Starting phenix.real_space_refine
on Tue Feb 11 10:37:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctg_26989/02_2025/8ctg_26989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctg_26989/02_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_26989/02_2025/8ctg_26989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctg_26989/02_2025/8ctg_26989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctg_26989/02_2025/8ctg_26989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctg_26989/02_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-5592/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: 4.47, per 1000 atoms: 0.88
  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: 1.56
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.91
  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: 1.99

  Time building geometry restraints manager: 1.71 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:             2.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.270
  Find NCS groups from input model:        0.060
  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:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.780
-------------------------------------------------------------------------------
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   5134  Z= 0.292
  Angle     :  0.978   8.505   7138  Z= 0.582
  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 

*********************** 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  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0607
  time to fit residues: 4.6888
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  : 0.663 
-------------------------------------------------------------------------------
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 = 0.223413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.207065 restraints weight = 18426.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.208872 restraints weight = 14448.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.210134 restraints weight = 11578.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4762 r_free = 0.4762    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 = 0.4746 r_free = 0.4746    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      157 |
|-----------------------------------------------------------------------------|
r_final: 0.4746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3519
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5134  Z= 0.234
  Angle     :  0.666   7.626   7138  Z= 0.371
  Chirality :  0.045   0.165    931
  Planarity :  0.005   0.055   1040
  Dihedral  :  6.153  56.242   1016
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.14
  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: -2.07 (0.25), residues: 994
  helix:  0.63 (0.41), residues: 173
  sheet: -1.30 (0.29), residues: 253
  loop : -2.13 (0.23), residues: 568

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 

*********************** 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  : 0.493 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0532
  time to fit residues: 3.3204
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  : 0.507 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4877 r_free = 0.4877 target = 0.218640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.202232 restraints weight = 18950.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.203961 restraints weight = 14775.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.205221 restraints weight = 11901.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.4706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4706 r_free = 0.4706    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      157 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4702 r_free = 0.4702    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      175 |
|-----------------------------------------------------------------------------|
r_final: 0.4702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3678
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5134  Z= 0.175
  Angle     :  0.577   5.944   7138  Z= 0.318
  Chirality :  0.044   0.138    931
  Planarity :  0.005   0.071   1040
  Dihedral  :  5.325  55.163   1014
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.34 %
    Favored  : 92.45 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.25), residues: 994
  helix:  1.39 (0.41), residues: 175
  sheet: -0.71 (0.32), residues: 234
  loop : -1.96 (0.23), residues: 585

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 

*********************** 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  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.1107 (OUTLIER) cc_final: 0.0618 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0559
  time to fit residues: 3.6264
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  : 0.544 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 21 optimal weight:   30.0000
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 = 0.4741 r_free = 0.4741 target = 0.206275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.189141 restraints weight = 18776.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.190730 restraints weight = 14979.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.191974 restraints weight = 12233.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.4563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4563 r_free = 0.4563    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      175 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4562 r_free = 0.4562    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      172 |
|-----------------------------------------------------------------------------|
r_final: 0.4562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4369
moved from start:          0.6245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.106   5134  Z= 0.472
  Angle     :  0.989   9.873   7138  Z= 0.581
  Chirality :  0.051   0.195    931
  Planarity :  0.008   0.067   1040
  Dihedral  :  8.878  54.965   1014
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 13.48 %
    Favored  : 86.12 %
  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 : 0.21 %

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: -3.33 (0.23), residues: 994
  helix: -1.02 (0.35), residues: 170
  sheet: -1.31 (0.34), residues: 197
  loop : -3.06 (0.21), residues: 627

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 

*********************** 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
  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: 0.0914 (OUTLIER) cc_final: 0.0591 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0519
  time to fit residues: 3.3223
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  : 0.505 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0010
   chunk 37 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    0.6986

-------------------------------------------------------------------------------
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 = 0.4783 r_free = 0.4783 target = 0.210039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.192943 restraints weight = 18542.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.194632 restraints weight = 14678.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.195989 restraints weight = 11956.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.4611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4611 r_free = 0.4611    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      172 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4610 r_free = 0.4610    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
r_final: 0.4610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4153
moved from start:          0.6031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5134  Z= 0.199
  Angle     :  0.628   5.699   7138  Z= 0.356
  Chirality :  0.045   0.139    931
  Planarity :  0.006   0.051   1040
  Dihedral  :  6.582  51.560   1014
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.76 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.34 %
    Favored  : 86.21 %
  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: -2.95 (0.24), residues: 994
  helix: -0.07 (0.38), residues: 180
  sheet: -1.37 (0.33), residues: 222
  loop : -2.98 (0.22), residues: 592

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 

*********************** 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  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: B  320 CYS cc_start: 0.0590 (OUTLIER) cc_final: 0.0241 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0554
  time to fit residues: 3.3067
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  : 0.564 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 67 optimal weight:    0.0670
   chunk 6 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.3924

-------------------------------------------------------------------------------
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 = 0.4716 r_free = 0.4716 target = 0.203770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.188343 restraints weight = 18384.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.188896 restraints weight = 15101.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.189733 restraints weight = 13458.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.4541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4541 r_free = 0.4541    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4541 r_free = 0.4541    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      177 |
|-----------------------------------------------------------------------------|
r_final: 0.4541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4435
moved from start:          0.7591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   5134  Z= 0.383
  Angle     :  0.853   6.984   7138  Z= 0.503
  Chirality :  0.048   0.143    931
  Planarity :  0.007   0.072   1040
  Dihedral  :  8.192  59.875   1014
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 15.59 %
    Favored  : 83.90 %
  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 : 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: -3.63 (0.23), residues: 994
  helix: -1.10 (0.35), residues: 177
  sheet: -1.76 (0.33), residues: 203
  loop : -3.24 (0.21), residues: 614

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 

*********************** 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  : 0.496 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0539
  time to fit residues: 3.4276
Evaluate side-chains
  24 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 67 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0070
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 21 optimal weight:   30.0000
   overall best weight:    2.2402

-------------------------------------------------------------------------------
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 = 0.4729 r_free = 0.4729 target = 0.203866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.188693 restraints weight = 18115.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.189150 restraints weight = 15565.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.189899 restraints weight = 13347.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4547 r_free = 0.4547    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      177 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4547 r_free = 0.4547    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      187 |
|-----------------------------------------------------------------------------|
r_final: 0.4547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4392
moved from start:          0.8125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   5134  Z= 0.357
  Angle     :  0.819  10.608   7138  Z= 0.472
  Chirality :  0.046   0.156    931
  Planarity :  0.007   0.080   1040
  Dihedral  :  7.815  55.254   1014
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.98 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.34 %
    Favored  : 86.21 %
  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: -3.83 (0.23), residues: 994
  helix: -1.41 (0.33), residues: 194
  sheet: -2.15 (0.31), residues: 205
  loop : -3.25 (0.22), residues: 595

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 

*********************** 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  : 0.431 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0564
  time to fit residues: 3.3737
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  : 0.567 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   overall best weight:    1.8384

-------------------------------------------------------------------------------
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 = 0.4737 r_free = 0.4737 target = 0.203772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.188545 restraints weight = 18020.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.188592 restraints weight = 16039.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.189732 restraints weight = 14083.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4556 r_free = 0.4556    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      187 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4555 r_free = 0.4555    target_work(ls_wunit_k1) = 0.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
r_final: 0.4555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4402
moved from start:          0.8834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   5134  Z= 0.325
  Angle     :  0.754   7.446   7138  Z= 0.432
  Chirality :  0.046   0.138    931
  Planarity :  0.006   0.071   1040
  Dihedral  :  7.444  54.851   1014
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 16.60 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.34 %
    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: -3.81 (0.23), residues: 994
  helix: -1.03 (0.35), residues: 194
  sheet: -2.29 (0.32), residues: 200
  loop : -3.30 (0.22), residues: 600

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 

*********************** 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
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0531
  time to fit residues: 3.3994
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  : 0.502 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   chunk 80 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 27 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0060
   chunk 43 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.0998

-------------------------------------------------------------------------------
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 = 0.4753 r_free = 0.4753 target = 0.205166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.189845 restraints weight = 17990.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.189993 restraints weight = 15623.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.190967 restraints weight = 13792.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.4568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4568 r_free = 0.4568    target_work(ls_wunit_k1) = 0.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4568 r_free = 0.4568    target_work(ls_wunit_k1) = 0.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
r_final: 0.4568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4330
moved from start:          0.8880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5134  Z= 0.227
  Angle     :  0.655   7.030   7138  Z= 0.369
  Chirality :  0.045   0.136    931
  Planarity :  0.005   0.066   1040
  Dihedral  :  6.738  51.901   1014
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.17 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.34 %
    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: -3.56 (0.24), residues: 994
  helix: -0.66 (0.36), residues: 192
  sheet: -2.19 (0.33), residues: 203
  loop : -3.18 (0.22), residues: 599

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 

*********************** 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
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0539
  time to fit residues: 3.4450
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  : 0.552 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 52 optimal weight:    0.0030
   chunk 98 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0980
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0050
   overall best weight:    0.3206

-------------------------------------------------------------------------------
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 = 0.4790 r_free = 0.4790 target = 0.208486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.191738 restraints weight = 18379.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.193319 restraints weight = 14554.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.194370 restraints weight = 11844.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4602 r_free = 0.4602    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4601 r_free = 0.4601    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      187 |
|-----------------------------------------------------------------------------|
r_final: 0.4601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4187
moved from start:          0.8738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   5134  Z= 0.174
  Angle     :  0.564   6.596   7138  Z= 0.309
  Chirality :  0.044   0.126    931
  Planarity :  0.005   0.058   1040
  Dihedral  :  5.630  43.461   1014
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.86 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.49 %
    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: -3.01 (0.25), residues: 994
  helix:  0.30 (0.39), residues: 187
  sheet: -1.96 (0.32), residues: 225
  loop : -2.94 (0.23), residues: 582

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 

********************** 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
  27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.651 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0506
  time to fit residues: 3.2253
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  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain B residue  328 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:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 29 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.4756 r_free = 0.4756 target = 0.205238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.189606 restraints weight = 18343.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.190334 restraints weight = 16548.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.191498 restraints weight = 14008.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4572 r_free = 0.4572    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      187 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4572 r_free = 0.4572    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      182 |
|-----------------------------------------------------------------------------|
r_final: 0.4572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4280
moved from start:          0.9068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   5134  Z= 0.278
  Angle     :  0.712  21.718   7138  Z= 0.393
  Chirality :  0.045   0.183    931
  Planarity :  0.005   0.057   1040
  Dihedral  :  6.358  51.712   1014
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.59 %
    Favored  : 84.10 %
  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: -3.14 (0.25), residues: 994
  helix: -0.10 (0.38), residues: 192
  sheet: -1.97 (0.33), residues: 213
  loop : -2.97 (0.23), residues: 589

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 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1952.31 seconds
wall clock time: 35 minutes 16.31 seconds (2116.31 seconds total)