Starting phenix.real_space_refine
on Thu Jul 31 10:54:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z9q_39867/07_2025/8z9q_39867.cif"
  }
  resolution = 2.33
  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=  -0.000 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      74      5.16       5
     C    7803      2.51       5
     N    2153      2.21       5
     O    2320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12362
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5020
          Classifications: {'peptide': 621}
          Link IDs: {'PTRANS': 31, 'TRANS': 589}
    Chain: "B"
      Number of atoms: 5190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5190
          Classifications: {'peptide': 647}
          Link IDs: {'PTRANS': 33, 'TRANS': 613}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1926
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 16, 'TRANS': 220}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 226
          Unusual residues: {'ATP': 1}
          Classifications: {'RNA': 9, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 5, None: 1}
            Not linked:
              pdbres="ATP D   1 "
              pdbres="  G D   2 "
  Time building chain proxies: 7.24, per 1000 atoms: 0.59
  Number of scatterers: 12362
  At special positions: 0
  Unit cell: (91.104, 100.74, 134.028, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      74     16.00
     P      12     15.00
     O    2320      8.00
     N    2153      7.00
     C    7803      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.72
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2878

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 14 sheets defined
      50.8% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 20
      removed outlier: 4.964A  pdb=" N   THR A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLN A  19 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   GLU A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 47
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 80 through 84
      removed outlier: 4.024A  pdb=" N   THR A  84 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 133
    Processing helix  chain 'A' and resid 134 through 146
    Processing helix  chain 'A' and resid 148 through 155
    Processing helix  chain 'A' and resid 157 through 167
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 246 through 257
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.559A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 305 through 316
      removed outlier: 4.121A  pdb=" N   GLN A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 3.879A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 345 " --> pdb=" O   MET A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.375A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 400
    Processing helix  chain 'A' and resid 485 through 493
      removed outlier: 3.593A  pdb=" N   ASN A 493 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 517
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.458A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 4.052A  pdb=" N   LYS A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 616
    Processing helix  chain 'B' and resid 1 through 5
    Processing helix  chain 'B' and resid 11 through 16
      removed outlier: 3.527A  pdb=" N   THR B  15 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 19
      No H-bonds generated for 'chain 'B' and resid 17 through 19'
    Processing helix  chain 'B' and resid 33 through 47
      Proline residue:  B  44  - end of helix
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 95
    Processing helix  chain 'B' and resid 95 through 108
    Processing helix  chain 'B' and resid 108 through 113
      removed outlier: 3.946A  pdb=" N   LYS B 112 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 121
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 169
    Processing helix  chain 'B' and resid 215 through 225
    Processing helix  chain 'B' and resid 247 through 266
      removed outlier: 4.398A  pdb=" N   GLY B 252 " --> pdb=" O   MET B 248 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   PHE B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 286
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.797A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      Proline residue:  B 338  - end of helix
      removed outlier: 3.541A  pdb=" N   SER B 344 " --> pdb=" O   MET B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 378
      removed outlier: 4.315A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 409
      removed outlier: 3.543A  pdb=" N   SER B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR B 401 " --> pdb=" O   ASN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 449
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 543 through 552
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 587 through 595
    Processing helix  chain 'B' and resid 648 through 662
    Processing helix  chain 'B' and resid 666 through 671
      removed outlier: 3.505A  pdb=" N   VAL B 669 " --> pdb=" O   PHE B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 694
    Processing helix  chain 'B' and resid 698 through 708
      removed outlier: 3.559A  pdb=" N   ARG B 708 " --> pdb=" O   ARG B 704 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 27
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'C' and resid 33 through 36
      removed outlier: 6.158A  pdb=" N   THR C  36 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 33 through 36'
    Processing helix  chain 'C' and resid 37 through 42
    Processing helix  chain 'C' and resid 56 through 63
    Processing helix  chain 'C' and resid 102 through 111
      removed outlier: 3.853A  pdb=" N   LYS C 109 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 126 through 135
    Processing helix  chain 'C' and resid 166 through 176
    Processing helix  chain 'C' and resid 181 through 187
    Processing helix  chain 'C' and resid 191 through 201
      removed outlier: 3.525A  pdb=" N   LYS C 195 " --> pdb=" O   GLY C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 204
      No H-bonds generated for 'chain 'C' and resid 202 through 204'
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.598A  pdb=" N   ILE C 220 " --> pdb=" O   ALA C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 239
      removed outlier: 3.789A  pdb=" N   GLU C 239 " --> pdb=" O   PRO C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 245
      removed outlier: 3.926A  pdb=" N   CYS C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 238
      removed outlier: 4.255A  pdb=" N   ILE A 450 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 423 through 431
    current: chain 'A' and resid 463 through 469
      removed outlier: 6.777A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.345A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 442 through 451
    current: chain 'A' and resid 290 through 291
    Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 531
    Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.502A  pdb=" N   ARG B 131 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230
    Processing sheet with id=AA9, first strand: chain 'B' and resid 380 through 381
    Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 470
    Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 69
      removed outlier: 3.867A  pdb=" N   THR C  97 " --> pdb=" O   MET C  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 143
      removed outlier: 4.900A  pdb=" N   HIS C 252 " --> pdb=" O   GLY C 139 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ILE C 141 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TYR C 250 " --> pdb=" O   ILE C 141 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154
      removed outlier: 3.605A  pdb=" N   LYS C 151 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)

    549 hydrogen bonds defined for protein.
    1533 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: 3.42

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3994
        1.34 -     1.46: 1800
        1.46 -     1.57: 6720
        1.57 -     1.69: 22
        1.69 -     1.81: 120
  Bond restraints: 12656
  Sorted by residual:
  bond pdb=" CB  ARG B 315 "
       pdb=" CG  ARG B 315 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.31e+00
  bond pdb=" CB  ILE B 452 "
       pdb=" CG2 ILE B 452 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.19e+00
  bond pdb=" CA  ARG A 147 "
       pdb=" CB  ARG A 147 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.69e-02 3.50e+03 1.17e+00
  bond pdb=" CG1 ILE A 606 "
       pdb=" CD1 ILE A 606 "
    ideal  model  delta    sigma   weight residual
    1.513  1.482  0.031 3.90e-02 6.57e+02 6.14e-01
  bond pdb=" N   LYS B 357 "
       pdb=" CA  LYS B 357 "
    ideal  model  delta    sigma   weight residual
    1.468  1.458  0.010 1.24e-02 6.50e+03 6.12e-01
  ... (remaining 12651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 17027
        2.28 -     4.56: 141
        4.56 -     6.85: 13
        6.85 -     9.13: 2
        9.13 -    11.41: 1
  Bond angle restraints: 17184
  Sorted by residual:
  angle pdb=" C   CYS A 146 "
        pdb=" N   ARG A 147 "
        pdb=" CA  ARG A 147 "
      ideal   model   delta    sigma   weight residual
     121.54  132.95  -11.41 1.91e+00 2.74e-01 3.57e+01
  angle pdb=" N   ARG A 147 "
        pdb=" CA  ARG A 147 "
        pdb=" CB  ARG A 147 "
      ideal   model   delta    sigma   weight residual
     110.49  115.74   -5.25 1.69e+00 3.50e-01 9.64e+00
  angle pdb=" CA  ARG A 147 "
        pdb=" CB  ARG A 147 "
        pdb=" CG  ARG A 147 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.63e+00
  angle pdb=" CG1 ILE B 452 "
        pdb=" CB  ILE B 452 "
        pdb=" CG2 ILE B 452 "
      ideal   model   delta    sigma   weight residual
     110.70  102.97    7.73 3.00e+00 1.11e-01 6.63e+00
  angle pdb=" CA  LEU B 487 "
        pdb=" CB  LEU B 487 "
        pdb=" CG  LEU B 487 "
      ideal   model   delta    sigma   weight residual
     116.30  124.66   -8.36 3.50e+00 8.16e-02 5.71e+00
  ... (remaining 17179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 7114
       17.77 -    35.53: 493
       35.53 -    53.30: 87
       53.30 -    71.07: 25
       71.07 -    88.83: 14
  Dihedral angle restraints: 7733
    sinusoidal: 3307
      harmonic: 4426
  Sorted by residual:
  dihedral pdb=" CA  ARG A 147 "
           pdb=" C   ARG A 147 "
           pdb=" N   ALA A 148 "
           pdb=" CA  ALA A 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.47   26.53     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  LEU A 145 "
           pdb=" C   LEU A 145 "
           pdb=" N   CYS A 146 "
           pdb=" CA  CYS A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.91   22.09     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  HIS C 233 "
           pdb=" C   HIS C 233 "
           pdb=" N   THR C 234 "
           pdb=" CA  THR C 234 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.35   18.65     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 7730 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1354
       0.036 -    0.072: 417
       0.072 -    0.108: 115
       0.108 -    0.145: 31
       0.145 -    0.181: 2
  Chirality restraints: 1919
  Sorted by residual:
  chirality pdb=" CB  ILE B 452 "
            pdb=" CA  ILE B 452 "
            pdb=" CG1 ILE B 452 "
            pdb=" CG2 ILE B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CG  LEU A 550 "
            pdb=" CB  LEU A 550 "
            pdb=" CD1 LEU A 550 "
            pdb=" CD2 LEU A 550 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.63e-01
  chirality pdb=" CA  ARG A 147 "
            pdb=" N   ARG A 147 "
            pdb=" C   ARG A 147 "
            pdb=" CB  ARG A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.08e-01
  ... (remaining 1916 not shown)

  Planarity restraints: 2158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 463 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO B 464 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 464 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 464 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 604 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO A 605 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  11 "   -0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO B  12 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  12 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  12 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2155 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 234
        2.67 -     3.23: 11908
        3.23 -     3.79: 19866
        3.79 -     4.34: 28172
        4.34 -     4.90: 45310
  Nonbonded interactions: 105490
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 472 "
            pdb=" O   VAL B 483 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OD2 ASP B 500 "
            pdb=" OH  TYR B 537 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" O   ASN C 163 "
            pdb=" OG  SER C 166 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   THR A 269 "
            pdb=" OG  SER A 463 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OD1 ASP B 172 "
            pdb=" NH2 ARG B 216 "
     model   vdw
     2.243 3.120
  ... (remaining 105485 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.820
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  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:10.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
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      :  0.003   0.036  12657  Z= 0.116
  Angle     :  0.534  11.412  17184  Z= 0.277
  Chirality :  0.040   0.181   1919
  Planarity :  0.005   0.042   2158
  Dihedral  : 13.208  88.832   4855
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.22), residues: 1489
  helix:  1.12 (0.20), residues: 688
  sheet:  0.62 (0.47), residues: 124
  loop : -0.35 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 336 
 HIS   0.006   0.001   HIS A 573 
 PHE   0.027   0.002   PHE A 483 
 TYR   0.019   0.001   TYR B 104 
 ARG   0.006   0.000   ARG B 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15861 (  544)
  hydrogen bonds       : angle       6.19319 ( 1533)
  covalent geometry    : bond        0.00261 (12656)
  covalent geometry    : angle       0.53447 (17184)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.7653 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  139 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7133 (tm-30)
REVERT: A  163 GLU cc_start: 0.8261 (tp30) cc_final: 0.7851 (tp30)
REVERT: A  307 GLN cc_start: 0.7293 (pp30) cc_final: 0.7090 (pp30)
REVERT: B   30 TYR cc_start: 0.7834 (m-80) cc_final: 0.7596 (m-80)
REVERT: B  243 ILE cc_start: 0.9069 (pt) cc_final: 0.8855 (pp)
REVERT: B  283 LYS cc_start: 0.8272 (tptt) cc_final: 0.8033 (tppt)
REVERT: B  287 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7626 (tmtt)
REVERT: B  672 GLN cc_start: 0.7878 (mt0) cc_final: 0.7360 (pt0)
REVERT: C  127 ASP cc_start: 0.7121 (t0) cc_final: 0.6828 (t0)
REVERT: C  201 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: C  210 GLU cc_start: 0.7759 (pm20) cc_final: 0.7545 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 1.7500
  time to fit residues: 423.0770
Evaluate side-chains
  174 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0980
   chunk 136 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 156 ASN
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 GLN
B  71 ASN
B 267 ASN
B 302 GLN
B 397 ASN
B 433 HIS
B 506 ASN
C 214 HIS
C 252 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.130964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099628 restraints weight = 15201.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.15
r_work: 0.3141 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12657  Z= 0.195
  Angle     :  0.601   7.628  17184  Z= 0.318
  Chirality :  0.043   0.150   1919
  Planarity :  0.005   0.052   2158
  Dihedral  :  8.769  82.122   1797
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.36 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.22), residues: 1489
  helix:  1.32 (0.20), residues: 683
  sheet:  0.56 (0.48), residues: 118
  loop : -0.36 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 336 
 HIS   0.011   0.002   HIS A 577 
 PHE   0.028   0.002   PHE C  41 
 TYR   0.017   0.002   TYR B 115 
 ARG   0.008   0.001   ARG A 576 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04671 (  544)
  hydrogen bonds       : angle       4.86359 ( 1533)
  covalent geometry    : bond        0.00462 (12656)
  covalent geometry    : angle       0.60054 (17184)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 1.335 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8062 (p0) cc_final: 0.7695 (t70)
REVERT: A   17 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7542 (tp30)
REVERT: A   49 HIS cc_start: 0.7868 (m90) cc_final: 0.7636 (m90)
REVERT: A   58 ASP cc_start: 0.8161 (m-30) cc_final: 0.7944 (m-30)
REVERT: A   86 ASP cc_start: 0.8031 (m-30) cc_final: 0.7713 (m-30)
REVERT: A  122 GLU cc_start: 0.7774 (pm20) cc_final: 0.7569 (pm20)
REVERT: A  139 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: A  147 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.7539 (ptm-80)
REVERT: A  163 GLU cc_start: 0.8412 (tp30) cc_final: 0.7951 (tp30)
REVERT: B   30 TYR cc_start: 0.7952 (m-80) cc_final: 0.7716 (m-80)
REVERT: B  100 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7526 (pt0)
REVERT: B  283 LYS cc_start: 0.8559 (tptt) cc_final: 0.8205 (tppt)
REVERT: B  287 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7755 (tmtt)
REVERT: B  469 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: B  576 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7388 (tt0)
REVERT: B  672 GLN cc_start: 0.7940 (mt0) cc_final: 0.7251 (pt0)
REVERT: B  693 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: C  127 ASP cc_start: 0.7961 (t0) cc_final: 0.7524 (m-30)
REVERT: C  201 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: C  210 GLU cc_start: 0.8013 (pm20) cc_final: 0.7725 (mp0)
  outliers start: 29
  outliers final: 8
  residues processed: 205
  average time/residue: 1.6018
  time to fit residues: 351.7127
Evaluate side-chains
  192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain C residue   18 GLU
Chi-restraints excluded: chain C residue   54 GLN
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  163 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 107 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 143 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 507 GLN
B 123 GLN
B 336 ASN
B 397 ASN
B 433 HIS
B 506 ASN
C 154 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.100242 restraints weight = 15265.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.16
r_work: 0.3149 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12657  Z= 0.145
  Angle     :  0.550   6.366  17184  Z= 0.289
  Chirality :  0.040   0.135   1919
  Planarity :  0.005   0.050   2158
  Dihedral  :  8.519  82.364   1797
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.28 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.22), residues: 1489
  helix:  1.43 (0.21), residues: 684
  sheet:  0.34 (0.47), residues: 118
  loop : -0.38 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 336 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.025   0.002   PHE C  41 
 TYR   0.018   0.001   TYR B 533 
 ARG   0.007   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  544)
  hydrogen bonds       : angle       4.62248 ( 1533)
  covalent geometry    : bond        0.00337 (12656)
  covalent geometry    : angle       0.54956 (17184)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 1.372 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7996 (p0) cc_final: 0.7595 (t70)
REVERT: A   18 THR cc_start: 0.8890 (m) cc_final: 0.8579 (p)
REVERT: A   47 ASN cc_start: 0.7824 (t0) cc_final: 0.7546 (t0)
REVERT: A   49 HIS cc_start: 0.7931 (m90) cc_final: 0.7652 (m90)
REVERT: A   64 ASP cc_start: 0.7255 (t0) cc_final: 0.6970 (t0)
REVERT: A   86 ASP cc_start: 0.8102 (m-30) cc_final: 0.7750 (m-30)
REVERT: A  122 GLU cc_start: 0.7734 (pm20) cc_final: 0.7482 (pm20)
REVERT: A  139 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: A  147 ARG cc_start: 0.7721 (ptm-80) cc_final: 0.7505 (ptm-80)
REVERT: A  163 GLU cc_start: 0.8418 (tp30) cc_final: 0.7913 (tp30)
REVERT: A  212 MET cc_start: 0.7858 (ttp) cc_final: 0.7609 (ttm)
REVERT: B   30 TYR cc_start: 0.7988 (m-80) cc_final: 0.7707 (m-80)
REVERT: B  100 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7506 (pt0)
REVERT: B  283 LYS cc_start: 0.8551 (tptt) cc_final: 0.8172 (tppt)
REVERT: B  469 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: B  482 ASN cc_start: 0.8834 (t0) cc_final: 0.8533 (t0)
REVERT: B  672 GLN cc_start: 0.7845 (mt0) cc_final: 0.7163 (pt0)
REVERT: C   18 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8292 (tp30)
REVERT: C  127 ASP cc_start: 0.8001 (t0) cc_final: 0.7611 (m-30)
REVERT: C  146 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7228 (mtt)
REVERT: C  201 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: C  210 GLU cc_start: 0.8038 (pm20) cc_final: 0.7731 (mp0)
  outliers start: 27
  outliers final: 7
  residues processed: 202
  average time/residue: 2.0608
  time to fit residues: 446.2654
Evaluate side-chains
  184 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 175
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain C residue   18 GLU
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 142 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 105 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 135 optimal weight:    1.9990
   chunk 143 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0770
   chunk 59 optimal weight:    0.0000
   overall best weight:    0.7946

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
B  55 GLN
B 397 ASN
C 154 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.132167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101127 restraints weight = 15150.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.12
r_work: 0.3158 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12657  Z= 0.128
  Angle     :  0.526   5.755  17184  Z= 0.276
  Chirality :  0.039   0.131   1919
  Planarity :  0.004   0.049   2158
  Dihedral  :  8.313  81.936   1797
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.02 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1489
  helix:  1.51 (0.21), residues: 684
  sheet:  0.22 (0.46), residues: 118
  loop : -0.39 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 336 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.023   0.002   PHE C  41 
 TYR   0.018   0.001   TYR B 533 
 ARG   0.008   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  544)
  hydrogen bonds       : angle       4.47702 ( 1533)
  covalent geometry    : bond        0.00295 (12656)
  covalent geometry    : angle       0.52604 (17184)
  Misc. bond           : bond        0.00029 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7990 (p0) cc_final: 0.7616 (t70)
REVERT: A   18 THR cc_start: 0.8752 (m) cc_final: 0.8443 (p)
REVERT: A   47 ASN cc_start: 0.7778 (t0) cc_final: 0.7529 (t0)
REVERT: A   49 HIS cc_start: 0.7940 (m90) cc_final: 0.7628 (m90)
REVERT: A   64 ASP cc_start: 0.7280 (t0) cc_final: 0.6967 (t0)
REVERT: A   86 ASP cc_start: 0.8085 (m-30) cc_final: 0.7739 (m-30)
REVERT: A  139 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7193 (tm-30)
REVERT: A  163 GLU cc_start: 0.8419 (tp30) cc_final: 0.7905 (tp30)
REVERT: A  212 MET cc_start: 0.7778 (ttp) cc_final: 0.7525 (ttm)
REVERT: A  307 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8439 (tp40)
REVERT: B  100 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7498 (pt0)
REVERT: B  283 LYS cc_start: 0.8536 (tptt) cc_final: 0.8154 (tppt)
REVERT: B  287 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7664 (tmtt)
REVERT: B  469 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: B  482 ASN cc_start: 0.8765 (t0) cc_final: 0.8495 (t0)
REVERT: B  576 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7494 (tt0)
REVERT: B  672 GLN cc_start: 0.7859 (mt0) cc_final: 0.7155 (pt0)
REVERT: B  693 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7798 (tm-30)
REVERT: C   25 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8288 (ttpp)
REVERT: C  127 ASP cc_start: 0.7995 (t0) cc_final: 0.7608 (m-30)
REVERT: C  146 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7323 (mtt)
REVERT: C  201 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: C  210 GLU cc_start: 0.8060 (pm20) cc_final: 0.7728 (mp0)
  outliers start: 27
  outliers final: 10
  residues processed: 204
  average time/residue: 1.7367
  time to fit residues: 380.6658
Evaluate side-chains
  189 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 2.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  147 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0470
   chunk 22 optimal weight:    0.0570
   chunk 2 optimal weight:    8.9990
   chunk 75 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
C 154 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.133598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.102619 restraints weight = 15160.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.11
r_work: 0.3184 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12657  Z= 0.110
  Angle     :  0.512   7.804  17184  Z= 0.268
  Chirality :  0.039   0.129   1919
  Planarity :  0.004   0.045   2158
  Dihedral  :  8.108  80.321   1797
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.54 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.22), residues: 1489
  helix:  1.59 (0.21), residues: 685
  sheet:  0.14 (0.45), residues: 118
  loop : -0.36 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 330 
 HIS   0.007   0.001   HIS A 434 
 PHE   0.022   0.001   PHE C  41 
 TYR   0.017   0.001   TYR B 533 
 ARG   0.009   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  544)
  hydrogen bonds       : angle       4.35935 ( 1533)
  covalent geometry    : bond        0.00250 (12656)
  covalent geometry    : angle       0.51169 (17184)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 1.358 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7941 (p0) cc_final: 0.7616 (t70)
REVERT: A   18 THR cc_start: 0.8743 (m) cc_final: 0.8457 (p)
REVERT: A   49 HIS cc_start: 0.7992 (m90) cc_final: 0.7680 (m90)
REVERT: A   64 ASP cc_start: 0.7351 (t0) cc_final: 0.6989 (t0)
REVERT: A   86 ASP cc_start: 0.8093 (m-30) cc_final: 0.7737 (m-30)
REVERT: A  139 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7237 (tm-30)
REVERT: A  153 VAL cc_start: 0.8587 (t) cc_final: 0.8356 (m)
REVERT: A  163 GLU cc_start: 0.8420 (tp30) cc_final: 0.7905 (tp30)
REVERT: A  212 MET cc_start: 0.7844 (ttp) cc_final: 0.7559 (ttm)
REVERT: B  100 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7491 (pt0)
REVERT: B  283 LYS cc_start: 0.8533 (tptt) cc_final: 0.8158 (tppt)
REVERT: B  469 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: B  482 ASN cc_start: 0.8718 (t0) cc_final: 0.8409 (t0)
REVERT: B  576 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7382 (tt0)
REVERT: B  672 GLN cc_start: 0.7938 (mt0) cc_final: 0.7187 (pt0)
REVERT: C  127 ASP cc_start: 0.7992 (t0) cc_final: 0.7635 (m-30)
REVERT: C  146 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7309 (mtt)
REVERT: C  201 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: C  210 GLU cc_start: 0.8085 (pm20) cc_final: 0.7756 (mp0)
REVERT: C  222 SER cc_start: 0.8449 (t) cc_final: 0.8207 (m)
  outliers start: 27
  outliers final: 8
  residues processed: 200
  average time/residue: 1.5068
  time to fit residues: 323.5471
Evaluate side-chains
  183 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 146 optimal weight:    4.9990
   chunk 122 optimal weight:    0.0770
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
B  55 GLN
C  80 ASN
C 154 GLN
C 214 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.099192 restraints weight = 15292.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.12
r_work: 0.3133 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12657  Z= 0.168
  Angle     :  0.557   6.056  17184  Z= 0.294
  Chirality :  0.041   0.136   1919
  Planarity :  0.005   0.051   2158
  Dihedral  :  8.242  84.801   1797
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.98 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.22), residues: 1489
  helix:  1.47 (0.21), residues: 688
  sheet:  0.03 (0.45), residues: 118
  loop : -0.41 (0.24), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 253 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.025   0.002   PHE C  41 
 TYR   0.019   0.002   TYR B 533 
 ARG   0.005   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  544)
  hydrogen bonds       : angle       4.40955 ( 1533)
  covalent geometry    : bond        0.00399 (12656)
  covalent geometry    : angle       0.55654 (17184)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 1.508 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7953 (p0) cc_final: 0.7636 (t70)
REVERT: A   18 THR cc_start: 0.8852 (m) cc_final: 0.8559 (p)
REVERT: A   64 ASP cc_start: 0.7363 (t0) cc_final: 0.7001 (t0)
REVERT: A   86 ASP cc_start: 0.8143 (m-30) cc_final: 0.7702 (m-30)
REVERT: A  139 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: A  163 GLU cc_start: 0.8455 (tp30) cc_final: 0.7947 (tp30)
REVERT: A  205 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6612 (mm-30)
REVERT: B  100 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7501 (pt0)
REVERT: B  283 LYS cc_start: 0.8556 (tptt) cc_final: 0.8179 (tppt)
REVERT: B  469 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: B  482 ASN cc_start: 0.8797 (t0) cc_final: 0.8558 (t0)
REVERT: B  576 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7745 (tt0)
REVERT: B  672 GLN cc_start: 0.7862 (mt0) cc_final: 0.7117 (pt0)
REVERT: B  693 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: C   75 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7944 (pt)
REVERT: C  127 ASP cc_start: 0.8046 (t0) cc_final: 0.7673 (m-30)
REVERT: C  146 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7343 (mtt)
REVERT: C  201 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: C  210 GLU cc_start: 0.8093 (pm20) cc_final: 0.7747 (mp0)
  outliers start: 27
  outliers final: 10
  residues processed: 194
  average time/residue: 1.5995
  time to fit residues: 332.9526
Evaluate side-chains
  187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  180 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 90 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
C  80 ASN
C 154 GLN
C 214 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.132278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.100933 restraints weight = 15145.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.12
r_work: 0.3160 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12657  Z= 0.123
  Angle     :  0.530   9.323  17184  Z= 0.277
  Chirality :  0.039   0.150   1919
  Planarity :  0.004   0.047   2158
  Dihedral  :  8.114  82.687   1797
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.31 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.22), residues: 1489
  helix:  1.54 (0.21), residues: 687
  sheet:  0.02 (0.45), residues: 118
  loop : -0.42 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 330 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.023   0.001   PHE C  41 
 TYR   0.019   0.001   TYR B 104 
 ARG   0.006   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  544)
  hydrogen bonds       : angle       4.34008 ( 1533)
  covalent geometry    : bond        0.00286 (12656)
  covalent geometry    : angle       0.52988 (17184)
  Misc. bond           : bond        0.00029 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 1.418 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7927 (p0) cc_final: 0.7612 (t70)
REVERT: A   18 THR cc_start: 0.8780 (m) cc_final: 0.8505 (p)
REVERT: A   64 ASP cc_start: 0.7363 (t0) cc_final: 0.6977 (t0)
REVERT: A   86 ASP cc_start: 0.8135 (m-30) cc_final: 0.7677 (m-30)
REVERT: A  139 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: A  153 VAL cc_start: 0.8569 (t) cc_final: 0.8328 (m)
REVERT: A  163 GLU cc_start: 0.8440 (tp30) cc_final: 0.7934 (tp30)
REVERT: A  205 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6540 (mm-30)
REVERT: A  532 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6569 (pm20)
REVERT: B  100 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7491 (pt0)
REVERT: B  118 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7821 (mp)
REVERT: B  283 LYS cc_start: 0.8538 (tptt) cc_final: 0.8165 (tppt)
REVERT: B  469 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: B  576 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7660 (tt0)
REVERT: B  672 GLN cc_start: 0.7805 (mt0) cc_final: 0.7062 (pt0)
REVERT: B  693 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: C   75 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7959 (pt)
REVERT: C  127 ASP cc_start: 0.8004 (t0) cc_final: 0.7641 (m-30)
REVERT: C  201 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: C  210 GLU cc_start: 0.8064 (pm20) cc_final: 0.7719 (mp0)
REVERT: C  222 SER cc_start: 0.8476 (t) cc_final: 0.8226 (m)
  outliers start: 23
  outliers final: 8
  residues processed: 187
  average time/residue: 1.6134
  time to fit residues: 323.9353
Evaluate side-chains
  185 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  180 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
C  80 ASN
C 154 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.130989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099808 restraints weight = 15426.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.14
r_work: 0.3142 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12657  Z= 0.148
  Angle     :  0.544   6.425  17184  Z= 0.286
  Chirality :  0.040   0.133   1919
  Planarity :  0.004   0.050   2158
  Dihedral  :  8.140  84.301   1797
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.61 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.22), residues: 1489
  helix:  1.52 (0.21), residues: 687
  sheet:  0.00 (0.45), residues: 118
  loop : -0.45 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 253 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.024   0.002   PHE C  41 
 TYR   0.018   0.001   TYR B 533 
 ARG   0.006   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  544)
  hydrogen bonds       : angle       4.36586 ( 1533)
  covalent geometry    : bond        0.00350 (12656)
  covalent geometry    : angle       0.54442 (17184)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 1.327 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7950 (p0) cc_final: 0.7658 (t70)
REVERT: A   18 THR cc_start: 0.8781 (m) cc_final: 0.8505 (p)
REVERT: A   64 ASP cc_start: 0.7385 (t0) cc_final: 0.6972 (t0)
REVERT: A   86 ASP cc_start: 0.8143 (m-30) cc_final: 0.7702 (m-30)
REVERT: A  139 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7257 (tm-30)
REVERT: A  153 VAL cc_start: 0.8564 (t) cc_final: 0.8318 (m)
REVERT: A  163 GLU cc_start: 0.8449 (tp30) cc_final: 0.7944 (tp30)
REVERT: A  205 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6566 (mm-30)
REVERT: B  100 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7504 (pt0)
REVERT: B  283 LYS cc_start: 0.8546 (tptt) cc_final: 0.8169 (tppt)
REVERT: B  469 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: B  576 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7693 (tt0)
REVERT: B  693 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7563 (tm-30)
REVERT: C   75 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7971 (pt)
REVERT: C  127 ASP cc_start: 0.8018 (t0) cc_final: 0.7657 (m-30)
REVERT: C  201 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: C  210 GLU cc_start: 0.8080 (pm20) cc_final: 0.7701 (mp0)
REVERT: C  222 SER cc_start: 0.8464 (t) cc_final: 0.8215 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 190
  average time/residue: 1.5131
  time to fit residues: 308.2810
Evaluate side-chains
  186 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  180 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 107 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 129 optimal weight:    0.0000
   chunk 0 optimal weight:   10.0000
   chunk 146 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 663 ASN
B 672 GLN
C  80 ASN
C 154 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.131108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099863 restraints weight = 15178.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.13
r_work: 0.3141 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12657  Z= 0.149
  Angle     :  0.555  10.758  17184  Z= 0.290
  Chirality :  0.040   0.133   1919
  Planarity :  0.004   0.049   2158
  Dihedral  :  8.145  85.104   1797
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.76 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.22), residues: 1489
  helix:  1.51 (0.21), residues: 687
  sheet: -0.02 (0.45), residues: 118
  loop : -0.47 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 253 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.024   0.002   PHE C  41 
 TYR   0.021   0.002   TYR B 104 
 ARG   0.007   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  544)
  hydrogen bonds       : angle       4.37658 ( 1533)
  covalent geometry    : bond        0.00352 (12656)
  covalent geometry    : angle       0.55542 (17184)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 1.609 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7949 (p0) cc_final: 0.7666 (t70)
REVERT: A   18 THR cc_start: 0.8820 (m) cc_final: 0.8550 (p)
REVERT: A   64 ASP cc_start: 0.7307 (t0) cc_final: 0.6919 (t0)
REVERT: A   86 ASP cc_start: 0.8153 (m-30) cc_final: 0.7701 (m-30)
REVERT: A  139 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7285 (tm-30)
REVERT: A  153 VAL cc_start: 0.8559 (t) cc_final: 0.8314 (m)
REVERT: A  163 GLU cc_start: 0.8441 (tp30) cc_final: 0.7932 (tp30)
REVERT: A  205 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6583 (mm-30)
REVERT: A  532 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6609 (pm20)
REVERT: B  100 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7504 (pt0)
REVERT: B  283 LYS cc_start: 0.8546 (tptt) cc_final: 0.8167 (tppt)
REVERT: B  469 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: B  576 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7692 (tt0)
REVERT: B  682 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.7005 (mt-10)
REVERT: B  693 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: C   75 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7980 (pt)
REVERT: C  127 ASP cc_start: 0.8014 (t0) cc_final: 0.7645 (m-30)
REVERT: C  201 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7903 (tm-30)
REVERT: C  210 GLU cc_start: 0.8082 (pm20) cc_final: 0.7685 (mp0)
REVERT: C  222 SER cc_start: 0.8463 (t) cc_final: 0.8206 (m)
  outliers start: 21
  outliers final: 8
  residues processed: 187
  average time/residue: 2.2330
  time to fit residues: 447.6724
Evaluate side-chains
  183 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 2.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain B residue  682 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  180 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 135 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 ASN
C 131 GLN
C 154 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.130434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099128 restraints weight = 15186.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.10
r_work: 0.3132 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12657  Z= 0.168
  Angle     :  0.571   6.979  17184  Z= 0.301
  Chirality :  0.041   0.135   1919
  Planarity :  0.005   0.051   2158
  Dihedral  :  8.227  87.646   1797
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.28 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.22), residues: 1489
  helix:  1.45 (0.20), residues: 688
  sheet: -0.01 (0.45), residues: 118
  loop : -0.48 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 253 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.025   0.002   PHE C  41 
 TYR   0.018   0.002   TYR B 533 
 ARG   0.006   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  544)
  hydrogen bonds       : angle       4.42336 ( 1533)
  covalent geometry    : bond        0.00400 (12656)
  covalent geometry    : angle       0.57126 (17184)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2978 Ramachandran restraints generated.
    1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 2.631 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7957 (p0) cc_final: 0.7686 (t70)
REVERT: A   18 THR cc_start: 0.8901 (m) cc_final: 0.8569 (p)
REVERT: A   64 ASP cc_start: 0.7358 (t0) cc_final: 0.6969 (t0)
REVERT: A   86 ASP cc_start: 0.8159 (m-30) cc_final: 0.7720 (m-30)
REVERT: A  139 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: A  163 GLU cc_start: 0.8453 (tp30) cc_final: 0.7946 (tp30)
REVERT: A  205 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6568 (mm-30)
REVERT: B  100 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7520 (pt0)
REVERT: B  283 LYS cc_start: 0.8549 (tptt) cc_final: 0.8173 (tppt)
REVERT: B  469 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: B  576 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7766 (tt0)
REVERT: B  682 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6853 (mt-10)
REVERT: B  693 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: C   75 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.8003 (pt)
REVERT: C  127 ASP cc_start: 0.8025 (t0) cc_final: 0.7696 (m-30)
REVERT: C  201 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: C  210 GLU cc_start: 0.8099 (pm20) cc_final: 0.7631 (mp0)
REVERT: C  222 SER cc_start: 0.8464 (t) cc_final: 0.8208 (m)
  outliers start: 16
  outliers final: 9
  residues processed: 179
  average time/residue: 2.4102
  time to fit residues: 463.8773
Evaluate side-chains
  180 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain B residue  670 LEU
Chi-restraints excluded: chain B residue  682 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  180 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 142 optimal weight:    0.3980
   chunk 71 optimal weight:    0.7980
   chunk 140 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 154 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.131959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100826 restraints weight = 15167.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.13
r_work: 0.3157 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12657  Z= 0.126
  Angle     :  0.544   9.661  17184  Z= 0.283
  Chirality :  0.039   0.129   1919
  Planarity :  0.004   0.047   2158
  Dihedral  :  8.095  85.799   1797
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.50 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.22), residues: 1489
  helix:  1.56 (0.21), residues: 684
  sheet: -0.04 (0.45), residues: 115
  loop : -0.43 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 330 
 HIS   0.008   0.001   HIS A 434 
 PHE   0.023   0.001   PHE C  41 
 TYR   0.023   0.001   TYR B 104 
 ARG   0.007   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03604 (  544)
  hydrogen bonds       : angle       4.34872 ( 1533)
  covalent geometry    : bond        0.00295 (12656)
  covalent geometry    : angle       0.54362 (17184)
  Misc. bond           : bond        0.00027 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13869.45 seconds
wall clock time: 249 minutes 27.35 seconds (14967.35 seconds total)