  EUJ B1000 "
            pdb=" O2  EUJ B1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.44   -2.12   -0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 1645 not shown)

  Planarity restraints: 1706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 191 "    0.049 5.00e-02 4.00e+02   7.36e-02 8.67e+00
        pdb=" N   PRO B 192 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 192 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 192 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 191 "   -0.049 5.00e-02 4.00e+02   7.35e-02 8.65e+00
        pdb=" N   PRO A 192 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 192 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 192 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 655 "    0.020 2.00e-02 2.50e+03   1.41e-02 4.94e+00
        pdb=" CG  TRP B 655 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 655 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 655 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 655 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 655 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 655 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 655 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 655 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 655 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1703 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1070
        2.74 -     3.28: 9776
        3.28 -     3.82: 15874
        3.82 -     4.36: 18626
        4.36 -     4.90: 31284
  Nonbonded interactions: 76630
  Sorted by model distance:
  nonbonded pdb=" O2  EUJ B1000 "
            pdb=" O3  EUJ B1000 "
     model   vdw
     2.200 2.432
  nonbonded pdb=" O2  EUJ A1000 "
            pdb=" O3  EUJ A1000 "
     model   vdw
     2.200 2.432
  nonbonded pdb=" O11 EUJ A1000 "
            pdb=" O2  EUJ A1000 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O11 EUJ B1000 "
            pdb=" O2  EUJ B1000 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER B 666 "
            pdb=" OG  SER B 666 "
     model   vdw
     2.309 3.040
  ... (remaining 76625 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.120
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
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      :  0.006   0.081  10399  Z= 0.272
  Angle     :  1.000  21.116  14150  Z= 0.489
  Chirality :  0.056   0.331   1648
  Planarity :  0.006   0.074   1706
  Dihedral  : 16.825 155.611   3770
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  7.80 %
    Favored  : 91.65 %
  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 are not related in a simple way.
  whole: -6.31 (0.14), residues: 1222
  helix: -4.38 (0.07), residues: 860
  sheet:  None (None), residues: 0
  loop : -2.95 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 185 
 TYR   0.021   0.002   TYR A 432 
 PHE   0.020   0.002   PHE B 626 
 TRP   0.037   0.002   TRP B 655 
 HIS   0.005   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00587 /  0.27 (10396)
  covalent geometry    : angle       0.99990 /  0.49 (14144)
  SS BOND              : bond        0.01166 /  0.55 (    3)
  SS BOND              : angle       1.02569 /  0.60 (    6)
  hydrogen bonds       : bond        0.31358 / 20.28 (  494)
  hydrogen bonds       : angle       9.27585 /  6.45 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 186
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 TRP cc_start: 0.7922 (t-100) cc_final: 0.7682 (t-100)
REVERT: A   47 ASP cc_start: 0.9245 (m-30) cc_final: 0.8964 (m-30)
REVERT: A  290 ILE cc_start: 0.9256 (tt) cc_final: 0.9017 (mt)
REVERT: A  434 PHE cc_start: 0.8147 (t80) cc_final: 0.7700 (t80)
REVERT: A  436 TYR cc_start: 0.7504 (t80) cc_final: 0.6651 (m-80)
REVERT: A  437 LEU cc_start: 0.8940 (mm) cc_final: 0.8687 (pp)
REVERT: A  459 VAL cc_start: 0.6389 (OUTLIER) cc_final: 0.5820 (t)
REVERT: A  467 PHE cc_start: 0.6564 (t80) cc_final: 0.5680 (m-80)
REVERT: A  484 MET cc_start: 0.7370 (ttt) cc_final: 0.7152 (tpp)
REVERT: A  562 MET cc_start: 0.8832 (mmt) cc_final: 0.8478 (mmm)
REVERT: A  652 VAL cc_start: 0.8568 (m) cc_final: 0.8289 (t)
REVERT: A  688 LEU cc_start: 0.8987 (mp) cc_final: 0.8786 (mp)
REVERT: B   47 ASP cc_start: 0.9244 (m-30) cc_final: 0.8959 (m-30)
REVERT: B   72 TRP cc_start: 0.8814 (t60) cc_final: 0.8608 (t60)
REVERT: B  290 ILE cc_start: 0.9272 (tt) cc_final: 0.9029 (mt)
REVERT: B  434 PHE cc_start: 0.8072 (t80) cc_final: 0.7645 (t80)
REVERT: B  436 TYR cc_start: 0.7522 (t80) cc_final: 0.6651 (m-80)
REVERT: B  437 LEU cc_start: 0.8947 (mm) cc_final: 0.8680 (pp)
REVERT: B  459 VAL cc_start: 0.6159 (OUTLIER) cc_final: 0.5615 (t)
REVERT: B  467 PHE cc_start: 0.6296 (t80) cc_final: 0.5663 (m-80)
REVERT: B  562 MET cc_start: 0.8833 (mmt) cc_final: 0.8430 (mmm)
REVERT: B  652 VAL cc_start: 0.8591 (m) cc_final: 0.8311 (t)
REVERT: B  688 LEU cc_start: 0.9000 (mp) cc_final: 0.8794 (mp)
  outliers start: 6
  outliers final: 2
  residues processed: 192
  average time/residue: 0.0735
  time to fit residues: 22.2812
Evaluate side-chains
  126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  459 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   30.0000
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   overall best weight:    1.3300

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 GLN
A 305 ASN
A 401 ASN
A 431 HIS
A 502 ASN
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 GLN
B 305 ASN
B 401 ASN
B 431 HIS
B 502 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.114162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.084107 restraints weight = 22240.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.084720 restraints weight = 11768.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.085434 restraints weight = 8652.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.085555 restraints weight = 7735.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.085694 restraints weight = 7523.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10399  Z= 0.143
  Angle     :  0.623   7.394  14150  Z= 0.318
  Chirality :  0.041   0.154   1648
  Planarity :  0.005   0.039   1706
  Dihedral  : 14.299 158.443   1494
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 13.79 %
    Favored  : 85.30 %
  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 are not related in a simple way.
  whole: -3.50 (0.20), residues: 1222
  helix: -2.13 (0.14), residues: 854
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 557 
 TYR   0.018   0.001   TYR A 432 
 PHE   0.025   0.002   PHE A 427 
 TRP   0.016   0.001   TRP B 655 
 HIS   0.007   0.001   HIS A 431 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (10396)
  covalent geometry    : angle       0.62291 /  0.32 (14144)
  SS BOND              : bond        0.00109 /  0.05 (    3)
  SS BOND              : angle       0.82480 /  0.52 (    6)
  hydrogen bonds       : bond        0.06070 /  4.05 (  494)
  hydrogen bonds       : angle       4.72325 /  3.32 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.9148 (m-30) cc_final: 0.8809 (m-30)
REVERT: A  467 PHE cc_start: 0.6516 (t80) cc_final: 0.5731 (m-80)
REVERT: A  484 MET cc_start: 0.7521 (ttt) cc_final: 0.7298 (tpp)
REVERT: A  557 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8351 (ptt90)
REVERT: A  562 MET cc_start: 0.8797 (mmt) cc_final: 0.8342 (mmm)
REVERT: A  565 MET cc_start: 0.7858 (mtm) cc_final: 0.7642 (mtm)
REVERT: A  579 MET cc_start: 0.7093 (tmm) cc_final: 0.6661 (tmm)
REVERT: A  688 LEU cc_start: 0.8828 (mp) cc_final: 0.8522 (mp)
REVERT: B   47 ASP cc_start: 0.9173 (m-30) cc_final: 0.8822 (m-30)
REVERT: B   72 TRP cc_start: 0.8825 (t60) cc_final: 0.8619 (t60)
REVERT: B  467 PHE cc_start: 0.6484 (t80) cc_final: 0.5755 (m-80)
REVERT: B  557 ARG cc_start: 0.8603 (ptm-80) cc_final: 0.8381 (ptt90)
REVERT: B  562 MET cc_start: 0.8749 (mmt) cc_final: 0.8245 (mmm)
REVERT: B  565 MET cc_start: 0.7833 (mtm) cc_final: 0.7611 (mtm)
REVERT: B  579 MET cc_start: 0.6999 (tmm) cc_final: 0.6565 (tmm)
REVERT: B  688 LEU cc_start: 0.8832 (mp) cc_final: 0.8516 (mp)
  outliers start: 10
  outliers final: 4
  residues processed: 149
  average time/residue: 0.0702
  time to fit residues: 16.8418
Evaluate side-chains
  115 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  402 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   overall best weight:    2.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.111668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.079799 restraints weight = 22500.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.081926 restraints weight = 11630.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.083154 restraints weight = 8067.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.083677 restraints weight = 6734.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.084175 restraints weight = 6160.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10399  Z= 0.183
  Angle     :  0.625  11.076  14150  Z= 0.314
  Chirality :  0.041   0.136   1648
  Planarity :  0.004   0.035   1706
  Dihedral  : 13.472 155.956   1488
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.70 %
    Favored  : 81.67 %
  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 are not related in a simple way.
  whole: -2.05 (0.22), residues: 1222
  helix: -0.88 (0.16), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.18 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 557 
 TYR   0.016   0.001   TYR A 432 
 PHE   0.026   0.002   PHE A 338 
 TRP   0.016   0.001   TRP A 655 
 HIS   0.004   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.18 (10396)
  covalent geometry    : angle       0.62520 /  0.31 (14144)
  SS BOND              : bond        0.00286 /  0.12 (    3)
  SS BOND              : angle       0.97327 /  0.62 (    6)
  hydrogen bonds       : bond        0.04865 /  3.27 (  494)
  hydrogen bonds       : angle       4.39687 /  3.06 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A  380 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7319 (mpp)
REVERT: A  467 PHE cc_start: 0.6733 (t80) cc_final: 0.5859 (m-80)
REVERT: A  562 MET cc_start: 0.8814 (mmt) cc_final: 0.8502 (mmm)
REVERT: A  579 MET cc_start: 0.7187 (tmm) cc_final: 0.6745 (tmm)
REVERT: B   47 ASP cc_start: 0.9182 (m-30) cc_final: 0.8838 (m-30)
REVERT: B   72 TRP cc_start: 0.8777 (t60) cc_final: 0.8577 (t60)
REVERT: B  380 MET cc_start: 0.7621 (mpp) cc_final: 0.7342 (mpp)
REVERT: B  467 PHE cc_start: 0.6750 (t80) cc_final: 0.5870 (m-80)
REVERT: B  472 LEU cc_start: 0.9253 (tp) cc_final: 0.8812 (pp)
REVERT: B  562 MET cc_start: 0.8799 (mmt) cc_final: 0.8451 (mmm)
REVERT: B  579 MET cc_start: 0.7207 (tmm) cc_final: 0.6765 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 139
  average time/residue: 0.0689
  time to fit residues: 15.6339
Evaluate side-chains
  127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  681 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 8 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.111325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.079836 restraints weight = 22544.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.081943 restraints weight = 11535.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.083170 restraints weight = 7991.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.083657 restraints weight = 6647.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.083956 restraints weight = 6113.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10399  Z= 0.175
  Angle     :  0.598   8.942  14150  Z= 0.299
  Chirality :  0.041   0.131   1648
  Planarity :  0.003   0.032   1706
  Dihedral  : 13.340 161.879   1488
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.15 %
    Favored  : 80.31 %
  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 are not related in a simple way.
  whole: -1.38 (0.23), residues: 1222
  helix: -0.30 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.12 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.015   0.001   TYR B 432 
 PHE   0.019   0.002   PHE A 582 
 TRP   0.012   0.001   TRP B 655 
 HIS   0.003   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 (10396)
  covalent geometry    : angle       0.59736 /  0.30 (14144)
  SS BOND              : bond        0.00246 /  0.11 (    3)
  SS BOND              : angle       1.08646 /  0.69 (    6)
  hydrogen bonds       : bond        0.04332 /  2.90 (  494)
  hydrogen bonds       : angle       4.20300 /  2.91 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 MET cc_start: 0.8025 (ttm) cc_final: 0.7785 (ttm)
REVERT: A  453 LEU cc_start: 0.9506 (tp) cc_final: 0.9164 (tp)
REVERT: A  479 TYR cc_start: 0.9142 (t80) cc_final: 0.8830 (t80)
REVERT: A  562 MET cc_start: 0.8783 (mmt) cc_final: 0.8395 (mmm)
REVERT: A  565 MET cc_start: 0.7897 (mtm) cc_final: 0.7619 (mtm)
REVERT: B   47 ASP cc_start: 0.9239 (m-30) cc_final: 0.8831 (m-30)
REVERT: B  472 LEU cc_start: 0.9245 (tp) cc_final: 0.8788 (pp)
REVERT: B  479 TYR cc_start: 0.9145 (t80) cc_final: 0.8825 (t80)
REVERT: B  562 MET cc_start: 0.8767 (mmt) cc_final: 0.8396 (mmm)
REVERT: B  565 MET cc_start: 0.7917 (mtm) cc_final: 0.7628 (mtm)
REVERT: B  579 MET cc_start: 0.7041 (tmm) cc_final: 0.6625 (tmm)
  outliers start: 28
  outliers final: 23
  residues processed: 152
  average time/residue: 0.0708
  time to fit residues: 17.1908
Evaluate side-chains
  145 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  699 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  681 SER
Chi-restraints excluded: chain B residue  699 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0770
   chunk 122 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    2.4146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 151 HIS
B 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.111231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.079829 restraints weight = 22671.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.081970 restraints weight = 11483.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.083235 restraints weight = 7909.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.083612 restraints weight = 6522.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.084218 restraints weight = 6068.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10399  Z= 0.168
  Angle     :  0.590   7.968  14150  Z= 0.295
  Chirality :  0.041   0.144   1648
  Planarity :  0.003   0.031   1706
  Dihedral  : 13.290 167.758   1488
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.33 %
    Favored  : 78.68 %
  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 are not related in a simple way.
  whole: -0.92 (0.23), residues: 1222
  helix:  0.10 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -2.05 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 557 
 TYR   0.013   0.001   TYR B 432 
 PHE   0.027   0.002   PHE A 338 
 TRP   0.010   0.001   TRP B 685 
 HIS   0.003   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.17 (10396)
  covalent geometry    : angle       0.58939 /  0.29 (14144)
  SS BOND              : bond        0.00267 /  0.11 (    3)
  SS BOND              : angle       1.08453 /  0.68 (    6)
  hydrogen bonds       : bond        0.04192 /  2.82 (  494)
  hydrogen bonds       : angle       4.11599 /  2.85 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.9290 (m-30) cc_final: 0.8850 (m-30)
REVERT: A  235 MET cc_start: 0.8242 (ttm) cc_final: 0.8020 (ttm)
REVERT: A  380 MET cc_start: 0.7614 (mpp) cc_final: 0.7373 (mpp)
REVERT: A  453 LEU cc_start: 0.9489 (tp) cc_final: 0.9271 (tp)
REVERT: A  479 TYR cc_start: 0.9152 (t80) cc_final: 0.8826 (t80)
REVERT: A  483 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7636 (mp0)
REVERT: A  562 MET cc_start: 0.8776 (mmt) cc_final: 0.8364 (mmm)
REVERT: A  565 MET cc_start: 0.8001 (mtm) cc_final: 0.7692 (mtm)
REVERT: A  579 MET cc_start: 0.7023 (tmm) cc_final: 0.6781 (tmm)
REVERT: B   47 ASP cc_start: 0.9283 (m-30) cc_final: 0.8843 (m-30)
REVERT: B  472 LEU cc_start: 0.9174 (tp) cc_final: 0.8726 (pp)
REVERT: B  479 TYR cc_start: 0.9152 (t80) cc_final: 0.8809 (t80)
REVERT: B  562 MET cc_start: 0.8775 (mmt) cc_final: 0.8368 (mmm)
REVERT: B  565 MET cc_start: 0.8001 (mtm) cc_final: 0.7695 (mtm)
REVERT: B  579 MET cc_start: 0.7024 (tmm) cc_final: 0.6714 (tmm)
  outliers start: 33
  outliers final: 24
  residues processed: 157
  average time/residue: 0.0685
  time to fit residues: 17.1562
Evaluate side-chains
  149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  699 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  681 SER
Chi-restraints excluded: chain B residue  699 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 97 optimal weight:   50.0000
   chunk 60 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 117 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.111469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.080171 restraints weight = 22784.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.082299 restraints weight = 11394.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.083555 restraints weight = 7830.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.084182 restraints weight = 6473.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.084445 restraints weight = 5901.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10399  Z= 0.156
  Angle     :  0.578   7.901  14150  Z= 0.291
  Chirality :  0.040   0.144   1648
  Planarity :  0.003   0.031   1706
  Dihedral  : 13.261 171.878   1488
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.69 %
    Favored  : 78.22 %
  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 are not related in a simple way.
  whole: -0.69 (0.24), residues: 1222
  helix:  0.27 (0.18), residues: 834
  sheet:  None (None), residues: 0
  loop : -1.98 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 331 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.027   0.002   PHE A 338 
 TRP   0.012   0.001   TRP A 685 
 HIS   0.007   0.001   HIS A 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 (10396)
  covalent geometry    : angle       0.57811 /  0.29 (14144)
  SS BOND              : bond        0.00196 /  0.08 (    3)
  SS BOND              : angle       0.95430 /  0.60 (    6)
  hydrogen bonds       : bond        0.04026 /  2.70 (  494)
  hydrogen bonds       : angle       4.10217 /  2.84 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.9271 (m-30) cc_final: 0.8829 (m-30)
REVERT: A  235 MET cc_start: 0.8163 (ttm) cc_final: 0.7921 (ttm)
REVERT: A  380 MET cc_start: 0.7659 (mpp) cc_final: 0.7329 (mpp)
REVERT: A  479 TYR cc_start: 0.9124 (t80) cc_final: 0.8810 (t80)
REVERT: A  562 MET cc_start: 0.8730 (mmt) cc_final: 0.8322 (mmm)
REVERT: A  565 MET cc_start: 0.7966 (mtm) cc_final: 0.7652 (mtm)
REVERT: A  579 MET cc_start: 0.6946 (tmm) cc_final: 0.6735 (tmm)
REVERT: B   47 ASP cc_start: 0.9288 (m-30) cc_final: 0.8843 (m-30)
REVERT: B  472 LEU cc_start: 0.9162 (tp) cc_final: 0.8729 (pp)
REVERT: B  479 TYR cc_start: 0.9224 (t80) cc_final: 0.8898 (t80)
REVERT: B  562 MET cc_start: 0.8733 (mmt) cc_final: 0.8319 (mmm)
REVERT: B  565 MET cc_start: 0.7960 (mtm) cc_final: 0.7648 (mtm)
REVERT: B  579 MET cc_start: 0.6982 (tmm) cc_final: 0.6692 (tmm)
  outliers start: 34
  outliers final: 27
  residues processed: 158
  average time/residue: 0.0696
  time to fit residues: 17.8559
Evaluate side-chains
  153 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  699 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  467 PHE
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  676 LEU
Chi-restraints excluded: chain B residue  681 SER
Chi-restraints excluded: chain B residue  699 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 82 optimal weight:    0.4980
   chunk 107 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 151 HIS
B 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.112654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.081211 restraints weight = 22309.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.083369 restraints weight = 11303.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.084613 restraints weight = 7846.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.085167 restraints weight = 6517.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.085654 restraints weight = 5966.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10399  Z= 0.125
  Angle     :  0.555   7.860  14150  Z= 0.278
  Chirality :  0.040   0.201   1648
  Planarity :  0.003   0.031   1706
  Dihedral  : 13.141 175.985   1488
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.78 %
    Favored  : 77.77 %
  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 are not related in a simple way.
  whole: -0.42 (0.24), residues: 1222
  helix:  0.50 (0.18), residues: 834
  sheet:  None (None), residues: 0
  loop : -1.93 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 580 
 TYR   0.013   0.001   TYR B 432 
 PHE   0.031   0.001   PHE B 338 
 TRP   0.007   0.001   TRP A  42 
 HIS   0.002   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 (10396)
  covalent geometry    : angle       0.55473 /  0.28 (14144)
  SS BOND              : bond        0.00157 /  0.07 (    3)
  SS BOND              : angle       0.83857 /  0.52 (    6)
  hydrogen bonds       : bond        0.03851 /  2.58 (  494)
  hydrogen bonds       : angle       3.95158 /  2.74 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.9286 (m-30) cc_final: 0.8835 (m-30)
REVERT: A  235 MET cc_start: 0.8200 (ttm) cc_final: 0.7930 (ttm)
REVERT: A  479 TYR cc_start: 0.9156 (t80) cc_final: 0.8866 (t80)
REVERT: A  562 MET cc_start: 0.8702 (mmt) cc_final: 0.8254 (mmm)
REVERT: A  565 MET cc_start: 0.7891 (mtm) cc_final: 0.7591 (mtm)
REVERT: B   47 ASP cc_start: 0.9285 (m-30) cc_final: 0.8834 (m-30)
REVERT: B  472 LEU cc_start: 0.9137 (tp) cc_final: 0.8698 (pp)
REVERT: B  479 TYR cc_start: 0.9158 (t80) cc_final: 0.8815 (t80)
REVERT: B  481 LEU cc_start: 0.9173 (tp) cc_final: 0.8966 (pp)
REVERT: B  562 MET cc_start: 0.8708 (mmt) cc_final: 0.8261 (mmm)
REVERT: B  565 MET cc_start: 0.7933 (mtm) cc_final: 0.7642 (mtm)
  outliers start: 27
  outliers final: 19
  residues processed: 160
  average time/residue: 0.0695
  time to fit residues: 17.8026
Evaluate side-chains
  144 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  467 PHE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  681 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 29 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 22 optimal weight:    0.1980
   chunk 123 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 105 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.114143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.082834 restraints weight = 22349.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.085096 restraints weight = 10935.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.086451 restraints weight = 7424.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.086997 restraints weight = 6112.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.086997 restraints weight = 5587.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10399  Z= 0.110
  Angle     :  0.563  10.137  14150  Z= 0.280
  Chirality :  0.039   0.192   1648
  Planarity :  0.003   0.031   1706
  Dihedral  : 12.983 177.389   1488
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.05 %
    Favored  : 77.04 %
  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 are not related in a simple way.
  whole: -0.35 (0.24), residues: 1222
  helix:  0.55 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -1.88 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 580 
 TYR   0.015   0.001   TYR A 432 
 PHE   0.031   0.002   PHE A 338 
 TRP   0.016   0.001   TRP B 685 
 HIS   0.009   0.001   HIS B 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 (10396)
  covalent geometry    : angle       0.56305 /  0.28 (14144)
  SS BOND              : bond        0.00085 /  0.04 (    3)
  SS BOND              : angle       0.77431 /  0.48 (    6)
  hydrogen bonds       : bond        0.03654 /  2.45 (  494)
  hydrogen bonds       : angle       3.89663 /  2.71 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.9302 (m-30) cc_final: 0.8837 (m-30)
REVERT: A  472 LEU cc_start: 0.9027 (tp) cc_final: 0.8790 (pp)
REVERT: A  479 TYR cc_start: 0.9150 (t80) cc_final: 0.8863 (t80)
REVERT: A  562 MET cc_start: 0.8771 (mmt) cc_final: 0.8244 (mmm)
REVERT: A  565 MET cc_start: 0.7927 (mtm) cc_final: 0.7634 (mtm)
REVERT: A  579 MET cc_start: 0.6987 (tmm) cc_final: 0.6572 (tmm)
REVERT: B   47 ASP cc_start: 0.9304 (m-30) cc_final: 0.8834 (m-30)
REVERT: B  472 LEU cc_start: 0.9151 (tp) cc_final: 0.8679 (pp)
REVERT: B  479 TYR cc_start: 0.9140 (t80) cc_final: 0.8852 (t80)
REVERT: B  562 MET cc_start: 0.8775 (mmt) cc_final: 0.8255 (mmm)
REVERT: B  565 MET cc_start: 0.7932 (mtm) cc_final: 0.7627 (mtm)
REVERT: B  579 MET cc_start: 0.6983 (tmm) cc_final: 0.6586 (tmm)
REVERT: B  690 LEU cc_start: 0.8714 (mt) cc_final: 0.8486 (mt)
  outliers start: 21
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0659
  time to fit residues: 16.3036
Evaluate side-chains
  143 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  467 PHE
Chi-restraints excluded: chain B residue  491 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0870
   chunk 86 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0370
   chunk 72 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    0.1980
   chunk 46 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3636

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 151 HIS
A 401 ASN
B 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.087774 restraints weight = 22432.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.088352 restraints weight = 13689.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.088891 restraints weight = 11194.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.089391 restraints weight = 9236.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.089629 restraints weight = 8806.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10399  Z= 0.105
  Angle     :  0.559   9.873  14150  Z= 0.275
  Chirality :  0.039   0.166   1648
  Planarity :  0.003   0.030   1706
  Dihedral  : 12.740 178.167   1488
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.87 %
    Favored  : 77.22 %
  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 are not related in a simple way.
  whole: -0.26 (0.24), residues: 1222
  helix:  0.59 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -1.86 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 580 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.032   0.001   PHE A 338 
 TRP   0.019   0.001   TRP A 685 
 HIS   0.006   0.001   HIS B 431 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 (10396)
  covalent geometry    : angle       0.55902 /  0.27 (14144)
  SS BOND              : bond        0.00039 /  0.02 (    3)
  SS BOND              : angle       0.53712 /  0.34 (    6)
  hydrogen bonds       : bond        0.03360 /  2.24 (  494)
  hydrogen bonds       : angle       3.78071 /  2.63 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.9188 (m-30) cc_final: 0.8762 (m-30)
REVERT: A  479 TYR cc_start: 0.9035 (t80) cc_final: 0.8813 (t80)
REVERT: A  562 MET cc_start: 0.8676 (mmt) cc_final: 0.8137 (mmm)
REVERT: A  565 MET cc_start: 0.7834 (mtm) cc_final: 0.7579 (mtm)
REVERT: A  579 MET cc_start: 0.6990 (tmm) cc_final: 0.6631 (tmm)
REVERT: B   47 ASP cc_start: 0.9174 (m-30) cc_final: 0.8751 (m-30)
REVERT: B  472 LEU cc_start: 0.9151 (tp) cc_final: 0.8711 (pp)
REVERT: B  479 TYR cc_start: 0.9022 (t80) cc_final: 0.8803 (t80)
REVERT: B  562 MET cc_start: 0.8674 (mmt) cc_final: 0.8130 (mmm)
REVERT: B  565 MET cc_start: 0.7868 (mtm) cc_final: 0.7565 (mtm)
REVERT: B  579 MET cc_start: 0.6891 (tmm) cc_final: 0.6552 (tmm)
  outliers start: 21
  outliers final: 16
  residues processed: 156
  average time/residue: 0.0652
  time to fit residues: 16.7639
Evaluate side-chains
  151 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  699 HIS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  467 PHE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  681 SER
Chi-restraints excluded: chain B residue  699 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   overall best weight:    1.4184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.086179 restraints weight = 22180.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.086997 restraints weight = 13822.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.087447 restraints weight = 11216.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.087766 restraints weight = 9471.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.087986 restraints weight = 8956.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10399  Z= 0.124
  Angle     :  0.577   9.865  14150  Z= 0.284
  Chirality :  0.040   0.180   1648
  Planarity :  0.003   0.029   1706
  Dihedral  : 12.760 177.873   1488
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 21.42 %
    Favored  : 77.04 %
  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 are not related in a simple way.
  whole: -0.14 (0.24), residues: 1222
  helix:  0.70 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -1.87 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 112 
 TYR   0.014   0.001   TYR B 432 
 PHE   0.032   0.002   PHE B 338 
 TRP   0.021   0.001   TRP A 685 
 HIS   0.005   0.001   HIS B 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 (10396)
  covalent geometry    : angle       0.57647 /  0.28 (14144)
  SS BOND              : bond        0.00129 /  0.05 (    3)
  SS BOND              : angle       0.79372 /  0.49 (    6)
  hydrogen bonds       : bond        0.03438 /  2.30 (  494)
  hydrogen bonds       : angle       3.84728 /  2.67 ( 1452)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.9189 (m-30) cc_final: 0.8769 (m-30)
REVERT: A  479 TYR cc_start: 0.9064 (t80) cc_final: 0.8796 (t80)
REVERT: A  562 MET cc_start: 0.8698 (mmt) cc_final: 0.8175 (mmm)
REVERT: A  565 MET cc_start: 0.7824 (mtm) cc_final: 0.7588 (mtm)
REVERT: B   47 ASP cc_start: 0.9182 (m-30) cc_final: 0.8763 (m-30)
REVERT: B  472 LEU cc_start: 0.9135 (tp) cc_final: 0.8727 (pp)
REVERT: B  479 TYR cc_start: 0.9050 (t80) cc_final: 0.8789 (t80)
REVERT: B  562 MET cc_start: 0.8699 (mmt) cc_final: 0.8181 (mmm)
REVERT: B  565 MET cc_start: 0.7858 (mtm) cc_final: 0.7572 (mtm)
REVERT: B  579 MET cc_start: 0.6925 (tmm) cc_final: 0.6515 (tmm)
  outliers start: 17
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0667
  time to fit residues: 16.0190
Evaluate side-chains
  149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  699 HIS
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  467 PHE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  699 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 117 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:   40.0000
   overall best weight:    2.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.112741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.084217 restraints weight = 22394.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.085490 restraints weight = 13898.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.085799 restraints weight = 10820.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.086097 restraints weight = 9511.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.086238 restraints weight = 8952.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  10399  Z= 0.153
  Angle     :  0.601  10.047  14150  Z= 0.295
  Chirality :  0.041   0.172   1648
  Planarity :  0.003   0.029   1706
  Dihedral  : 12.924 178.219   1488
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.78 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.24), residues: 1222
  helix:  0.73 (0.18), residues: 844
  sheet:  None (None), residues: 0
  loop : -1.83 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 112 
 TYR   0.014   0.001   TYR B 432 
 PHE   0.033   0.002   PHE B 338 
 TRP   0.020   0.001   TRP A 685 
 HIS   0.003   0.001   HIS B 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 (10396)
  covalent geometry    : angle       0.60108 /  0.29 (14144)
  SS BOND              : bond        0.00247 /  0.11 (    3)
  SS BOND              : angle       1.08432 /  0.67 (    6)
  hydrogen bonds       : bond        0.03730 /  2.50 (  494)
  hydrogen bonds       : angle       3.94459 /  2.73 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1581.25 seconds
wall clock time: 28 minutes 2.58 seconds (1682.58 seconds total)