Starting phenix.real_space_refine
on Thu May 15 15:26:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k87_36946/05_2025/8k87_36946.cif"
  }
  resolution = 2.9
  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=   0.005 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    8248      2.51       5
     N    2300      2.21       5
     O    2690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13372
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 469
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "D"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 444
          Classifications: {'DNA': 1, 'RNA': 20}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 4, 'rna3p': 16}
    Chain: "A"
      Number of atoms: 3719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3719
          Classifications: {'peptide': 468}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439}
    Chain: "B"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2053
          Classifications: {'peptide': 258}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247}
    Chain: "H"
      Number of atoms: 469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 469
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "I"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 444
          Classifications: {'DNA': 1, 'RNA': 20}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 4, 'rna3p': 16}
    Chain: "F"
      Number of atoms: 3719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3719
          Classifications: {'peptide': 468}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439}
    Chain: "G"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2053
          Classifications: {'peptide': 258}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.25, per 1000 atoms: 0.62
  Number of scatterers: 13372
  At special positions: 0
  Unit cell: (92.828, 107.963, 165.476, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P      88     15.00
     Mg      2     11.99
     O    2690      8.00
     N    2300      7.00
     C    8248      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=0, symmetry=0
  Time building additional restraints: 3.16
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 20 sheets defined
      38.2% alpha, 25.1% beta
      33 base pairs and 52 stacking pairs defined.
    Time for finding SS restraints: 4.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 37
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 57 through 59
      No H-bonds generated for 'chain 'A' and resid 57 through 59'
    Processing helix  chain 'A' and resid 60 through 73
      removed outlier: 3.825A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 95
    Processing helix  chain 'A' and resid 111 through 120
      removed outlier: 3.879A  pdb=" N   GLY A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
    Processing helix  chain 'A' and resid 134 through 137
    Processing helix  chain 'A' and resid 139 through 143
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 5.004A  pdb=" N   LYS A 156 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 174
    Processing helix  chain 'A' and resid 184 through 189
      removed outlier: 3.859A  pdb=" N   LEU A 188 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 208
      removed outlier: 3.748A  pdb=" N   VAL A 196 " --> pdb=" O   CYS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 295
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.785A  pdb=" N   PHE A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 4.337A  pdb=" N   THR A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
    Processing helix  chain 'A' and resid 460 through 463
      removed outlier: 4.071A  pdb=" N   VAL A 463 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 460 through 463'
    Processing helix  chain 'A' and resid 470 through 472
      No H-bonds generated for 'chain 'A' and resid 470 through 472'
    Processing helix  chain 'B' and resid 355 through 367
    Processing helix  chain 'B' and resid 383 through 391
      removed outlier: 3.930A  pdb=" N   ILE B 387 " --> pdb=" O   GLY B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 414
    Processing helix  chain 'B' and resid 414 through 430
    Processing helix  chain 'B' and resid 455 through 457
      No H-bonds generated for 'chain 'B' and resid 455 through 457'
    Processing helix  chain 'B' and resid 458 through 465
    Processing helix  chain 'B' and resid 513 through 519
      removed outlier: 4.829A  pdb=" N   GLU B 518 " --> pdb=" O   ASP B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 528
    Processing helix  chain 'B' and resid 532 through 549
    Processing helix  chain 'F' and resid 29 through 37
    Processing helix  chain 'F' and resid 39 through 43
      removed outlier: 3.898A  pdb=" N   CYS F  43 " --> pdb=" O   TYR F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 73
      removed outlier: 3.792A  pdb=" N   LEU F  64 " --> pdb=" O   HIS F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 95
    Processing helix  chain 'F' and resid 102 through 104
      No H-bonds generated for 'chain 'F' and resid 102 through 104'
    Processing helix  chain 'F' and resid 111 through 120
      removed outlier: 3.816A  pdb=" N   GLY F 115 " --> pdb=" O   ASP F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 133
    Processing helix  chain 'F' and resid 133 through 140
      removed outlier: 3.761A  pdb=" N   PHE F 137 " --> pdb=" O   MET F 133 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG F 138 " --> pdb=" O   SER F 134 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 141 through 143
      No H-bonds generated for 'chain 'F' and resid 141 through 143'
    Processing helix  chain 'F' and resid 151 through 158
      removed outlier: 5.017A  pdb=" N   LYS F 156 " --> pdb=" O   SER F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 164 through 174
    Processing helix  chain 'F' and resid 184 through 189
      removed outlier: 3.806A  pdb=" N   LEU F 188 " --> pdb=" O   ASN F 184 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 192 through 208
      removed outlier: 3.905A  pdb=" N   VAL F 196 " --> pdb=" O   CYS F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 276 through 294
    Processing helix  chain 'F' and resid 312 through 323
      removed outlier: 4.094A  pdb=" N   PHE F 323 " --> pdb=" O   ALA F 319 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 397 through 399
      No H-bonds generated for 'chain 'F' and resid 397 through 399'
    Processing helix  chain 'F' and resid 417 through 428
      removed outlier: 4.641A  pdb=" N   THR F 421 " --> pdb=" O   GLY F 417 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 443 through 459
    Processing helix  chain 'F' and resid 460 through 463
      removed outlier: 4.215A  pdb=" N   VAL F 463 " --> pdb=" O   PRO F 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 460 through 463'
    Processing helix  chain 'F' and resid 470 through 472
      No H-bonds generated for 'chain 'F' and resid 470 through 472'
    Processing helix  chain 'G' and resid 355 through 367
    Processing helix  chain 'G' and resid 383 through 391
      removed outlier: 3.533A  pdb=" N   ILE G 387 " --> pdb=" O   GLY G 383 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 406 through 414
    Processing helix  chain 'G' and resid 414 through 430
    Processing helix  chain 'G' and resid 455 through 457
      No H-bonds generated for 'chain 'G' and resid 455 through 457'
    Processing helix  chain 'G' and resid 458 through 466
    Processing helix  chain 'G' and resid 513 through 519
      removed outlier: 4.938A  pdb=" N   GLU G 518 " --> pdb=" O   ASP G 515 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 520 through 529
    Processing helix  chain 'G' and resid 532 through 549
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
      removed outlier: 3.535A  pdb=" N   SER A  12 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU A 331 " --> pdb=" O   PHE A 412 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE A 303 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   VAL A 332 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE A 305 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ILE A 334 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LYS A 307 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA A 223 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   HIS A 306 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE A 225 " --> pdb=" O   HIS A 306 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS A 232 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 248 " --> pdb=" O   GLU A 256 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLU A 256 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99
      removed outlier: 6.688A  pdb=" N   VAL A  50 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   CYS A 107 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   TYR A  54 " --> pdb=" O   CYS A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99
      removed outlier: 6.688A  pdb=" N   VAL A  50 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ARG A  51 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   LEU A 147 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ALA A  53 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   TYR A 149 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A  55 " --> pdb=" O   TYR A 149 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU A 146 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   ILE A 183 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   VAL A 148 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356
    Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382
    Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 338
      removed outlier: 4.816A  pdb=" N   LEU B 501 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   HIS B 444 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 338
      removed outlier: 4.816A  pdb=" N   LEU B 501 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 371 through 374
      removed outlier: 3.584A  pdb=" N   LEU B 371 " --> pdb=" O   LEU B 381 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL B 378 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 346 " --> pdb=" O   PHE B 380 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 556 through 561
      removed outlier: 3.607A  pdb=" N   ALA B 569 " --> pdb=" O   CYS B 561 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13
      removed outlier: 6.626A  pdb=" N   LEU F 331 " --> pdb=" O   PHE F 412 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ALA F 223 " --> pdb=" O   PHE F 304 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   HIS F 306 " --> pdb=" O   ALA F 223 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ILE F 225 " --> pdb=" O   HIS F 306 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 25 through 27
      removed outlier: 3.581A  pdb=" N   LYS F 214 " --> pdb=" O   LEU F  20 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 98 through 99
      removed outlier: 7.073A  pdb=" N   VAL F  50 " --> pdb=" O   VAL F  99 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   CYS F 107 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   TYR F  54 " --> pdb=" O   CYS F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'F' and resid 98 through 99
      removed outlier: 7.073A  pdb=" N   VAL F  50 " --> pdb=" O   VAL F  99 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ARG F  51 " --> pdb=" O   VAL F 145 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU F 147 " --> pdb=" O   ARG F  51 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ALA F  53 " --> pdb=" O   LEU F 147 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   TYR F 149 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LEU F  55 " --> pdb=" O   TYR F 149 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 355 through 356
      removed outlier: 3.562A  pdb=" N   ALA F 355 " --> pdb=" O   ASP F 346 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 381 through 382
      removed outlier: 3.523A  pdb=" N   VAL F 394 " --> pdb=" O   VAL F 382 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 335 through 337
      removed outlier: 3.979A  pdb=" N   HIS G 444 " --> pdb=" O   ILE G 492 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 335 through 337
    Processing sheet with id=AC1, first strand: chain 'G' and resid 371 through 374
      removed outlier: 3.569A  pdb=" N   VAL G 378 " --> pdb=" O   VAL G 348 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER G 398 " --> pdb=" O   THR G 349 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 556 through 561
      removed outlier: 3.694A  pdb=" N   ALA G 569 " --> pdb=" O   CYS G 561 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      82 hydrogen bonds
      164 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      52 stacking parallelities
  Total time for adding SS restraints: 4.96

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3304
        1.33 -     1.45: 3132
        1.45 -     1.57: 7192
        1.57 -     1.69: 176
        1.69 -     1.81: 64
  Bond restraints: 13868
  Sorted by residual:
  bond pdb=" CB  PRO B 353 "
       pdb=" CG  PRO B 353 "
    ideal  model  delta    sigma   weight residual
    1.492  1.635 -0.143 5.00e-02 4.00e+02 8.14e+00
  bond pdb=" N3    U I  10 "
       pdb=" C4    U I  10 "
    ideal  model  delta    sigma   weight residual
    1.380  1.331  0.049 2.00e-02 2.50e+03 6.02e+00
  bond pdb=" CB  PRO F  17 "
       pdb=" CG  PRO F  17 "
    ideal  model  delta    sigma   weight residual
    1.492  1.603 -0.111 5.00e-02 4.00e+02 4.94e+00
  bond pdb=" CB  PRO A 179 "
       pdb=" CG  PRO A 179 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.87e+00
  bond pdb=" CB  GLU G 432 "
       pdb=" CG  GLU G 432 "
    ideal  model  delta    sigma   weight residual
    1.520  1.578 -0.058 3.00e-02 1.11e+03 3.75e+00
  ... (remaining 13863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 18944
        2.91 -     5.82: 218
        5.82 -     8.73: 21
        8.73 -    11.64: 3
       11.64 -    14.55: 2
  Bond angle restraints: 19188
  Sorted by residual:
  angle pdb=" CA  PRO B 353 "
        pdb=" N   PRO B 353 "
        pdb=" CD  PRO B 353 "
      ideal   model   delta    sigma   weight residual
     112.00   97.45   14.55 1.40e+00 5.10e-01 1.08e+02
  angle pdb=" CA  PRO F  17 "
        pdb=" N   PRO F  17 "
        pdb=" CD  PRO F  17 "
      ideal   model   delta    sigma   weight residual
     112.00  104.72    7.28 1.40e+00 5.10e-01 2.70e+01
  angle pdb=" CA  PRO A 179 "
        pdb=" N   PRO A 179 "
        pdb=" CD  PRO A 179 "
      ideal   model   delta    sigma   weight residual
     112.00  104.75    7.25 1.40e+00 5.10e-01 2.68e+01
  angle pdb=" CA  GLU G 432 "
        pdb=" CB  GLU G 432 "
        pdb=" CG  GLU G 432 "
      ideal   model   delta    sigma   weight residual
     114.10  122.99   -8.89 2.00e+00 2.50e-01 1.98e+01
  angle pdb=" CB  MET A 383 "
        pdb=" CG  MET A 383 "
        pdb=" SD  MET A 383 "
      ideal   model   delta    sigma   weight residual
     112.70  125.17  -12.47 3.00e+00 1.11e-01 1.73e+01
  ... (remaining 19183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.24: 7710
       35.24 -    70.48: 492
       70.48 -   105.72: 25
      105.72 -   140.96: 2
      140.96 -   176.20: 5
  Dihedral angle restraints: 8234
    sinusoidal: 4014
      harmonic: 4220
  Sorted by residual:
  dihedral pdb=" O4'   U I  10 "
           pdb=" C1'   U I  10 "
           pdb=" N1    U I  10 "
           pdb=" C2    U I  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   23.80  176.20     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   U I   8 "
           pdb=" C1'   U I   8 "
           pdb=" N1    U I   8 "
           pdb=" C2    U I   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   30.20  169.80     1      1.50e+01 4.44e-03 8.47e+01
  dihedral pdb=" O4'   U I   2 "
           pdb=" C1'   U I   2 "
           pdb=" N1    U I   2 "
           pdb=" C2    U I   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -1.21 -158.79     1      1.50e+01 4.44e-03 8.24e+01
  ... (remaining 8231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1815
       0.057 -    0.113: 291
       0.113 -    0.170: 35
       0.170 -    0.226: 5
       0.226 -    0.283: 2
  Chirality restraints: 2148
  Sorted by residual:
  chirality pdb=" C1'   G D   7 "
            pdb=" O4'   G D   7 "
            pdb=" C2'   G D   7 "
            pdb=" N9    G D   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.17    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  PRO B 353 "
            pdb=" N   PRO B 353 "
            pdb=" C   PRO B 353 "
            pdb=" CB  PRO B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CG  LEU A  46 "
            pdb=" CB  LEU A  46 "
            pdb=" CD1 LEU A  46 "
            pdb=" CD2 LEU A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 2145 not shown)

  Planarity restraints: 2152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 352 "    0.094 5.00e-02 4.00e+02   1.30e-01 2.71e+01
        pdb=" N   PRO B 353 "   -0.224 5.00e-02 4.00e+02
        pdb=" CA  PRO B 353 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO B 353 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 178 "   -0.085 5.00e-02 4.00e+02   1.25e-01 2.50e+01
        pdb=" N   PRO A 179 "    0.216 5.00e-02 4.00e+02
        pdb=" CA  PRO A 179 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A 179 "   -0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 367 "   -0.070 5.00e-02 4.00e+02   1.05e-01 1.75e+01
        pdb=" N   PRO B 368 "    0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO B 368 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B 368 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 2149 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 125
        2.52 -     3.12: 9715
        3.12 -     3.71: 21751
        3.71 -     4.31: 29834
        4.31 -     4.90: 48733
  Nonbonded interactions: 110158
  Sorted by model distance:
  nonbonded pdb=" OP2   A D   1 "
            pdb="MG    MG A 501 "
     model   vdw
     1.929 2.170
  nonbonded pdb=" OXT MET A 473 "
            pdb="MG    MG A 501 "
     model   vdw
     1.969 2.170
  nonbonded pdb=" ND2 ASN A 434 "
            pdb="MG    MG A 501 "
     model   vdw
     2.001 2.250
  nonbonded pdb=" OG1 THR F 312 "
            pdb=" OD1 ASP F 314 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" O   LEU A 426 "
            pdb=" OG1 THR A 429 "
     model   vdw
     2.133 3.040
  ... (remaining 110153 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'I'
}

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:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     34.970
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.143  13868  Z= 0.174
  Angle     :  0.766  14.548  19188  Z= 0.418
  Chirality :  0.043   0.283   2148
  Planarity :  0.007   0.130   2152
  Dihedral  : 20.688 176.198   5522
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 36.90 %
    Favored  : 61.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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:  0.41 (0.22), residues: 1444
  helix:  1.50 (0.25), residues: 430
  sheet:  0.98 (0.30), residues: 314
  loop : -0.86 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 218 
 HIS   0.008   0.001   HIS A 114 
 PHE   0.027   0.002   PHE A 143 
 TYR   0.046   0.002   TYR F  84 
 ARG   0.014   0.001   ARG G 527 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17360 (  589)
  hydrogen bonds       : angle       7.13231 ( 1631)
  covalent geometry    : bond        0.00406 (13868)
  covalent geometry    : angle       0.76629 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 250
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.8858 (mm) cc_final: 0.8585 (mt)
REVERT: A   70 GLU cc_start: 0.8822 (tt0) cc_final: 0.8214 (tt0)
REVERT: A  133 MET cc_start: 0.8162 (ptt) cc_final: 0.7912 (ptp)
REVERT: A  197 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6245 (mpp)
REVERT: A  439 TYR cc_start: 0.7710 (p90) cc_final: 0.7326 (p90)
REVERT: B  360 LYS cc_start: 0.8839 (mtpm) cc_final: 0.8469 (pptt)
REVERT: B  561 CYS cc_start: 0.7575 (t) cc_final: 0.6489 (p)
REVERT: F  214 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8393 (ptpp)
REVERT: F  220 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7950 (ptmt)
REVERT: F  264 GLU cc_start: 0.8204 (tt0) cc_final: 0.7962 (tp30)
REVERT: F  299 MET cc_start: 0.8531 (ptp) cc_final: 0.7886 (ppp)
REVERT: F  428 LEU cc_start: 0.8768 (mm) cc_final: 0.8416 (tp)
REVERT: F  467 TYR cc_start: 0.7944 (m-80) cc_final: 0.7692 (m-80)
REVERT: G  506 LYS cc_start: 0.8825 (mttp) cc_final: 0.8558 (tptp)
  outliers start: 26
  outliers final: 22
  residues processed: 270
  average time/residue: 0.9170
  time to fit residues: 277.6374
Evaluate side-chains
  251 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  392 GLN
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  485 SER
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  385 VAL
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  375 THR
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  478 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 117 optimal weight:    0.0370
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 136 optimal weight:    5.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 392 GLN
F 184 ASN
F 310 HIS
G 441 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.101945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.087427 restraints weight = 26650.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 3.03
r_work: 0.3387 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13868  Z= 0.137
  Angle     :  0.629   7.953  19188  Z= 0.332
  Chirality :  0.042   0.166   2148
  Planarity :  0.006   0.069   2152
  Dihedral  : 19.573 163.539   2777
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 28.54 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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:  0.51 (0.22), residues: 1444
  helix:  1.34 (0.24), residues: 456
  sheet:  0.82 (0.28), residues: 352
  loop : -0.65 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G 510 
 HIS   0.023   0.001   HIS G 441 
 PHE   0.027   0.002   PHE A 143 
 TYR   0.024   0.002   TYR F  84 
 ARG   0.008   0.001   ARG G 527 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04085 (  589)
  hydrogen bonds       : angle       5.25218 ( 1631)
  covalent geometry    : bond        0.00306 (13868)
  covalent geometry    : angle       0.62865 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 258
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8696 (tt0) cc_final: 0.8316 (tt0)
REVERT: A  221 ASP cc_start: 0.8164 (m-30) cc_final: 0.7894 (m-30)
REVERT: A  385 VAL cc_start: 0.8713 (m) cc_final: 0.8427 (t)
REVERT: A  392 GLN cc_start: 0.8464 (tt0) cc_final: 0.8227 (tt0)
REVERT: B  360 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8407 (pptt)
REVERT: B  369 LYS cc_start: 0.8587 (mmpt) cc_final: 0.8268 (mmpt)
REVERT: B  384 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8456 (mp0)
REVERT: B  401 GLN cc_start: 0.8574 (pm20) cc_final: 0.8125 (pp30)
REVERT: B  561 CYS cc_start: 0.7560 (t) cc_final: 0.6734 (p)
REVERT: F   61 MET cc_start: 0.8691 (mmt) cc_final: 0.8279 (mmt)
REVERT: F  107 CYS cc_start: 0.8029 (t) cc_final: 0.7587 (p)
REVERT: F  220 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8220 (ptpt)
REVERT: F  299 MET cc_start: 0.8695 (ptp) cc_final: 0.7989 (ppp)
REVERT: F  370 THR cc_start: 0.8682 (t) cc_final: 0.8455 (p)
REVERT: F  392 GLN cc_start: 0.8176 (tt0) cc_final: 0.7975 (tt0)
REVERT: F  428 LEU cc_start: 0.8495 (mm) cc_final: 0.8188 (tp)
REVERT: G  477 ASN cc_start: 0.8709 (m-40) cc_final: 0.8462 (t0)
  outliers start: 51
  outliers final: 24
  residues processed: 284
  average time/residue: 0.8827
  time to fit residues: 282.2040
Evaluate side-chains
  263 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  485 SER
Chi-restraints excluded: chain G residue  509 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 121 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 30 optimal weight:    0.0670
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 195 ASN
G 437 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.102084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.087661 restraints weight = 26677.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 3.02
r_work: 0.3392 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13868  Z= 0.127
  Angle     :  0.597   7.846  19188  Z= 0.313
  Chirality :  0.041   0.177   2148
  Planarity :  0.005   0.053   2152
  Dihedral  : 19.461 167.398   2759
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 29.74 %
    Favored  : 66.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: 1444
  helix:  1.73 (0.25), residues: 430
  sheet:  0.72 (0.28), residues: 342
  loop : -0.45 (0.23), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 510 
 HIS   0.006   0.001   HIS A 114 
 PHE   0.015   0.001   PHE F 323 
 TYR   0.023   0.002   TYR F  84 
 ARG   0.008   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  589)
  hydrogen bonds       : angle       4.81959 ( 1631)
  covalent geometry    : bond        0.00284 (13868)
  covalent geometry    : angle       0.59717 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 260
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8384 (t0) cc_final: 0.8162 (t0)
REVERT: A  220 LYS cc_start: 0.8155 (mttm) cc_final: 0.7911 (mttt)
REVERT: A  392 GLN cc_start: 0.8468 (tt0) cc_final: 0.8212 (tt0)
REVERT: B  360 LYS cc_start: 0.8787 (mtpm) cc_final: 0.8406 (pptt)
REVERT: B  384 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8472 (mp0)
REVERT: B  401 GLN cc_start: 0.8634 (pm20) cc_final: 0.8161 (pp30)
REVERT: B  442 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8312 (mtp-110)
REVERT: B  519 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (mt-10)
REVERT: B  561 CYS cc_start: 0.7438 (t) cc_final: 0.6567 (p)
REVERT: F  107 CYS cc_start: 0.8035 (t) cc_final: 0.7551 (p)
REVERT: F  220 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8144 (ptmt)
REVERT: F  232 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8704 (tttm)
REVERT: F  392 GLN cc_start: 0.8251 (tt0) cc_final: 0.7982 (tt0)
REVERT: F  428 LEU cc_start: 0.8513 (mm) cc_final: 0.8241 (tp)
REVERT: G  377 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8141 (mptt)
REVERT: G  477 ASN cc_start: 0.8683 (m-40) cc_final: 0.8438 (t0)
REVERT: G  506 LYS cc_start: 0.8769 (mttp) cc_final: 0.8426 (tptt)
REVERT: G  512 LYS cc_start: 0.8850 (tttt) cc_final: 0.8639 (tttp)
  outliers start: 44
  outliers final: 27
  residues processed: 288
  average time/residue: 0.9329
  time to fit residues: 304.4556
Evaluate side-chains
  271 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 241
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  485 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 47 optimal weight:    0.0050
   chunk 17 optimal weight:    1.9990
   chunk 147 optimal weight:    0.0770
   chunk 50 optimal weight:    0.0570
   chunk 114 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.3870

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

Flipped N/Q/H residues before XYZ refinement:
A 278 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.103466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.089003 restraints weight = 26337.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.97
r_work: 0.3420 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13868  Z= 0.119
  Angle     :  0.588   9.217  19188  Z= 0.306
  Chirality :  0.041   0.166   2148
  Planarity :  0.005   0.050   2152
  Dihedral  : 19.224 167.083   2755
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 29.66 %
    Favored  : 66.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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:  0.83 (0.22), residues: 1444
  helix:  1.88 (0.25), residues: 430
  sheet:  0.70 (0.28), residues: 354
  loop : -0.39 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 510 
 HIS   0.006   0.001   HIS A 114 
 PHE   0.028   0.001   PHE A 143 
 TYR   0.024   0.002   TYR A 439 
 ARG   0.010   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  589)
  hydrogen bonds       : angle       4.62805 ( 1631)
  covalent geometry    : bond        0.00267 (13868)
  covalent geometry    : angle       0.58796 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 265
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8609 (tt0) cc_final: 0.7999 (tt0)
REVERT: A  121 ASN cc_start: 0.8377 (t0) cc_final: 0.8131 (t0)
REVERT: A  197 MET cc_start: 0.7525 (mpp) cc_final: 0.7035 (mpp)
REVERT: A  220 LYS cc_start: 0.8047 (mttm) cc_final: 0.7780 (mttt)
REVERT: A  221 ASP cc_start: 0.7988 (m-30) cc_final: 0.7295 (p0)
REVERT: A  222 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5933 (mm-30)
REVERT: A  392 GLN cc_start: 0.8477 (tt0) cc_final: 0.8221 (tt0)
REVERT: A  430 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7921 (mtmt)
REVERT: B  360 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8396 (pptt)
REVERT: B  384 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8422 (mp0)
REVERT: B  401 GLN cc_start: 0.8565 (pm20) cc_final: 0.8048 (pp30)
REVERT: B  519 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7829 (mt-10)
REVERT: F   61 MET cc_start: 0.8705 (mmt) cc_final: 0.8324 (mmt)
REVERT: F  107 CYS cc_start: 0.8038 (t) cc_final: 0.7633 (p)
REVERT: F  214 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8613 (ptmm)
REVERT: F  220 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8196 (ptmt)
REVERT: F  232 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8718 (tttp)
REVERT: F  392 GLN cc_start: 0.8269 (tt0) cc_final: 0.8003 (tt0)
REVERT: F  428 LEU cc_start: 0.8556 (mm) cc_final: 0.8336 (tp)
REVERT: G  342 SER cc_start: 0.8273 (p) cc_final: 0.7968 (m)
REVERT: G  377 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8092 (mptt)
REVERT: G  477 ASN cc_start: 0.8628 (m-40) cc_final: 0.8396 (t0)
REVERT: G  506 LYS cc_start: 0.8707 (mttp) cc_final: 0.8383 (tptt)
REVERT: G  512 LYS cc_start: 0.8772 (tttt) cc_final: 0.8561 (tttp)
  outliers start: 49
  outliers final: 27
  residues processed: 297
  average time/residue: 0.8980
  time to fit residues: 299.1079
Evaluate side-chains
  277 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  396 ILE
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Chi-restraints excluded: chain G residue  485 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0370
   chunk 94 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0062

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

Flipped N/Q/H residues before XYZ refinement:
A 389 ASN
B 534 GLN
F 195 ASN
G 441 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.100325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085890 restraints weight = 26787.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 3.02
r_work: 0.3365 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13868  Z= 0.155
  Angle     :  0.612   9.168  19188  Z= 0.321
  Chirality :  0.041   0.194   2148
  Planarity :  0.005   0.048   2152
  Dihedral  : 19.101 170.020   2753
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 29.26 %
    Favored  : 66.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: 1444
  helix:  1.83 (0.25), residues: 430
  sheet:  0.62 (0.29), residues: 354
  loop : -0.45 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 340 
 HIS   0.018   0.001   HIS G 441 
 PHE   0.027   0.002   PHE A 143 
 TYR   0.024   0.002   TYR F  84 
 ARG   0.011   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  589)
  hydrogen bonds       : angle       4.57212 ( 1631)
  covalent geometry    : bond        0.00357 (13868)
  covalent geometry    : angle       0.61154 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 261
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8681 (tp)
REVERT: A   70 GLU cc_start: 0.8651 (tt0) cc_final: 0.7912 (tt0)
REVERT: A  121 ASN cc_start: 0.8468 (t0) cc_final: 0.8168 (t0)
REVERT: A  197 MET cc_start: 0.7641 (mpp) cc_final: 0.6989 (mpp)
REVERT: A  221 ASP cc_start: 0.7982 (m-30) cc_final: 0.7462 (p0)
REVERT: A  222 GLU cc_start: 0.6417 (mm-30) cc_final: 0.6092 (mm-30)
REVERT: A  248 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7108 (p90)
REVERT: A  285 SER cc_start: 0.8343 (m) cc_final: 0.7884 (p)
REVERT: A  392 GLN cc_start: 0.8506 (tt0) cc_final: 0.8207 (tt0)
REVERT: A  430 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8092 (mtmt)
REVERT: B  360 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8378 (pptt)
REVERT: B  384 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8477 (mp0)
REVERT: B  401 GLN cc_start: 0.8629 (pm20) cc_final: 0.8161 (pp30)
REVERT: B  519 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7876 (mt-10)
REVERT: F   46 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8572 (pp)
REVERT: F   55 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7597 (tp)
REVERT: F   61 MET cc_start: 0.8769 (mmt) cc_final: 0.8400 (mmt)
REVERT: F  214 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8628 (ptmm)
REVERT: F  220 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8188 (ptmt)
REVERT: F  392 GLN cc_start: 0.8289 (tt0) cc_final: 0.7992 (tt0)
REVERT: F  428 LEU cc_start: 0.8538 (mm) cc_final: 0.8230 (tp)
REVERT: G  342 SER cc_start: 0.8286 (p) cc_final: 0.7976 (m)
REVERT: G  357 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.9096 (p)
REVERT: G  377 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (mptt)
REVERT: G  477 ASN cc_start: 0.8651 (m-40) cc_final: 0.8408 (t0)
REVERT: G  512 LYS cc_start: 0.8796 (tttt) cc_final: 0.8593 (tttp)
  outliers start: 59
  outliers final: 28
  residues processed: 296
  average time/residue: 0.8141
  time to fit residues: 273.0825
Evaluate side-chains
  286 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 249
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  248 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0980
   chunk 88 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 135 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.099865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.085397 restraints weight = 26949.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 3.04
r_work: 0.3355 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13868  Z= 0.150
  Angle     :  0.612   9.397  19188  Z= 0.321
  Chirality :  0.042   0.236   2148
  Planarity :  0.005   0.049   2152
  Dihedral  : 19.081 170.067   2752
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 30.06 %
    Favored  : 65.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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:  0.59 (0.22), residues: 1444
  helix:  1.69 (0.25), residues: 442
  sheet:  0.63 (0.29), residues: 342
  loop : -0.62 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 340 
 HIS   0.005   0.001   HIS A 114 
 PHE   0.027   0.002   PHE A 143 
 TYR   0.025   0.002   TYR F  84 
 ARG   0.011   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  589)
  hydrogen bonds       : angle       4.57242 ( 1631)
  covalent geometry    : bond        0.00345 (13868)
  covalent geometry    : angle       0.61186 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 258
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8661 (tp)
REVERT: A   70 GLU cc_start: 0.8632 (tt0) cc_final: 0.8168 (tt0)
REVERT: A  121 ASN cc_start: 0.8507 (t0) cc_final: 0.8227 (t0)
REVERT: A  248 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7192 (p90)
REVERT: A  285 SER cc_start: 0.8320 (m) cc_final: 0.7867 (p)
REVERT: A  392 GLN cc_start: 0.8491 (tt0) cc_final: 0.8223 (tt0)
REVERT: A  430 LYS cc_start: 0.8268 (mtpt) cc_final: 0.8042 (mtmt)
REVERT: B  384 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8453 (mp0)
REVERT: B  401 GLN cc_start: 0.8599 (pm20) cc_final: 0.8132 (pp30)
REVERT: B  411 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (t)
REVERT: B  442 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8294 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8557 (pp)
REVERT: F   61 MET cc_start: 0.8768 (mmt) cc_final: 0.8381 (mmt)
REVERT: F   69 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8281 (ptm-80)
REVERT: F  107 CYS cc_start: 0.8169 (t) cc_final: 0.7631 (p)
REVERT: F  214 LYS cc_start: 0.9117 (ptmm) cc_final: 0.8612 (ptmm)
REVERT: F  220 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8217 (ptmt)
REVERT: F  392 GLN cc_start: 0.8291 (tt0) cc_final: 0.8008 (tt0)
REVERT: F  428 LEU cc_start: 0.8532 (mm) cc_final: 0.8204 (tp)
REVERT: G  342 SER cc_start: 0.8285 (p) cc_final: 0.7978 (m)
REVERT: G  357 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9114 (p)
REVERT: G  377 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8050 (mptt)
REVERT: G  477 ASN cc_start: 0.8618 (m-40) cc_final: 0.8376 (t0)
REVERT: G  506 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8338 (tttp)
  outliers start: 60
  outliers final: 34
  residues processed: 291
  average time/residue: 0.8732
  time to fit residues: 288.1182
Evaluate side-chains
  294 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 251
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  248 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  508 GLU
Chi-restraints excluded: chain B residue  564 ASP
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   69 ARG
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Chi-restraints excluded: chain G residue  506 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 129 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0980
   chunk 96 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 146 optimal weight:    0.6980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 405 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.101012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.086519 restraints weight = 26751.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 3.03
r_work: 0.3376 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13868  Z= 0.137
  Angle     :  0.634   9.854  19188  Z= 0.331
  Chirality :  0.041   0.186   2148
  Planarity :  0.005   0.058   2152
  Dihedral  : 19.060 169.442   2752
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 31.27 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: 1444
  helix:  1.84 (0.25), residues: 432
  sheet:  0.64 (0.29), residues: 342
  loop : -0.51 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 340 
 HIS   0.005   0.001   HIS A 114 
 PHE   0.029   0.001   PHE A 143 
 TYR   0.039   0.002   TYR F  84 
 ARG   0.012   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  589)
  hydrogen bonds       : angle       4.46404 ( 1631)
  covalent geometry    : bond        0.00312 (13868)
  covalent geometry    : angle       0.63413 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 259
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8667 (tp)
REVERT: A   70 GLU cc_start: 0.8623 (tt0) cc_final: 0.8132 (tt0)
REVERT: A  121 ASN cc_start: 0.8492 (t0) cc_final: 0.8200 (t0)
REVERT: A  221 ASP cc_start: 0.8047 (m-30) cc_final: 0.7565 (p0)
REVERT: A  248 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7296 (p90)
REVERT: A  285 SER cc_start: 0.8332 (m) cc_final: 0.7879 (p)
REVERT: A  392 GLN cc_start: 0.8492 (tt0) cc_final: 0.8243 (tt0)
REVERT: A  430 LYS cc_start: 0.8229 (mtpt) cc_final: 0.8009 (mtmt)
REVERT: B  384 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8429 (mp0)
REVERT: B  401 GLN cc_start: 0.8552 (pm20) cc_final: 0.7828 (pp30)
REVERT: B  403 TYR cc_start: 0.8173 (m-10) cc_final: 0.7943 (m-10)
REVERT: B  411 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8128 (t)
REVERT: B  442 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8278 (mtp-110)
REVERT: B  561 CYS cc_start: 0.7576 (t) cc_final: 0.6595 (p)
REVERT: F   46 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: F   61 MET cc_start: 0.8760 (mmt) cc_final: 0.8358 (mmt)
REVERT: F   69 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8152 (ppp80)
REVERT: F  107 CYS cc_start: 0.8157 (t) cc_final: 0.7661 (p)
REVERT: F  214 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8593 (ptmm)
REVERT: F  220 LYS cc_start: 0.8595 (ptpt) cc_final: 0.8234 (ptmt)
REVERT: F  328 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7886 (mm-30)
REVERT: F  428 LEU cc_start: 0.8542 (mm) cc_final: 0.8262 (tp)
REVERT: G  342 SER cc_start: 0.8274 (p) cc_final: 0.7987 (m)
REVERT: G  357 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9119 (p)
REVERT: G  377 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8048 (mptt)
REVERT: G  477 ASN cc_start: 0.8608 (m-40) cc_final: 0.8373 (t0)
  outliers start: 52
  outliers final: 28
  residues processed: 286
  average time/residue: 0.8306
  time to fit residues: 269.4695
Evaluate side-chains
  289 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 252
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  248 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  508 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   69 ARG
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  328 GLU
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain F residue  473 MET
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Chi-restraints excluded: chain G residue  485 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 130 optimal weight:    0.0980
   chunk 28 optimal weight:    0.0980
   chunk 69 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 142 optimal weight:    0.7980
   chunk 135 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 128 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.101529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.087120 restraints weight = 26926.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.04
r_work: 0.3386 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13868  Z= 0.136
  Angle     :  0.639  10.979  19188  Z= 0.335
  Chirality :  0.041   0.200   2148
  Planarity :  0.005   0.055   2152
  Dihedral  : 19.021 169.425   2749
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 32.23 %
    Favored  : 63.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: 1444
  helix:  1.90 (0.25), residues: 432
  sheet:  0.52 (0.29), residues: 354
  loop : -0.42 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 340 
 HIS   0.005   0.001   HIS A 114 
 PHE   0.027   0.001   PHE A 143 
 TYR   0.029   0.002   TYR F 240 
 ARG   0.014   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  589)
  hydrogen bonds       : angle       4.45352 ( 1631)
  covalent geometry    : bond        0.00313 (13868)
  covalent geometry    : angle       0.63875 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 266
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8486 (t0) cc_final: 0.8193 (t0)
REVERT: A  221 ASP cc_start: 0.8062 (m-30) cc_final: 0.7521 (p0)
REVERT: A  285 SER cc_start: 0.8409 (m) cc_final: 0.7928 (p)
REVERT: A  392 GLN cc_start: 0.8486 (tt0) cc_final: 0.8255 (tt0)
REVERT: A  430 LYS cc_start: 0.8216 (mtpt) cc_final: 0.8000 (mtmt)
REVERT: B  384 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8421 (mp0)
REVERT: B  401 GLN cc_start: 0.8569 (pm20) cc_final: 0.7947 (pp30)
REVERT: B  411 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8133 (t)
REVERT: B  442 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8272 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8527 (pp)
REVERT: F   61 MET cc_start: 0.8752 (mmt) cc_final: 0.8388 (mmt)
REVERT: F   69 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8250 (ppp80)
REVERT: F  107 CYS cc_start: 0.8161 (t) cc_final: 0.7699 (p)
REVERT: F  214 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8599 (ptmm)
REVERT: F  220 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8288 (ptmt)
REVERT: F  428 LEU cc_start: 0.8470 (mm) cc_final: 0.8199 (tp)
REVERT: F  454 ASP cc_start: 0.7259 (m-30) cc_final: 0.7049 (t0)
REVERT: G  342 SER cc_start: 0.8273 (p) cc_final: 0.7979 (m)
REVERT: G  357 SER cc_start: 0.9344 (OUTLIER) cc_final: 0.9121 (p)
REVERT: G  377 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8205 (mppt)
REVERT: G  477 ASN cc_start: 0.8615 (m-40) cc_final: 0.8381 (t0)
  outliers start: 48
  outliers final: 30
  residues processed: 289
  average time/residue: 0.7933
  time to fit residues: 260.1713
Evaluate side-chains
  292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 256
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  508 GLU
Chi-restraints excluded: chain B residue  564 ASP
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   35 SER
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   69 ARG
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  385 VAL
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 129 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0050
   chunk 99 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 246 GLN
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 334 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.101247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086857 restraints weight = 26578.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 3.02
r_work: 0.3382 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13868  Z= 0.146
  Angle     :  0.677  15.227  19188  Z= 0.351
  Chirality :  0.042   0.225   2148
  Planarity :  0.005   0.061   2152
  Dihedral  : 18.978 169.968   2749
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 32.64 %
    Favored  : 63.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.22), residues: 1444
  helix:  1.87 (0.25), residues: 428
  sheet:  0.57 (0.29), residues: 342
  loop : -0.50 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 340 
 HIS   0.005   0.001   HIS A 114 
 PHE   0.029   0.002   PHE A 143 
 TYR   0.025   0.002   TYR F 240 
 ARG   0.015   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  589)
  hydrogen bonds       : angle       4.46067 ( 1631)
  covalent geometry    : bond        0.00340 (13868)
  covalent geometry    : angle       0.67697 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 256
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8585 (tt0) cc_final: 0.8225 (tt0)
REVERT: A  121 ASN cc_start: 0.8491 (t0) cc_final: 0.8193 (t0)
REVERT: A  197 MET cc_start: 0.7521 (mpp) cc_final: 0.7114 (mpp)
REVERT: A  285 SER cc_start: 0.8427 (m) cc_final: 0.7953 (p)
REVERT: A  392 GLN cc_start: 0.8489 (tt0) cc_final: 0.8249 (tt0)
REVERT: B  384 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8433 (mp0)
REVERT: B  401 GLN cc_start: 0.8604 (pm20) cc_final: 0.7948 (pp30)
REVERT: B  411 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8119 (t)
REVERT: F   46 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8472 (pp)
REVERT: F   61 MET cc_start: 0.8754 (mmt) cc_final: 0.8405 (mmt)
REVERT: F   69 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8296 (ptm-80)
REVERT: F  107 CYS cc_start: 0.8177 (t) cc_final: 0.7721 (p)
REVERT: F  214 LYS cc_start: 0.9124 (ptmm) cc_final: 0.8603 (ptmm)
REVERT: F  220 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8313 (ptmt)
REVERT: F  328 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7882 (mm-30)
REVERT: F  428 LEU cc_start: 0.8454 (mm) cc_final: 0.8169 (tp)
REVERT: G  342 SER cc_start: 0.8248 (p) cc_final: 0.7970 (m)
REVERT: G  357 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9123 (p)
REVERT: G  377 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8039 (mptt)
REVERT: G  441 HIS cc_start: 0.7939 (t-90) cc_final: 0.7729 (t70)
REVERT: G  477 ASN cc_start: 0.8611 (m-40) cc_final: 0.8378 (t0)
  outliers start: 44
  outliers final: 32
  residues processed: 280
  average time/residue: 0.8052
  time to fit residues: 256.4982
Evaluate side-chains
  292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 253
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  508 GLU
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   35 SER
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   69 ARG
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  328 GLU
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  385 VAL
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Chi-restraints excluded: chain G residue  485 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0170
   chunk 93 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 119 ASN
A 195 ASN
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 392 GLN
G 334 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.101279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086858 restraints weight = 26636.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.02
r_work: 0.3384 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13868  Z= 0.147
  Angle     :  0.685  15.195  19188  Z= 0.354
  Chirality :  0.042   0.219   2148
  Planarity :  0.005   0.065   2152
  Dihedral  : 18.946 170.161   2749
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 33.36 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: 1444
  helix:  1.91 (0.25), residues: 416
  sheet:  0.55 (0.29), residues: 342
  loop : -0.53 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 340 
 HIS   0.005   0.001   HIS A 114 
 PHE   0.030   0.001   PHE A 143 
 TYR   0.022   0.002   TYR F 240 
 ARG   0.015   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  589)
  hydrogen bonds       : angle       4.46174 ( 1631)
  covalent geometry    : bond        0.00341 (13868)
  covalent geometry    : angle       0.68502 (19188)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 257
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8572 (tt0) cc_final: 0.8189 (tt0)
REVERT: A  121 ASN cc_start: 0.8487 (t0) cc_final: 0.8189 (t0)
REVERT: A  197 MET cc_start: 0.7533 (mpp) cc_final: 0.7184 (mpp)
REVERT: A  285 SER cc_start: 0.8422 (m) cc_final: 0.7949 (p)
REVERT: A  392 GLN cc_start: 0.8481 (tt0) cc_final: 0.8241 (tt0)
REVERT: B  384 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8431 (mp0)
REVERT: B  401 GLN cc_start: 0.8576 (pm20) cc_final: 0.7930 (pp30)
REVERT: B  411 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8169 (t)
REVERT: B  442 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8289 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8455 (pp)
REVERT: F   61 MET cc_start: 0.8760 (mmt) cc_final: 0.8401 (mmt)
REVERT: F   69 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8278 (ppp80)
REVERT: F  107 CYS cc_start: 0.8174 (t) cc_final: 0.7878 (p)
REVERT: F  214 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8597 (ptmm)
REVERT: F  220 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8335 (ptmt)
REVERT: F  295 HIS cc_start: 0.8207 (t-90) cc_final: 0.7987 (t-90)
REVERT: F  328 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7852 (mm-30)
REVERT: F  428 LEU cc_start: 0.8448 (mm) cc_final: 0.8152 (tp)
REVERT: G  342 SER cc_start: 0.8294 (p) cc_final: 0.8050 (m)
REVERT: G  357 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9115 (p)
REVERT: G  377 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8039 (mptt)
REVERT: G  477 ASN cc_start: 0.8629 (m-40) cc_final: 0.8401 (t0)
  outliers start: 41
  outliers final: 32
  residues processed: 280
  average time/residue: 0.8526
  time to fit residues: 270.3670
Evaluate side-chains
  292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 253
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  464 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  508 GLU
Chi-restraints excluded: chain B residue  564 ASP
Chi-restraints excluded: chain F residue   28 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   69 ARG
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  227 LEU
Chi-restraints excluded: chain F residue  262 THR
Chi-restraints excluded: chain F residue  327 THR
Chi-restraints excluded: chain F residue  328 GLU
Chi-restraints excluded: chain F residue  337 SER
Chi-restraints excluded: chain F residue  385 VAL
Chi-restraints excluded: chain F residue  401 THR
Chi-restraints excluded: chain F residue  403 LEU
Chi-restraints excluded: chain F residue  405 ASN
Chi-restraints excluded: chain F residue  421 THR
Chi-restraints excluded: chain G residue  339 VAL
Chi-restraints excluded: chain G residue  347 VAL
Chi-restraints excluded: chain G residue  348 VAL
Chi-restraints excluded: chain G residue  355 THR
Chi-restraints excluded: chain G residue  357 SER
Chi-restraints excluded: chain G residue  372 LEU
Chi-restraints excluded: chain G residue  377 LYS
Chi-restraints excluded: chain G residue  459 LEU
Chi-restraints excluded: chain G residue  478 VAL
Chi-restraints excluded: chain G residue  485 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    0.0870
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 139 optimal weight:    0.2980
   chunk 93 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 119 ASN
A 195 ASN
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 GLN
G 334 ASN
G 441 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.101045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.086544 restraints weight = 26953.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.05
r_work: 0.3378 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13868  Z= 0.152
  Angle     :  0.693  14.640  19188  Z= 0.360
  Chirality :  0.042   0.211   2148
  Planarity :  0.005   0.065   2152
  Dihedral  : 18.935 170.355   2749
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 33.68 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.22), residues: 1444
  helix:  1.84 (0.25), residues: 416
  sheet:  0.52 (0.29), residues: 342
  loop : -0.54 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 340 
 HIS   0.023   0.001   HIS G 441 
 PHE   0.031   0.001   PHE A 143 
 TYR   0.027   0.002   TYR F 341 
 ARG   0.015   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  589)
  hydrogen bonds       : angle       4.50874 ( 1631)
  covalent geometry    : bond        0.00356 (13868)
  covalent geometry    : angle       0.69348 (19188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8885.63 seconds
wall clock time: 154 minutes 7.05 seconds (9247.05 seconds total)