Starting phenix.real_space_refine
on Sun Jan 26 04:12:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rn7_19389/01_2025/8rn7_19389.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S     101      5.16       5
     C    7685      2.51       5
     N    2073      2.21       5
     O    2245      1.98       5
     H   12184      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 24289
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8275
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 518, 8275
          Classifications: {'peptide': 518}
          Link IDs: {'PTRANS': 21, 'TRANS': 496}
    Chain: "B"
      Number of atoms: 11267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 11267
          Classifications: {'peptide': 718}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 684}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 3921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 3921
          Classifications: {'peptide': 236}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 222}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 379
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 2, 'TRANS': 20}
    Chain: "E"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 446
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 12.27, per 1000 atoms: 0.51
  Number of scatterers: 24289
  At special positions: 0
  Unit cell: (114.24, 110.04, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     101     16.00
     Mg      1     11.99
     O    2245      8.00
     N    2073      7.00
     C    7685      6.00
     H   12184      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.02
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2844

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 16 sheets defined
      52.2% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 206 through 214
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 237 through 246
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'A' and resid 301 through 313
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 332 through 349
    Processing helix  chain 'A' and resid 361 through 366
    Processing helix  chain 'A' and resid 376 through 383
      removed outlier: 3.585A  pdb=" N   ALA A 380 " --> pdb=" O   MET A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 410
      removed outlier: 4.410A  pdb=" N   GLN A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 448
      removed outlier: 4.609A  pdb=" N   TYR A 448 " --> pdb=" O   ASN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 472
      removed outlier: 3.582A  pdb=" N   THR A 453 " --> pdb=" O   CYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 4.224A  pdb=" N   SER A 530 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLY A 531 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 570
    Processing helix  chain 'A' and resid 573 through 595
      removed outlier: 3.871A  pdb=" N   LEU A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A 583 " --> pdb=" O   GLN A 579 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   MET A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 605
    Processing helix  chain 'A' and resid 629 through 646
    Processing helix  chain 'A' and resid 648 through 670
      removed outlier: 4.106A  pdb=" N   ARG A 660 " --> pdb=" O   ALA A 656 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   LEU A 661 " --> pdb=" O   GLU A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 688
      removed outlier: 3.700A  pdb=" N   MET A 682 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 714
    Processing helix  chain 'B' and resid 7 through 12
      removed outlier: 3.930A  pdb=" N   ASP B  11 " --> pdb=" O   PHE B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 35 through 49
    Processing helix  chain 'B' and resid 84 through 99
    Processing helix  chain 'B' and resid 101 through 116
      removed outlier: 3.748A  pdb=" N   ALA B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 124
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 162 through 174
      removed outlier: 3.836A  pdb=" N   PHE B 166 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 222
    Processing helix  chain 'B' and resid 248 through 266
      removed outlier: 4.254A  pdb=" N   ASN B 265 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU B 266 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 293
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 3.541A  pdb=" N   PHE B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 338
    Processing helix  chain 'B' and resid 339 through 346
    Processing helix  chain 'B' and resid 369 through 373
    Processing helix  chain 'B' and resid 377 through 381
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 394 through 396
      No H-bonds generated for 'chain 'B' and resid 394 through 396'
    Processing helix  chain 'B' and resid 414 through 426
    Processing helix  chain 'B' and resid 454 through 472
    Processing helix  chain 'B' and resid 517 through 536
    Processing helix  chain 'B' and resid 539 through 558
    Processing helix  chain 'B' and resid 569 through 582
      removed outlier: 4.199A  pdb=" N   ILE B 574 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU B 580 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 593
    Processing helix  chain 'B' and resid 606 through 611
    Processing helix  chain 'B' and resid 612 through 615
    Processing helix  chain 'B' and resid 616 through 624
    Processing helix  chain 'B' and resid 632 through 639
      removed outlier: 3.532A  pdb=" N   ILE B 636 " --> pdb=" O   HIS B 633 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLU B 637 " --> pdb=" O   LEU B 634 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLY B 638 " --> pdb=" O   SER B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 665
      removed outlier: 3.789A  pdb=" N   TRP B 665 " --> pdb=" O   THR B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 699
    Processing helix  chain 'B' and resid 712 through 731
      removed outlier: 3.595A  pdb=" N   ALA B 716 " --> pdb=" O   SER B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 735 through 750
    Processing helix  chain 'C' and resid 2 through 14
    Processing helix  chain 'C' and resid 15 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 44 through 55
      removed outlier: 3.789A  pdb=" N   CYS C  54 " --> pdb=" O   LYS C  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER C  55 " --> pdb=" O   TRP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 70
      removed outlier: 3.643A  pdb=" N   ASN C  68 " --> pdb=" O   ASP C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 104
      removed outlier: 3.810A  pdb=" N   VAL C  98 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 117 through 130
    Processing helix  chain 'C' and resid 157 through 170
    Processing helix  chain 'C' and resid 184 through 196
    Processing helix  chain 'C' and resid 201 through 214
      removed outlier: 3.543A  pdb=" N   LEU C 205 " --> pdb=" O   THR C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 233
      removed outlier: 4.003A  pdb=" N   MET C 233 " --> pdb=" O   GLU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 238
    Processing helix  chain 'D' and resid 369 through 375
      removed outlier: 4.364A  pdb=" N   PHE D 374 " --> pdb=" O   PRO D 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 360 through 366
      removed outlier: 3.808A  pdb=" N   TRP E 364 " --> pdb=" O   ASN E 360 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 383
    Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256
    Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 295
      removed outlier: 4.247A  pdb=" N   SER A 492 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR A 497 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A 521 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LYS A 551 " --> pdb=" O   SER A 543 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   SER A 543 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL A 553 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL A 538 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295
      removed outlier: 4.247A  pdb=" N   SER A 492 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ILE A 481 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   LEU A 499 " --> pdb=" O   ILE A 479 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ILE A 479 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL A 501 " --> pdb=" O   LYS A 477 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LYS A 477 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374
      removed outlier: 5.696A  pdb=" N   GLN A 373 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   GLN B 367 " --> pdb=" O   GLN A 373 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 623 through 628
      removed outlier: 6.048A  pdb=" N   LYS A 623 " --> pdb=" O   THR A 619 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   THR A 619 " --> pdb=" O   LYS A 623 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 617 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 188
    Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 243
      removed outlier: 4.013A  pdb=" N   THR B 226 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 491
    Processing sheet with id=AB2, first strand: chain 'B' and resid 641 through 642
    Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60
    Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74
    Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 136
      removed outlier: 5.436A  pdb=" N   TRP C 132 " --> pdb=" O   HIS C 247 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   HIS C 247 " --> pdb=" O   TRP C 132 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   ARG C 134 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 148
    Processing sheet with id=AB7, first strand: chain 'D' and resid 355 through 359

    621 hydrogen bonds defined for protein.
    1704 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: 9.84

  Time building geometry restraints manager: 8.02 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12152
        1.03 -     1.23: 33
        1.23 -     1.42: 5026
        1.42 -     1.62: 7147
        1.62 -     1.81: 170
  Bond restraints: 24528
  Sorted by residual:
  bond pdb=" N   PRO C 157 "
       pdb=" CA  PRO C 157 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.31e-02 5.83e+03 9.30e-01
  bond pdb=" CB  GLN B 104 "
       pdb=" CG  GLN B 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.82e-01
  bond pdb=" C   ASN B   4 "
       pdb=" O   ASN B   4 "
    ideal  model  delta    sigma   weight residual
    1.249  1.241  0.007 8.50e-03 1.38e+04 7.39e-01
  bond pdb=" C   ASN B 628 "
       pdb=" O   ASN B 628 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.28e-02 6.10e+03 7.14e-01
  bond pdb=" CA  TRP B 437 "
       pdb=" CB  TRP B 437 "
    ideal  model  delta    sigma   weight residual
    1.534  1.553 -0.019 2.33e-02 1.84e+03 6.44e-01
  ... (remaining 24523 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 42653
        1.21 -     2.41: 1619
        2.41 -     3.62: 113
        3.62 -     4.82: 22
        4.82 -     6.03: 1
  Bond angle restraints: 44408
  Sorted by residual:
  angle pdb=" N   ILE B 339 "
        pdb=" CA  ILE B 339 "
        pdb=" C   ILE B 339 "
      ideal   model   delta    sigma   weight residual
     112.96  109.73    3.23 1.00e+00 1.00e+00 1.04e+01
  angle pdb=" N   VAL B 516 "
        pdb=" CA  VAL B 516 "
        pdb=" C   VAL B 516 "
      ideal   model   delta    sigma   weight residual
     109.34  115.37   -6.03 2.08e+00 2.31e-01 8.40e+00
  angle pdb=" N   TRP B 309 "
        pdb=" CA  TRP B 309 "
        pdb=" CB  TRP B 309 "
      ideal   model   delta    sigma   weight residual
     113.65  109.46    4.19 1.47e+00 4.63e-01 8.13e+00
  angle pdb=" CA  GLY B 512 "
        pdb=" C   GLY B 512 "
        pdb=" N   VAL B 513 "
      ideal   model   delta    sigma   weight residual
     115.34  117.55   -2.21 8.10e-01 1.52e+00 7.44e+00
  angle pdb=" CA  VAL A 428 "
        pdb=" C   VAL A 428 "
        pdb=" N   ALA A 429 "
      ideal   model   delta    sigma   weight residual
     116.60  120.12   -3.52 1.45e+00 4.76e-01 5.90e+00
  ... (remaining 44403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 9983
       17.30 -    34.60: 1057
       34.60 -    51.89: 344
       51.89 -    69.19: 90
       69.19 -    86.49: 16
  Dihedral angle restraints: 11490
    sinusoidal: 6357
      harmonic: 5133
  Sorted by residual:
  dihedral pdb=" CA  GLY B 515 "
           pdb=" C   GLY B 515 "
           pdb=" N   VAL B 516 "
           pdb=" CA  VAL B 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.02  -25.98     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  LYS A 327 "
           pdb=" C   LYS A 327 "
           pdb=" N   SER A 328 "
           pdb=" CA  SER A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ASP A 678 "
           pdb=" CB  ASP A 678 "
           pdb=" CG  ASP A 678 "
           pdb=" OD1 ASP A 678 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.67   57.67     1      2.00e+01 2.50e-03 1.12e+01
  ... (remaining 11487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1218
       0.029 -    0.058: 432
       0.058 -    0.087: 99
       0.087 -    0.117: 59
       0.117 -    0.146: 18
  Chirality restraints: 1826
  Sorted by residual:
  chirality pdb=" CA  ILE B 368 "
            pdb=" N   ILE B 368 "
            pdb=" C   ILE B 368 "
            pdb=" CB  ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  ILE D 368 "
            pdb=" N   ILE D 368 "
            pdb=" C   ILE D 368 "
            pdb=" CB  ILE D 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.88e-01
  chirality pdb=" CA  ILE B 376 "
            pdb=" N   ILE B 376 "
            pdb=" C   ILE B 376 "
            pdb=" CB  ILE B 376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1823 not shown)

  Planarity restraints: 3571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 253 "    0.034 5.00e-02 4.00e+02   5.21e-02 4.35e+00
        pdb=" N   PRO A 254 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 254 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 254 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 429 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A 430 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 430 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 430 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 444 "    0.008 2.00e-02 2.50e+03   1.50e-02 2.25e+00
        pdb=" C   ASP B 444 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ASP B 444 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP B 445 "    0.009 2.00e-02 2.50e+03
  ... (remaining 3568 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 1106
        2.17 -     2.77: 48009
        2.77 -     3.38: 69651
        3.38 -     3.99: 88946
        3.99 -     4.60: 140435
  Nonbonded interactions: 348147
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 111 "
            pdb=" H   GLU C 111 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" OD1 ASP B 454 "
            pdb=" H   THR B 457 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" O   SER B  58 "
            pdb=" H   GLY B  62 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" H   GLY A 237 "
            pdb=" OE1 GLU B  90 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" OD2 ASP B 445 "
            pdb=" H   THR B 492 "
     model   vdw
     1.602 2.450
  ... (remaining 348142 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     53.440
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
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      :  0.002   0.027  12344  Z= 0.155
  Angle     :  0.484   6.029  16635  Z= 0.258
  Chirality :  0.036   0.146   1826
  Planarity :  0.003   0.052   2127
  Dihedral  : 16.657  86.490   4693
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.60 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.42 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.22), residues: 1502
  helix:  1.97 (0.20), residues: 704
  sheet: -1.26 (0.39), residues: 153
  loop : -0.24 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 309 
 HIS   0.002   0.001   HIS B 561 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.009   0.001   TYR B 556 
 ARG   0.004   0.000   ARG C 211 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 MET cc_start: 0.6205 (pmm) cc_final: 0.5571 (pmm)
REVERT: A  580 SER cc_start: 0.7807 (m) cc_final: 0.7323 (p)
REVERT: C  117 TYR cc_start: 0.6303 (m-80) cc_final: 0.5895 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.5600
  time to fit residues: 159.9189
Evaluate side-chains
  194 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 2.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 102 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.170226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.134576 restraints weight = 47032.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.39
r_work: 0.3519 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12344  Z= 0.417
  Angle     :  0.583   6.387  16635  Z= 0.315
  Chirality :  0.042   0.158   1826
  Planarity :  0.005   0.061   2127
  Dihedral  :  4.152  29.207   1643
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.79 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.76 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.21), residues: 1502
  helix:  1.26 (0.19), residues: 702
  sheet: -1.32 (0.39), residues: 150
  loop : -0.63 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 309 
 HIS   0.004   0.001   HIS C 235 
 PHE   0.021   0.002   PHE A 709 
 TYR   0.020   0.002   TYR A 313 
 ARG   0.004   0.000   ARG B 151 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ILE cc_start: 0.8750 (mp) cc_final: 0.8377 (mm)
REVERT: A  545 PHE cc_start: 0.8130 (m-80) cc_final: 0.7399 (m-80)
REVERT: A  580 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7385 (p)
REVERT: B  246 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8556 (tp)
REVERT: B  437 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.8832 (p90)
REVERT: B  572 MET cc_start: 0.6310 (mmm) cc_final: 0.5209 (mmm)
REVERT: C  245 ILE cc_start: 0.8082 (mt) cc_final: 0.7784 (mp)
  outliers start: 30
  outliers final: 19
  residues processed: 227
  average time/residue: 0.5541
  time to fit residues: 184.9721
Evaluate side-chains
  223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 2.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   36 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  437 TRP
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
B 136 ASN
C 102 ASN
C 129 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.173517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.138247 restraints weight = 46364.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.37
r_work: 0.3565 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12344  Z= 0.181
  Angle     :  0.489   5.735  16635  Z= 0.257
  Chirality :  0.037   0.160   1826
  Planarity :  0.004   0.057   2127
  Dihedral  :  3.930  27.336   1643
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.93 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.82 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.22), residues: 1502
  helix:  1.64 (0.20), residues: 690
  sheet: -1.25 (0.38), residues: 157
  loop : -0.43 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 437 
 HIS   0.002   0.000   HIS A 462 
 PHE   0.011   0.001   PHE A 442 
 TYR   0.011   0.001   TYR A 313 
 ARG   0.002   0.000   ARG C 144 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 1.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ILE cc_start: 0.8692 (mp) cc_final: 0.8351 (mm)
REVERT: A  473 MET cc_start: 0.6290 (pmm) cc_final: 0.5784 (pmm)
REVERT: A  545 PHE cc_start: 0.8026 (m-80) cc_final: 0.7379 (m-80)
REVERT: A  580 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7253 (p)
REVERT: B   41 ASP cc_start: 0.7461 (m-30) cc_final: 0.7259 (m-30)
REVERT: B  246 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (tp)
REVERT: B  437 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.8809 (p90)
REVERT: B  572 MET cc_start: 0.6195 (mmm) cc_final: 0.5222 (mmm)
REVERT: C  211 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6997 (tpp-160)
  outliers start: 20
  outliers final: 12
  residues processed: 223
  average time/residue: 0.5440
  time to fit residues: 179.4245
Evaluate side-chains
  218 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  437 TRP
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 148 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.171525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136318 restraints weight = 47127.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.39
r_work: 0.3538 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12344  Z= 0.241
  Angle     :  0.501   5.619  16635  Z= 0.264
  Chirality :  0.038   0.157   1826
  Planarity :  0.004   0.058   2127
  Dihedral  :  3.971  29.484   1643
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.26 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.14 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.22), residues: 1502
  helix:  1.57 (0.20), residues: 696
  sheet: -1.17 (0.39), residues: 155
  loop : -0.52 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 437 
 HIS   0.002   0.001   HIS C 235 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.017   0.001   TYR A 313 
 ARG   0.002   0.000   ARG A 540 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 201
  time to evaluate  : 1.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8412 (mtmm)
REVERT: A  323 ILE cc_start: 0.8686 (mp) cc_final: 0.8335 (mm)
REVERT: A  473 MET cc_start: 0.6359 (pmm) cc_final: 0.5942 (pmm)
REVERT: A  545 PHE cc_start: 0.8050 (m-80) cc_final: 0.7365 (m-80)
REVERT: A  580 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7318 (p)
REVERT: B  239 ARG cc_start: 0.4791 (OUTLIER) cc_final: 0.4563 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8509 (tp)
REVERT: B  705 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5905 (ttt180)
REVERT: C  101 TRP cc_start: 0.3787 (t-100) cc_final: 0.3420 (t-100)
  outliers start: 27
  outliers final: 16
  residues processed: 220
  average time/residue: 0.5783
  time to fit residues: 184.6610
Evaluate side-chains
  219 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 2.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain B residue  705 ARG
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 135 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.171756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.136955 restraints weight = 46767.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.37
r_work: 0.3558 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12344  Z= 0.175
  Angle     :  0.480   6.624  16635  Z= 0.251
  Chirality :  0.037   0.157   1826
  Planarity :  0.004   0.055   2127
  Dihedral  :  3.901  27.794   1643
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.60 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.37 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1502
  helix:  1.70 (0.20), residues: 690
  sheet: -1.27 (0.38), residues: 146
  loop : -0.43 (0.24), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 437 
 HIS   0.003   0.000   HIS C 235 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.013   0.001   TYR A 313 
 ARG   0.002   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 204
  time to evaluate  : 2.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8427 (mtmm)
REVERT: A  323 ILE cc_start: 0.8692 (mp) cc_final: 0.8335 (mm)
REVERT: A  360 ASN cc_start: 0.8052 (t0) cc_final: 0.7831 (t0)
REVERT: A  468 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7369 (mp0)
REVERT: A  473 MET cc_start: 0.6371 (pmm) cc_final: 0.5964 (pmm)
REVERT: A  545 PHE cc_start: 0.8040 (m-80) cc_final: 0.7416 (m-80)
REVERT: A  580 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7251 (p)
REVERT: B  239 ARG cc_start: 0.4810 (OUTLIER) cc_final: 0.4564 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8499 (tp)
REVERT: C  101 TRP cc_start: 0.3800 (t-100) cc_final: 0.3401 (t-100)
  outliers start: 26
  outliers final: 19
  residues processed: 224
  average time/residue: 0.5741
  time to fit residues: 187.8520
Evaluate side-chains
  220 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 1.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.173243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138038 restraints weight = 46708.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.38
r_work: 0.3561 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12344  Z= 0.173
  Angle     :  0.473   5.376  16635  Z= 0.247
  Chirality :  0.037   0.156   1826
  Planarity :  0.004   0.053   2127
  Dihedral  :  3.857  29.094   1643
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.99 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.07 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.22), residues: 1502
  helix:  1.70 (0.20), residues: 703
  sheet: -1.24 (0.38), residues: 145
  loop : -0.46 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 437 
 HIS   0.002   0.000   HIS C 235 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.012   0.001   TYR A 313 
 ARG   0.003   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 1.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8462 (mtmm)
REVERT: A  323 ILE cc_start: 0.8713 (mp) cc_final: 0.8361 (mm)
REVERT: A  468 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7370 (mp0)
REVERT: A  473 MET cc_start: 0.6364 (pmm) cc_final: 0.5986 (pmm)
REVERT: A  545 PHE cc_start: 0.8043 (m-80) cc_final: 0.7450 (m-80)
REVERT: A  580 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7383 (p)
REVERT: B  239 ARG cc_start: 0.4854 (OUTLIER) cc_final: 0.4624 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8487 (tp)
REVERT: C  101 TRP cc_start: 0.3697 (t-100) cc_final: 0.3366 (t-100)
  outliers start: 25
  outliers final: 19
  residues processed: 218
  average time/residue: 0.5813
  time to fit residues: 188.2199
Evaluate side-chains
  216 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 193
  time to evaluate  : 1.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  576 CYS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.170385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.134971 restraints weight = 47052.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.41
r_work: 0.3530 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12344  Z= 0.255
  Angle     :  0.507   6.831  16635  Z= 0.266
  Chirality :  0.038   0.157   1826
  Planarity :  0.004   0.056   2127
  Dihedral  :  3.974  28.282   1643
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.59 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.05 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.22), residues: 1502
  helix:  1.58 (0.20), residues: 696
  sheet: -1.28 (0.38), residues: 145
  loop : -0.51 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 437 
 HIS   0.004   0.001   HIS C 235 
 PHE   0.013   0.001   PHE A 709 
 TYR   0.015   0.001   TYR A 313 
 ARG   0.002   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 1.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8456 (mtmm)
REVERT: A  323 ILE cc_start: 0.8687 (mp) cc_final: 0.8326 (mm)
REVERT: A  473 MET cc_start: 0.6383 (pmm) cc_final: 0.6064 (pmm)
REVERT: A  545 PHE cc_start: 0.8167 (m-80) cc_final: 0.7466 (m-80)
REVERT: A  580 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7399 (p)
REVERT: B  239 ARG cc_start: 0.4890 (OUTLIER) cc_final: 0.4638 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8500 (tp)
REVERT: C  101 TRP cc_start: 0.3743 (t-100) cc_final: 0.3440 (t-100)
  outliers start: 27
  outliers final: 22
  residues processed: 217
  average time/residue: 0.5584
  time to fit residues: 177.0781
Evaluate side-chains
  222 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 1.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  576 CYS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.171628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136440 restraints weight = 46538.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.39
r_work: 0.3543 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12344  Z= 0.207
  Angle     :  0.491   5.247  16635  Z= 0.256
  Chirality :  0.038   0.157   1826
  Planarity :  0.004   0.054   2127
  Dihedral  :  3.952  29.397   1643
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.26 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.97 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1502
  helix:  1.58 (0.20), residues: 705
  sheet: -1.23 (0.38), residues: 146
  loop : -0.52 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 437 
 HIS   0.004   0.001   HIS B 745 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.013   0.001   TYR A 313 
 ARG   0.003   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 1.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8452 (mtmm)
REVERT: A  468 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7411 (mp0)
REVERT: A  473 MET cc_start: 0.6428 (pmm) cc_final: 0.6083 (pmm)
REVERT: A  545 PHE cc_start: 0.8165 (m-80) cc_final: 0.7480 (m-80)
REVERT: A  580 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7373 (p)
REVERT: B  239 ARG cc_start: 0.4874 (OUTLIER) cc_final: 0.4639 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8481 (tp)
REVERT: C  101 TRP cc_start: 0.3671 (t-100) cc_final: 0.3359 (t-100)
REVERT: C  211 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6755 (ttm-80)
  outliers start: 30
  outliers final: 25
  residues processed: 217
  average time/residue: 0.5611
  time to fit residues: 180.3197
Evaluate side-chains
  223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 1.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  576 CYS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue   51 TRP
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 126 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 135 optimal weight:    0.0670
   overall best weight:    0.9122

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

Flipped N/Q/H residues before XYZ refinement:
** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.170948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136406 restraints weight = 46752.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.36
r_work: 0.3547 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12344  Z= 0.187
  Angle     :  0.483   5.405  16635  Z= 0.252
  Chirality :  0.037   0.156   1826
  Planarity :  0.004   0.053   2127
  Dihedral  :  3.904  27.469   1643
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.19 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.57 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.22), residues: 1502
  helix:  1.63 (0.20), residues: 705
  sheet: -1.20 (0.38), residues: 146
  loop : -0.50 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 437 
 HIS   0.002   0.001   HIS C 235 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.011   0.001   TYR B 466 
 ARG   0.003   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 2.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8462 (mtmm)
REVERT: A  323 ILE cc_start: 0.8684 (mp) cc_final: 0.8299 (mm)
REVERT: A  360 ASN cc_start: 0.8196 (t0) cc_final: 0.7733 (p0)
REVERT: A  468 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7413 (mp0)
REVERT: A  545 PHE cc_start: 0.8141 (m-80) cc_final: 0.7483 (m-80)
REVERT: A  580 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7415 (p)
REVERT: B  226 THR cc_start: 0.8351 (t) cc_final: 0.8097 (p)
REVERT: B  239 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.4680 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8485 (tp)
REVERT: B  298 ILE cc_start: 0.8575 (mp) cc_final: 0.8219 (tt)
REVERT: C  101 TRP cc_start: 0.3646 (t-100) cc_final: 0.3345 (t-100)
REVERT: C  211 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6766 (ttm-80)
  outliers start: 27
  outliers final: 22
  residues processed: 214
  average time/residue: 0.5802
  time to fit residues: 180.6637
Evaluate side-chains
  221 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 1.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  576 CYS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue   51 TRP
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 137 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 140 optimal weight:    0.0770
   chunk 127 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.171865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.136897 restraints weight = 46769.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.36
r_work: 0.3546 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12344  Z= 0.197
  Angle     :  0.487   5.054  16635  Z= 0.254
  Chirality :  0.038   0.156   1826
  Planarity :  0.004   0.053   2127
  Dihedral  :  3.903  29.588   1643
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.19 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.65 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.22), residues: 1502
  helix:  1.62 (0.20), residues: 705
  sheet: -1.21 (0.38), residues: 146
  loop : -0.52 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 437 
 HIS   0.003   0.001   HIS C 235 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.012   0.001   TYR B 466 
 ARG   0.003   0.000   ARG C 185 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 2.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8474 (mtmm)
REVERT: A  323 ILE cc_start: 0.8711 (mp) cc_final: 0.8333 (mm)
REVERT: A  360 ASN cc_start: 0.8186 (t0) cc_final: 0.7771 (p0)
REVERT: A  468 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7440 (mp0)
REVERT: A  545 PHE cc_start: 0.8162 (m-80) cc_final: 0.7467 (m-80)
REVERT: A  550 GLU cc_start: 0.6348 (tt0) cc_final: 0.5741 (pm20)
REVERT: A  580 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7477 (p)
REVERT: B  226 THR cc_start: 0.8347 (t) cc_final: 0.8096 (p)
REVERT: B  239 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.4721 (ptp-170)
REVERT: B  246 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8468 (tp)
REVERT: B  298 ILE cc_start: 0.8600 (mp) cc_final: 0.8267 (tt)
REVERT: C   49 MET cc_start: 0.6799 (tpp) cc_final: 0.5987 (mmm)
REVERT: C  101 TRP cc_start: 0.3587 (t-100) cc_final: 0.3209 (t-100)
REVERT: C  211 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6805 (ttm-80)
  outliers start: 27
  outliers final: 23
  residues processed: 214
  average time/residue: 0.5787
  time to fit residues: 180.0007
Evaluate side-chains
  223 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 1.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  576 CYS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  246 ILE
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  337 CYS
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  660 SER
Chi-restraints excluded: chain C residue   51 TRP
Chi-restraints excluded: chain C residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 134 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 131 optimal weight:    8.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.171768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.136652 restraints weight = 46691.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.39
r_work: 0.3542 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12344  Z= 0.201
  Angle     :  0.488   5.554  16635  Z= 0.255
  Chirality :  0.038   0.156   1826
  Planarity :  0.004   0.053   2127
  Dihedral  :  3.887  26.910   1643
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.13 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.42 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.22), residues: 1502
  helix:  1.59 (0.20), residues: 705
  sheet: -1.21 (0.38), residues: 146
  loop : -0.52 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 437 
 HIS   0.003   0.001   HIS C 235 
 PHE   0.013   0.001   PHE A 442 
 TYR   0.012   0.001   TYR B 466 
 ARG   0.003   0.000   ARG C 185 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12496.88 seconds
wall clock time: 227 minutes 29.09 seconds (13649.09 seconds total)