Starting phenix.real_space_refine
on Thu Jun  5 05:29:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctg_26989/06_2025/8ctg_26989.cif"
  }
  resolution = 3.8
  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=   0.002 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    3041      2.51       5
     N    1006      2.21       5
     O    1008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5100
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 618
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 343
          Unresolved non-hydrogen angles: 440
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 222
    Chain: "B"
      Number of atoms: 1585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 1585
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 241}
          Link IDs: {'PTRANS': 4, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 908
          Unresolved non-hydrogen angles: 1156
          Unresolved non-hydrogen dihedrals: 769
          Unresolved non-hydrogen chiralities: 70
          Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 14, 'TYR:plan': 5, 'ASN:plan1': 18, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 21, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 541
    Chain: "C"
      Number of atoms: 2880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 2880
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 456}
          Link IDs: {'PTRANS': 24, 'TRANS': 547}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1778
          Unresolved non-hydrogen angles: 2320
          Unresolved non-hydrogen dihedrals: 1490
          Unresolved non-hydrogen chiralities: 166
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 12, 'TYR:plan': 21, 'ASN:plan1': 22, 'TRP:plan': 19, 'ASP:plan': 51, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 37}
          Unresolved non-hydrogen planarities: 1084
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 69
    residue:
      pdb=" N   LEU A  97 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU A  97 " occ=0.20
    residue:
      pdb=" N   GLU A  98 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLU A  98 " occ=0.20
    residue:
      pdb=" N   ASP A  99 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  ASP A  99 " occ=0.20
    residue:
      pdb=" N   TYR A 100 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  TYR A 100 " occ=0.20
    residue:
      pdb=" N   LYS A 101 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LYS A 101 " occ=0.20
    residue:
      pdb=" N   PRO B  67 " occ=0.20
      ... (5 atoms not shown)
      pdb=" CD  PRO B  67 " occ=0.20
    residue:
      pdb=" N   GLU B  68 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLU B  68 " occ=0.20
    residue:
      pdb=" N   SER B  69 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  SER B  69 " occ=0.20
    residue:
      pdb=" N   THR B  70 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  THR B  70 " occ=0.20
    residue:
      pdb=" N   LEU B  71 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU B  71 " occ=0.20
    residue:
      pdb=" N   GLN B  72 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  GLN B  72 " occ=0.20
    residue:
      pdb=" N   LEU B  73 " occ=0.20
      ... (3 atoms not shown)
      pdb=" CB  LEU B  73 " occ=0.20
    ... (remaining 57 not shown)
  Time building chain proxies: 4.74, per 1000 atoms: 0.93
  Number of scatterers: 5100
  At special positions: 0
  Unit cell: (69.0201, 97.9915, 134.632, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1008      8.00
     N    1006      7.00
     C    3041      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  80 " - pdb=" SG  CYS A 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 135 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 105 " - pdb=" SG  CYS B 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 115 " - pdb=" SG  CYS B 133 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 181 " - pdb=" SG  CYS B 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 183 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 260 " - pdb=" SG  CYS B 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 295 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 328 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 315 " - pdb=" SG  CYS B 325 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 320 " - pdb=" SG  CYS B 321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 286 " - pdb=" SG  CYS C 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 293 " - pdb=" SG  CYS C 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 310 " - pdb=" SG  CYS C 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 592 " - pdb=" SG  CYS C 603 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 599 " - pdb=" SG  CYS C 612 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1862

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 19 sheets defined
      22.1% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 44
    Processing helix  chain 'A' and resid 61 through 70
    Processing helix  chain 'A' and resid 72 through 79
    Processing helix  chain 'A' and resid 81 through 93
      removed outlier: 4.538A  pdb=" N   LYS A  85 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   PHE A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 125
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 130 through 134
      removed outlier: 3.511A  pdb=" N   ARG A 134 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 59
      removed outlier: 3.581A  pdb=" N   SER B  41 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   SER B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 76
    Processing helix  chain 'B' and resid 83 through 107
      removed outlier: 3.789A  pdb=" N   SER B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE B  88 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 5.995A  pdb=" N   ASN B 112 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 152
      removed outlier: 3.740A  pdb=" N   GLY B 150 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 176
    Processing helix  chain 'B' and resid 185 through 189
    Processing helix  chain 'B' and resid 201 through 215
      removed outlier: 3.521A  pdb=" N   ILE B 205 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 242
    Processing helix  chain 'B' and resid 284 through 295
      removed outlier: 4.118A  pdb=" N   CYS B 291 " --> pdb=" O   GLU B 287 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LYS B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'C' and resid 275 through 279
    Processing helix  chain 'C' and resid 289 through 293
    Processing helix  chain 'C' and resid 590 through 599
      removed outlier: 4.417A  pdb=" N   GLU C 595 " --> pdb=" O   CYS C 592 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ASN C 596 " --> pdb=" O   ALA C 593 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37
    Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 125
      removed outlier: 6.479A  pdb=" N   ILE B 123 " --> pdb=" O   TRP B 130 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TRP B 130 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY B 125 " --> pdb=" O   TRP B 128 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 129 " --> pdb=" O   CYS B 195 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   LEU B 197 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263
    Processing sheet with id=AA4, first strand: chain 'B' and resid 275 through 276
    Processing sheet with id=AA5, first strand: chain 'B' and resid 310 through 311
    Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 34
      removed outlier: 3.840A  pdb=" N   ARG C  32 " --> pdb=" O   TYR C  25 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 59
      removed outlier: 6.176A  pdb=" N   SER C  68 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL C  56 " --> pdb=" O   TYR C  66 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TYR C  66 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE C  58 " --> pdb=" O   LEU C  64 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU C  64 " --> pdb=" O   PHE C  58 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ILE C  75 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 103
      removed outlier: 3.647A  pdb=" N   GLY C  99 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG C 118 " --> pdb=" O   ASP C 113 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE C 119 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 140 through 146
      removed outlier: 4.665A  pdb=" N   ALA C 142 " --> pdb=" O   THR C 155 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE C 163 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190
      removed outlier: 5.200A  pdb=" N   GLY C 186 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA C 199 " --> pdb=" O   GLY C 186 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE C 206 " --> pdb=" O   GLN C 217 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 230 through 232
      removed outlier: 3.669A  pdb=" N   THR C 231 " --> pdb=" O   TYR C 238 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR C 238 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE C 247 " --> pdb=" O   ILE C 261 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 299
    Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 353
      removed outlier: 3.539A  pdb=" N   ILE C 342 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU C 330 " --> pdb=" O   THR C 581 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR C 581 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU C 332 " --> pdb=" O   LYS C 579 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LYS C 579 " --> pdb=" O   LEU C 332 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY C 577 " --> pdb=" O   ALA C 334 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 368
      removed outlier: 4.219A  pdb=" N   ALA C 364 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE C 384 " --> pdb=" O   VAL C 397 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 411
      removed outlier: 6.593A  pdb=" N   ILE C 427 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 448 through 454
      removed outlier: 4.753A  pdb=" N   ALA C 450 " --> pdb=" O   THR C 463 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ILE C 471 " --> pdb=" O   LEU C 484 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 498
      removed outlier: 3.532A  pdb=" N   GLY C 494 " --> pdb=" O   GLY C 507 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS C 513 " --> pdb=" O   ASP C 508 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ILE C 514 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 539 through 541
      removed outlier: 3.657A  pdb=" N   TYR C 544 " --> pdb=" O   LEU C 541 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ARG C 557 " --> pdb=" O   VAL C 567 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   VAL C 567 " --> pdb=" O   ARG C 557 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   HIS C 559 " --> pdb=" O   ARG C 565 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ARG C 565 " --> pdb=" O   HIS C 559 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 602 through 606

    286 hydrogen bonds defined for protein.
    702 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.16

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 1888
        1.34 -     1.47: 1123
        1.47 -     1.60: 2078
        1.60 -     1.74: 0
        1.74 -     1.87: 45
  Bond restraints: 5134
  Sorted by residual:
  bond pdb=" C   LYS C 303 "
       pdb=" N   PRO C 304 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 2.34e-02 1.83e+03 7.19e+00
  bond pdb=" C1  PAM B 401 "
       pdb=" O1  PAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.250  1.202  0.048 2.00e-02 2.50e+03 5.86e+00
  bond pdb=" CB  CYS B 321 "
       pdb=" SG  CYS B 321 "
    ideal  model  delta    sigma   weight residual
    1.808  1.873 -0.065 3.30e-02 9.18e+02 3.88e+00
  bond pdb=" CB  SER B 187 "
       pdb=" OG  SER B 187 "
    ideal  model  delta    sigma   weight residual
    1.417  1.451 -0.034 2.00e-02 2.50e+03 2.82e+00
  bond pdb=" C1  PAM B 401 "
       pdb=" C2  PAM B 401 "
    ideal  model  delta    sigma   weight residual
    1.538  1.504  0.034 2.00e-02 2.50e+03 2.81e+00
  ... (remaining 5129 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 6606
        1.70 -     3.40: 430
        3.40 -     5.10: 84
        5.10 -     6.80: 14
        6.80 -     8.50: 4
  Bond angle restraints: 7138
  Sorted by residual:
  angle pdb=" C   GLY B 114 "
        pdb=" N   CYS B 115 "
        pdb=" CA  CYS B 115 "
      ideal   model   delta    sigma   weight residual
     121.54  129.52   -7.98 1.91e+00 2.74e-01 1.74e+01
  angle pdb=" CA  ARG C 141 "
        pdb=" C   ARG C 141 "
        pdb=" N   ALA C 142 "
      ideal   model   delta    sigma   weight residual
     119.56  117.20    2.36 5.80e-01 2.97e+00 1.65e+01
  angle pdb=" N   VAL C 381 "
        pdb=" CA  VAL C 381 "
        pdb=" C   VAL C 381 "
      ideal   model   delta    sigma   weight residual
     112.04  107.30    4.74 1.40e+00 5.10e-01 1.14e+01
  angle pdb=" CA  LYS C 303 "
        pdb=" C   LYS C 303 "
        pdb=" N   PRO C 304 "
      ideal   model   delta    sigma   weight residual
     118.44  123.77   -5.33 1.59e+00 3.96e-01 1.12e+01
  angle pdb=" N   SER C 179 "
        pdb=" CA  SER C 179 "
        pdb=" C   SER C 179 "
      ideal   model   delta    sigma   weight residual
     108.67  113.78   -5.11 1.55e+00 4.16e-01 1.09e+01
  ... (remaining 7133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.04: 2980
       12.04 -    24.08: 84
       24.08 -    36.13: 23
       36.13 -    48.17: 10
       48.17 -    60.21: 10
  Dihedral angle restraints: 3107
    sinusoidal: 245
      harmonic: 2862
  Sorted by residual:
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 328 "
           pdb=" CB  CYS B 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.41   55.59     1      1.00e+01 1.00e-02 4.17e+01
  dihedral pdb=" CB  CYS B 105 "
           pdb=" SG  CYS B 105 "
           pdb=" SG  CYS B 113 "
           pdb=" CB  CYS B 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.59   52.59     1      1.00e+01 1.00e-02 3.77e+01
  dihedral pdb=" CA  CYS B 320 "
           pdb=" C   CYS B 320 "
           pdb=" N   CYS B 321 "
           pdb=" CA  CYS B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.06   20.94     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 3104 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 567
       0.036 -    0.072: 252
       0.072 -    0.108: 73
       0.108 -    0.144: 37
       0.144 -    0.180: 2
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CA  CYS B 321 "
            pdb=" N   CYS B 321 "
            pdb=" C   CYS B 321 "
            pdb=" CB  CYS B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  CYS B 115 "
            pdb=" N   CYS B 115 "
            pdb=" C   CYS B 115 "
            pdb=" CB  CYS B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 928 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 145 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.45e+00
        pdb=" C   LYS B 145 "    0.047 2.00e-02 2.50e+03
        pdb=" O   LYS B 145 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 146 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  72 "    0.012 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   GLN B  72 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLN B  72 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU B  73 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 267 "    0.038 5.00e-02 4.00e+02   5.68e-02 5.16e+00
        pdb=" N   PRO C 268 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 268 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 268 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 582
        2.74 -     3.28: 5035
        3.28 -     3.82: 7526
        3.82 -     4.36: 7462
        4.36 -     4.90: 13462
  Nonbonded interactions: 34067
  Sorted by model distance:
  nonbonded pdb=" O   MET A 122 "
            pdb=" N   PHE A 127 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   LYS B 292 "
            pdb=" N   ASP B 297 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   SER C  96 "
            pdb=" N   SER C 114 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   CYS B 320 "
            pdb=" N   THR B 322 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   TRP C 491 "
            pdb=" N   ALA C 509 "
     model   vdw
     2.342 3.120
  ... (remaining 34062 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=0.20 max=1.00 mean=0.95
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.730
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3443
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   5156  Z= 0.230
  Angle     :  0.992   8.505   7180  Z= 0.587
  Chirality :  0.047   0.180    931
  Planarity :  0.006   0.057   1040
  Dihedral  :  7.618  54.388   1182
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  1.81 %
    Allowed  :  9.66 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  :  8.05 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -3.04 (0.23), residues: 994
  helix: -1.41 (0.35), residues: 170
  sheet: -1.53 (0.30), residues: 238
  loop : -2.51 (0.22), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24769 (  286)
  hydrogen bonds       : angle       8.62775 (  702)
  SS BOND              : bond        0.00410 (   21)
  SS BOND              : angle       2.40563 (   42)
  covalent geometry    : bond        0.00397 ( 5134)
  covalent geometry    : angle       0.97807 ( 7138)
  Misc. bond           : bond        0.04417 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0573
  time to fit residues: 4.5012
Evaluate side-chains
  28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  328 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.2980
   chunk 75 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0570
   chunk 77 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0570
   chunk 47 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0670
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.6956

-------------------------------------------------------------------------------
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 = 0.4923 r_free = 0.4923 target = 0.223428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.206949 restraints weight = 18431.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.208788 restraints weight = 14520.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.210056 restraints weight = 11654.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4761 r_free = 0.4761    target_work(ls_wunit_k1) = 0.209         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4744 r_free = 0.4744    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
r_final: 0.4744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3524
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5156  Z= 0.159
  Angle     :  0.693  12.074   7180  Z= 0.381
  Chirality :  0.045   0.163    931
  Planarity :  0.005   0.055   1040
  Dihedral  :  6.155  56.326   1016
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.94 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.94 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -2.08 (0.25), residues: 994
  helix:  0.63 (0.41), residues: 173
  sheet: -1.34 (0.29), residues: 255
  loop : -2.11 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  286)
  hydrogen bonds       : angle       6.34436 (  702)
  SS BOND              : bond        0.00628 (   21)
  SS BOND              : angle       2.69118 (   42)
  covalent geometry    : bond        0.00308 ( 5134)
  covalent geometry    : angle       0.66405 ( 7138)
  Misc. bond           : bond        0.00132 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0571
  time to fit residues: 3.5911
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  599 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 81 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4859 r_free = 0.4859 target = 0.216775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.200193 restraints weight = 18809.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.201933 restraints weight = 14649.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.203070 restraints weight = 11832.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.4683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4683 r_free = 0.4683    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4679 r_free = 0.4679    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      180 |
|-----------------------------------------------------------------------------|
r_final: 0.4679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3801
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5156  Z= 0.159
  Angle     :  0.642   7.281   7180  Z= 0.353
  Chirality :  0.045   0.140    931
  Planarity :  0.005   0.070   1040
  Dihedral  :  5.766  55.707   1014
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.75 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  :  8.05 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.76 (0.25), residues: 994
  helix:  1.22 (0.41), residues: 175
  sheet: -1.00 (0.31), residues: 241
  loop : -2.10 (0.23), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  286)
  hydrogen bonds       : angle       5.74383 (  702)
  SS BOND              : bond        0.00487 (   21)
  SS BOND              : angle       1.59190 (   42)
  covalent geometry    : bond        0.00279 ( 5134)
  covalent geometry    : angle       0.63172 ( 7138)
  Misc. bond           : bond        0.00181 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.1134 (OUTLIER) cc_final: 0.0618 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0573
  time to fit residues: 3.7771
Evaluate side-chains
  26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  599 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0970
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    0.2980
   chunk 25 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 21 optimal weight:   30.0000
   overall best weight:    2.2782

-------------------------------------------------------------------------------
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 = 0.4757 r_free = 0.4757 target = 0.207714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.192203 restraints weight = 18823.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.192872 restraints weight = 15336.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.193479 restraints weight = 13371.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.4578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4578 r_free = 0.4578    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      180 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4577 r_free = 0.4577    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      175 |
|-----------------------------------------------------------------------------|
r_final: 0.4577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4283
moved from start:          0.6011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   5156  Z= 0.314
  Angle     :  0.906  10.363   7180  Z= 0.523
  Chirality :  0.048   0.186    931
  Planarity :  0.008   0.063   1040
  Dihedral  :  8.177  53.841   1014
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.37 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 11.49 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.08 (0.23), residues: 994
  helix: -0.60 (0.36), residues: 174
  sheet: -1.23 (0.35), residues: 204
  loop : -2.95 (0.21), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06584 (  286)
  hydrogen bonds       : angle       7.87553 (  702)
  SS BOND              : bond        0.01063 (   21)
  SS BOND              : angle       2.90784 (   42)
  covalent geometry    : bond        0.00520 ( 5134)
  covalent geometry    : angle       0.88035 ( 7138)
  Misc. bond           : bond        0.00320 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.2313 (OUTLIER) cc_final: 0.2030 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0581
  time to fit residues: 3.8925
Evaluate side-chains
  28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  599 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 98 optimal weight:    0.0270
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0970
   chunk 97 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   overall best weight:    0.5636

-------------------------------------------------------------------------------
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 = 0.4807 r_free = 0.4807 target = 0.211514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.194550 restraints weight = 18262.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.196057 restraints weight = 14507.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.197193 restraints weight = 11945.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4629 r_free = 0.4629    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      175 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4629 r_free = 0.4629    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4066
moved from start:          0.5874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5156  Z= 0.135
  Angle     :  0.609   5.681   7180  Z= 0.339
  Chirality :  0.045   0.134    931
  Planarity :  0.005   0.058   1040
  Dihedral  :  6.100  52.234   1014
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.24 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.64 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -2.62 (0.25), residues: 994
  helix:  0.23 (0.38), residues: 182
  sheet: -1.09 (0.34), residues: 219
  loop : -2.80 (0.22), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  286)
  hydrogen bonds       : angle       5.98393 (  702)
  SS BOND              : bond        0.00458 (   21)
  SS BOND              : angle       1.72461 (   42)
  covalent geometry    : bond        0.00257 ( 5134)
  covalent geometry    : angle       0.59668 ( 7138)
  Misc. bond           : bond        0.00037 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.1003 (OUTLIER) cc_final: 0.0665 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0575
  time to fit residues: 3.5129
Evaluate side-chains
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  599 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0570
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0670
   chunk 86 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.8240

-------------------------------------------------------------------------------
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 = 0.4751 r_free = 0.4751 target = 0.206405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.191267 restraints weight = 18322.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.191527 restraints weight = 15654.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.192322 restraints weight = 13670.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4567 r_free = 0.4567    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4566 r_free = 0.4566    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4297
moved from start:          0.7075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   5156  Z= 0.252
  Angle     :  0.765   6.055   7180  Z= 0.443
  Chirality :  0.046   0.136    931
  Planarity :  0.007   0.065   1040
  Dihedral  :  7.298  56.334   1014
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 14.69 %
    Favored  : 84.91 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  :  9.20 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.22 (0.24), residues: 994
  helix: -0.62 (0.35), residues: 187
  sheet: -1.53 (0.33), residues: 223
  loop : -3.06 (0.22), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05598 (  286)
  hydrogen bonds       : angle       7.23770 (  702)
  SS BOND              : bond        0.00707 (   21)
  SS BOND              : angle       2.05815 (   42)
  covalent geometry    : bond        0.00430 ( 5134)
  covalent geometry    : angle       0.75039 ( 7138)
  Misc. bond           : bond        0.00131 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.2025 (OUTLIER) cc_final: 0.1817 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0470
  time to fit residues: 3.1661
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  328 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0050
   chunk 30 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0010
   chunk 19 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 21 optimal weight:   30.0000
   overall best weight:    1.1004

-------------------------------------------------------------------------------
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 = 0.4771 r_free = 0.4771 target = 0.207950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.191059 restraints weight = 18259.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.192571 restraints weight = 14690.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.193834 restraints weight = 12035.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4591 r_free = 0.4591    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4591 r_free = 0.4591    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4240
moved from start:          0.7199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5156  Z= 0.162
  Angle     :  0.658  10.996   7180  Z= 0.369
  Chirality :  0.045   0.173    931
  Planarity :  0.006   0.069   1040
  Dihedral  :  6.443  52.003   1014
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.27 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.64 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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: -3.06 (0.24), residues: 994
  helix: -0.37 (0.36), residues: 193
  sheet: -1.61 (0.32), residues: 224
  loop : -2.94 (0.23), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  286)
  hydrogen bonds       : angle       6.39720 (  702)
  SS BOND              : bond        0.00879 (   21)
  SS BOND              : angle       1.86954 (   42)
  covalent geometry    : bond        0.00292 ( 5134)
  covalent geometry    : angle       0.64406 ( 7138)
  Misc. bond           : bond        0.00072 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.0845 (OUTLIER) cc_final: 0.0607 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0531
  time to fit residues: 3.2697
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  328 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 88 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0170
   chunk 25 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   overall best weight:    3.2026

-------------------------------------------------------------------------------
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 = 0.4702 r_free = 0.4702 target = 0.201346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.185283 restraints weight = 17989.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.186047 restraints weight = 17589.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.187475 restraints weight = 13974.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4519 r_free = 0.4519    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4520 r_free = 0.4520    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4507
moved from start:          0.8815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.091   5156  Z= 0.377
  Angle     :  0.978   9.634   7180  Z= 0.572
  Chirality :  0.050   0.199    931
  Planarity :  0.007   0.071   1040
  Dihedral  :  8.796  58.779   1014
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 18.41 %
    Favored  : 81.29 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 10.34 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    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: -3.96 (0.23), residues: 994
  helix: -1.44 (0.35), residues: 173
  sheet: -2.27 (0.32), residues: 196
  loop : -3.30 (0.21), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07642 (  286)
  hydrogen bonds       : angle       8.85963 (  702)
  SS BOND              : bond        0.01111 (   21)
  SS BOND              : angle       2.97669 (   42)
  covalent geometry    : bond        0.00626 ( 5134)
  covalent geometry    : angle       0.95370 ( 7138)
  Misc. bond           : bond        0.00109 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0548
  time to fit residues: 3.4373
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  323 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 96 optimal weight:    0.0980
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.4732 r_free = 0.4732 target = 0.203278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.187446 restraints weight = 17824.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.188171 restraints weight = 14867.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.189660 restraints weight = 12950.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4558 r_free = 0.4558    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4558 r_free = 0.4558    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4422
moved from start:          0.8989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109   5156  Z= 0.265
  Angle     :  0.851  10.937   7180  Z= 0.481
  Chirality :  0.046   0.160    931
  Planarity :  0.006   0.077   1040
  Dihedral  :  7.835  52.255   1014
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 15.69 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.49 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -4.04 (0.23), residues: 994
  helix: -1.45 (0.34), residues: 190
  sheet: -2.49 (0.32), residues: 196
  loop : -3.34 (0.21), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05895 (  286)
  hydrogen bonds       : angle       7.89929 (  702)
  SS BOND              : bond        0.00640 (   21)
  SS BOND              : angle       3.16929 (   42)
  covalent geometry    : bond        0.00481 ( 5134)
  covalent geometry    : angle       0.81815 ( 7138)
  Misc. bond           : bond        0.00096 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0509
  time to fit residues: 3.1475
Evaluate side-chains
  25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  323 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 98 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0030
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 23 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0020
   overall best weight:    0.3398

-------------------------------------------------------------------------------
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 = 0.4788 r_free = 0.4788 target = 0.208419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.193141 restraints weight = 18361.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.193807 restraints weight = 16381.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.195118 restraints weight = 13770.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4617 r_free = 0.4617    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4617 r_free = 0.4617    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4128
moved from start:          0.8716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   5156  Z= 0.131
  Angle     :  0.631   8.941   7180  Z= 0.344
  Chirality :  0.044   0.136    931
  Planarity :  0.005   0.065   1040
  Dihedral  :  6.017  44.019   1014
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.26 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.49 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.40 (0.24), residues: 994
  helix: -0.33 (0.36), residues: 198
  sheet: -2.19 (0.31), residues: 236
  loop : -3.14 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03062 (  286)
  hydrogen bonds       : angle       6.06505 (  702)
  SS BOND              : bond        0.00449 (   21)
  SS BOND              : angle       2.34081 (   42)
  covalent geometry    : bond        0.00275 ( 5134)
  covalent geometry    : angle       0.60710 ( 7138)
  Misc. bond           : bond        0.00066 (    1)

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0547
  time to fit residues: 3.6136
Evaluate side-chains
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain B residue  328 CYS
Chi-restraints excluded: chain C residue  323 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.4745 r_free = 0.4745 target = 0.204374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.188586 restraints weight = 18270.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.188909 restraints weight = 15559.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.190148 restraints weight = 13908.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.4561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4561 r_free = 0.4561    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4561 r_free = 0.4561    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      189 |
|-----------------------------------------------------------------------------|
r_final: 0.4561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4375
moved from start:          0.9119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   5156  Z= 0.206
  Angle     :  0.718   7.075   7180  Z= 0.404
  Chirality :  0.045   0.145    931
  Planarity :  0.006   0.064   1040
  Dihedral  :  6.821  52.689   1014
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 16.30 %
    Favored  : 83.60 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.49 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.48 (0.24), residues: 994
  helix: -0.46 (0.37), residues: 192
  sheet: -2.18 (0.33), residues: 200
  loop : -3.16 (0.22), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  73 
 PHE   0.000   0.000   PHE A  57 
 TYR   0.000   0.000   TYR A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04981 (  286)
  hydrogen bonds       : angle       6.86847 (  702)
  SS BOND              : bond        0.00580 (   21)
  SS BOND              : angle       2.47744 (   42)
  covalent geometry    : bond        0.00373 ( 5134)
  covalent geometry    : angle       0.69476 ( 7138)
  Misc. bond           : bond        0.00047 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2097.46 seconds
wall clock time: 36 minutes 35.90 seconds (2195.90 seconds total)