Starting phenix.real_space_refine
on Sun Apr  5 14:23:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhq_49421/04_2026/9nhq_49421.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    6719      2.51       5
     N    1891      2.21       5
     O    2107      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10738
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 849, 6595
          Classifications: {'peptide': 849}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 24, 'TRANS': 824}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "B"
      Number of atoms: 4143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4143
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 525}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 199
          Unresolved non-hydrogen angles: 236
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 6}
          Unresolved non-hydrogen planarities: 106
  Time building chain proxies: 2.47, per 1000 atoms: 0.23
  Number of scatterers: 10738
  At special positions: 0
  Unit cell: (82.712, 120.692, 181.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O    2107      8.00
     N    1891      7.00
     C    6719      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 272 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 455 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 572 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 412.1 milliseconds
  

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2518

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 15 sheets defined
      6.4% alpha, 34.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 58
      removed outlier: 4.257A  pdb=" N   GLY A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 72
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 4.487A  pdb=" N   TYR A  82 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.589A  pdb=" N   GLN A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 3.765A  pdb=" N   VAL A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 264
      removed outlier: 3.598A  pdb=" N   CYS A 264 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 350 through 362
      removed outlier: 3.519A  pdb=" N   PHE A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 451
      removed outlier: 4.199A  pdb=" N   SER A 451 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 451'
    Processing helix  chain 'A' and resid 652 through 658
      removed outlier: 3.740A  pdb=" N   GLY A 658 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'B' and resid 101 through 111
    Processing helix  chain 'B' and resid 669 through 672
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90
      removed outlier: 3.695A  pdb=" N   VAL A  89 " --> pdb=" O   GLY A  98 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   GLY A  98 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117
      removed outlier: 6.393A  pdb=" N   SER A 110 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   PHE A 173 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   THR A 112 " --> pdb=" O   PHE A 173 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   THR A 175 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   SER A 170 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ILE A 153 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ALA A 172 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL A 151 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN A 174 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 196
      removed outlier: 3.588A  pdb=" N   LYS A 193 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 305 through 314
    current: chain 'A' and resid 326 through 341
      removed outlier: 4.464A  pdb=" N   SER A 447 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   GLY A 396 " --> pdb=" O   HIS A 445 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   HIS A 445 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   PHE A 398 " --> pdb=" O   GLN A 443 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   GLN A 443 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   ASP A 400 " --> pdb=" O   PHE A 441 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   PHE A 441 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   THR A 402 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   ASN A 439 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   THR A 404 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   LEU A 437 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   SER A 406 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   VAL A 435 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   TYR A 408 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   GLN A 433 " --> pdb=" O   TYR A 408 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU A 410 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ASP A 431 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   TYR A 412 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   SER A 429 " --> pdb=" O   TYR A 412 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   TYR A 414 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ARG A 427 " --> pdb=" O   TYR A 414 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 482 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 494 through 509
    current: chain 'A' and resid 555 through 559
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 555 through 559
    current: chain 'A' and resid 596 through 611
      removed outlier: 9.335A  pdb=" N   LEU A 624 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   PHE A 648 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   TRP A 626 " --> pdb=" O   THR A 646 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 691 " --> pdb=" O   PHE A 684 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 755 through 764
    current: chain 'A' and resid 805 through 813
      removed outlier: 3.635A  pdb=" N   LEU A 862 " --> pdb=" O   TYR A 854 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 258
    Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 383
    Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 526
    Processing sheet with id=AA8, first strand: chain 'A' and resid 724 through 727
    Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 46
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 45 through 46
    current: chain 'B' and resid 582 through 585
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 582 through 585
    current: chain 'B' and resid 606 through 612
      removed outlier: 4.603A  pdb=" N   LYS B 662 " --> pdb=" O   ALA B 680 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ALA B 680 " --> pdb=" O   LYS B 662 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 89 through 90
      removed outlier: 3.751A  pdb=" N   ILE B 185 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 195 through 197
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 209
      removed outlier: 3.870A  pdb=" N   TRP B 208 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   PHE B 262 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY B 261 " --> pdb=" O   ASN B 282 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LEU B 275 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   GLU B 300 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLY B 277 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   SER B 298 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 279 " --> pdb=" O   TYR B 296 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE B 308 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   SER B 337 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLY B 310 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B 335 " --> pdb=" O   GLY B 310 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   SER B 335 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LEU B 353 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU B 347 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 207 " --> pdb=" O   SER B 364 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 419
    Processing sheet with id=AB5, first strand: chain 'B' and resid 428 through 431
    Processing sheet with id=AB6, first strand: chain 'B' and resid 643 through 644
      removed outlier: 3.605A  pdb=" N   PHE B 643 " --> pdb=" O   ALA B 656 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    900 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3612
        1.34 -     1.46: 2683
        1.46 -     1.58: 4645
        1.58 -     1.70: 0
        1.70 -     1.81: 34
  Bond restraints: 10974
  Sorted by residual:
  bond pdb=" C   GLN B 141 "
       pdb=" N   PRO B 142 "
    ideal  model  delta    sigma   weight residual
    1.333  1.355 -0.021 1.01e-02 9.80e+03 4.39e+00
  bond pdb=" C   TYR B 681 "
       pdb=" N   PRO B 682 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.13e+00
  bond pdb=" CA  GLU A 817 "
       pdb=" C   GLU A 817 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.34e-02 5.57e+03 2.44e+00
  bond pdb=" CA  ILE B 119 "
       pdb=" CB  ILE B 119 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.05e-02 9.07e+03 1.71e+00
  bond pdb=" CA  ARG A 873 "
       pdb=" C   ARG A 873 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.014 1.17e-02 7.31e+03 1.46e+00
  ... (remaining 10969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 13887
        1.28 -     2.57: 792
        2.57 -     3.85: 140
        3.85 -     5.13: 29
        5.13 -     6.42: 10
  Bond angle restraints: 14858
  Sorted by residual:
  angle pdb=" C   ASN A 893 "
        pdb=" CA  ASN A 893 "
        pdb=" CB  ASN A 893 "
      ideal   model   delta    sigma   weight residual
     109.71  114.84   -5.13 1.39e+00 5.18e-01 1.36e+01
  angle pdb=" N   ASP A 105 "
        pdb=" CA  ASP A 105 "
        pdb=" C   ASP A 105 "
      ideal   model   delta    sigma   weight residual
     113.43  108.98    4.45 1.26e+00 6.30e-01 1.25e+01
  angle pdb=" C   LYS B 628 "
        pdb=" N   ASP B 629 "
        pdb=" CA  ASP B 629 "
      ideal   model   delta    sigma   weight residual
     121.54  127.96   -6.42 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" N   ASP B 414 "
        pdb=" CA  ASP B 414 "
        pdb=" C   ASP B 414 "
      ideal   model   delta    sigma   weight residual
     114.75  110.80    3.95 1.26e+00 6.30e-01 9.84e+00
  angle pdb=" N   ARG B 194 "
        pdb=" CA  ARG B 194 "
        pdb=" C   ARG B 194 "
      ideal   model   delta    sigma   weight residual
     114.56  110.59    3.97 1.27e+00 6.20e-01 9.76e+00
  ... (remaining 14853 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 5855
       17.08 -    34.16: 468
       34.16 -    51.24: 89
       51.24 -    68.31: 12
       68.31 -    85.39: 11
  Dihedral angle restraints: 6435
    sinusoidal: 2450
      harmonic: 3985
  Sorted by residual:
  dihedral pdb=" CA  ASN B 288 "
           pdb=" C   ASN B 288 "
           pdb=" N   ASN B 289 "
           pdb=" CA  ASN B 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.58  -38.42     0      5.00e+00 4.00e-02 5.90e+01
  dihedral pdb=" CA  ASP B 287 "
           pdb=" C   ASP B 287 "
           pdb=" N   ASN B 288 "
           pdb=" CA  ASN B 288 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.24  -29.76     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  ASN A 745 "
           pdb=" C   ASN A 745 "
           pdb=" N   GLY A 746 "
           pdb=" CA  GLY A 746 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.50  -29.50     0      5.00e+00 4.00e-02 3.48e+01
  ... (remaining 6432 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1068
       0.035 -    0.071: 336
       0.071 -    0.106: 124
       0.106 -    0.142: 29
       0.142 -    0.177: 3
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CB  ILE B 119 "
            pdb=" CA  ILE B 119 "
            pdb=" CG1 ILE B 119 "
            pdb=" CG2 ILE B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CA  VAL A 856 "
            pdb=" N   VAL A 856 "
            pdb=" C   VAL A 856 "
            pdb=" CB  VAL A 856 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL B  81 "
            pdb=" N   VAL B  81 "
            pdb=" C   VAL B  81 "
            pdb=" CB  VAL B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 1557 not shown)

  Planarity restraints: 1970
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 628 "   -0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   LYS B 628 "    0.056 2.00e-02 2.50e+03
        pdb=" O   LYS B 628 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP B 629 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 100 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO B 101 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 101 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 101 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 288 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.69e+00
        pdb=" C   ASN B 288 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ASN B 288 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASN B 289 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1967 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1020
        2.74 -     3.28: 10582
        3.28 -     3.82: 17305
        3.82 -     4.36: 19561
        4.36 -     4.90: 34533
  Nonbonded interactions: 83001
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 298 "
            pdb=" OG1 THR B 313 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD1 ASN A 416 "
            pdb=" OG1 THR A 421 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A 798 "
            pdb=" OH  TYR A 853 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   ALA A 134 "
            pdb=" OH  TYR A 569 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OH  TYR B 124 "
            pdb=" NE2 HIS B 209 "
     model   vdw
     2.305 3.120
  ... (remaining 82996 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.100
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10977  Z= 0.143
  Angle     :  0.685   6.418  14864  Z= 0.425
  Chirality :  0.041   0.177   1560
  Planarity :  0.003   0.043   1970
  Dihedral  : 12.892  85.392   3908
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.35 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.98 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.32 (0.20), residues: 1378
  helix: -1.43 (0.62), residues: 55
  sheet: -1.01 (0.20), residues: 588
  loop : -3.43 (0.18), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.008   0.001   TYR A 583 
 PHE   0.008   0.001   PHE B 352 
 TRP   0.008   0.001   TRP A 637 
 HIS   0.004   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (10974)
  covalent geometry    : angle       0.68497 (14858)
  SS BOND              : bond        0.00114 (    3)
  SS BOND              : angle       0.93073 (    6)
  hydrogen bonds       : bond        0.15203 (  332)
  hydrogen bonds       : angle       7.17970 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 MET cc_start: 0.8524 (mmp) cc_final: 0.8241 (mmp)
REVERT: A  632 LEU cc_start: 0.9081 (tt) cc_final: 0.8312 (mp)
REVERT: A  639 ASP cc_start: 0.8684 (t0) cc_final: 0.8466 (t0)
REVERT: B  352 PHE cc_start: 0.8030 (p90) cc_final: 0.7710 (p90)
REVERT: B  425 ASN cc_start: 0.9435 (t0) cc_final: 0.9082 (t0)
REVERT: B  550 GLN cc_start: 0.8234 (pt0) cc_final: 0.7938 (pt0)
  outliers start: 3
  outliers final: 1
  residues processed: 99
  average time/residue: 0.1057
  time to fit residues: 14.8807
Evaluate side-chains
  59 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
A  75 ASN
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 445 HIS
A 519 HIS
A 745 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 ASN
B 594 ASN
B 647 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.054277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.042642 restraints weight = 65193.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.043787 restraints weight = 37564.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.044378 restraints weight = 25902.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.044967 restraints weight = 20913.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.045373 restraints weight = 17388.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  10977  Z= 0.317
  Angle     :  0.724   8.175  14864  Z= 0.390
  Chirality :  0.044   0.147   1560
  Planarity :  0.005   0.052   1970
  Dihedral  :  5.376  45.311   1539
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.47 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  8.03 %
    Favored  : 91.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.20), residues: 1378
  helix: -1.41 (0.63), residues: 61
  sheet: -0.82 (0.21), residues: 566
  loop : -3.15 (0.19), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 221 
 TYR   0.025   0.002   TYR A 307 
 PHE   0.023   0.002   PHE A 338 
 TRP   0.015   0.002   TRP B 159 
 HIS   0.012   0.002   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 (10974)
  covalent geometry    : angle       0.72244 (14858)
  SS BOND              : bond        0.00379 (    3)
  SS BOND              : angle       2.20301 (    6)
  hydrogen bonds       : bond        0.04121 (  332)
  hydrogen bonds       : angle       6.08990 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  544 THR cc_start: 0.9134 (m) cc_final: 0.8892 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0661
  time to fit residues: 5.8880
Evaluate side-chains
  42 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 124 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0070
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    2.4006

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 439 ASN
A 440 HIS
A 442 GLN
A 745 ASN
A 890 GLN
B 209 HIS
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.055014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.043278 restraints weight = 63748.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.044452 restraints weight = 37100.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.045209 restraints weight = 25330.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.045754 restraints weight = 19540.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.046057 restraints weight = 16284.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10977  Z= 0.183
  Angle     :  0.606   8.928  14864  Z= 0.326
  Chirality :  0.043   0.146   1560
  Planarity :  0.004   0.048   1970
  Dihedral  :  5.112  42.470   1539
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.16 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.21), residues: 1378
  helix: -0.74 (0.71), residues: 55
  sheet: -0.48 (0.21), residues: 555
  loop : -2.95 (0.19), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 281 
 TYR   0.012   0.001   TYR A 465 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.011   0.001   TRP B 159 
 HIS   0.005   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (10974)
  covalent geometry    : angle       0.60384 (14858)
  SS BOND              : bond        0.00535 (    3)
  SS BOND              : angle       2.70366 (    6)
  hydrogen bonds       : bond        0.03274 (  332)
  hydrogen bonds       : angle       5.75191 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8702 (tptm) cc_final: 0.8404 (tptm)
REVERT: A  682 ILE cc_start: 0.9598 (pt) cc_final: 0.9348 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0724
  time to fit residues: 6.9753
Evaluate side-chains
  41 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0270
   chunk 129 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0980
   overall best weight:    1.4244

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 890 GLN
B 209 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.055899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.044069 restraints weight = 63706.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.045244 restraints weight = 36098.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.046057 restraints weight = 24494.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.046622 restraints weight = 18691.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.046924 restraints weight = 15466.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10977  Z= 0.125
  Angle     :  0.570   8.487  14864  Z= 0.305
  Chirality :  0.042   0.147   1560
  Planarity :  0.004   0.044   1970
  Dihedral  :  4.857  42.967   1539
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.30 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.21), residues: 1378
  helix:  0.40 (0.80), residues: 49
  sheet: -0.35 (0.21), residues: 565
  loop : -2.77 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.013   0.001   TYR B 681 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.011   0.001   TRP A 548 
 HIS   0.004   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10974)
  covalent geometry    : angle       0.56928 (14858)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.68521 (    6)
  hydrogen bonds       : bond        0.02859 (  332)
  hydrogen bonds       : angle       5.48923 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8674 (tptm) cc_final: 0.8412 (tptm)
REVERT: B  361 VAL cc_start: 0.8909 (t) cc_final: 0.8699 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0882
  time to fit residues: 7.8707
Evaluate side-chains
  46 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 76 optimal weight:    0.0970
   chunk 98 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 82 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 889 ASN
B 209 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.056951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.045215 restraints weight = 62760.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.046400 restraints weight = 35328.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.047249 restraints weight = 24007.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.047716 restraints weight = 18236.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.048146 restraints weight = 15308.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10977  Z= 0.095
  Angle     :  0.562   8.252  14864  Z= 0.298
  Chirality :  0.043   0.148   1560
  Planarity :  0.004   0.044   1970
  Dihedral  :  4.709  42.373   1539
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.87 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.22), residues: 1378
  helix:  0.49 (0.80), residues: 49
  sheet: -0.13 (0.22), residues: 560
  loop : -2.64 (0.20), residues: 769

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 511 
 TYR   0.010   0.001   TYR B 204 
 PHE   0.009   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 748 
 HIS   0.009   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (10974)
  covalent geometry    : angle       0.56092 (14858)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       2.12019 (    6)
  hydrogen bonds       : bond        0.02675 (  332)
  hydrogen bonds       : angle       5.31336 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8614 (tptm) cc_final: 0.8374 (tptm)
REVERT: A  632 LEU cc_start: 0.9261 (tp) cc_final: 0.8755 (mp)
REVERT: B  361 VAL cc_start: 0.8913 (t) cc_final: 0.8685 (t)
REVERT: B  412 LEU cc_start: 0.8919 (tp) cc_final: 0.8642 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0923
  time to fit residues: 9.2579
Evaluate side-chains
  48 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 131 optimal weight:    0.0980
   chunk 53 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 126 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
B 209 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.054861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.043195 restraints weight = 63705.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.044337 restraints weight = 36682.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.045124 restraints weight = 25160.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.045638 restraints weight = 19329.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.045994 restraints weight = 16218.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10977  Z= 0.173
  Angle     :  0.594   9.017  14864  Z= 0.318
  Chirality :  0.042   0.146   1560
  Planarity :  0.004   0.045   1970
  Dihedral  :  4.974  42.940   1539
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.18 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.22), residues: 1378
  helix:  0.37 (0.79), residues: 49
  sheet: -0.21 (0.22), residues: 562
  loop : -2.61 (0.20), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 341 
 TYR   0.012   0.001   TYR A  82 
 PHE   0.012   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 312 
 HIS   0.010   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10974)
  covalent geometry    : angle       0.59214 (14858)
  SS BOND              : bond        0.00353 (    3)
  SS BOND              : angle       2.31590 (    6)
  hydrogen bonds       : bond        0.03061 (  332)
  hydrogen bonds       : angle       5.49941 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8738 (tptm) cc_final: 0.8472 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0744
  time to fit residues: 7.3545
Evaluate side-chains
  47 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 133 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 126 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 385 ASN
A 416 ASN
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 890 GLN
B  58 GLN
B 209 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.055415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.043693 restraints weight = 63562.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044809 restraints weight = 36386.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.045611 restraints weight = 25041.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.046112 restraints weight = 19342.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.046525 restraints weight = 16217.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10977  Z= 0.136
  Angle     :  0.574   8.527  14864  Z= 0.305
  Chirality :  0.042   0.156   1560
  Planarity :  0.004   0.044   1970
  Dihedral  :  4.863  42.375   1539
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.01 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.22), residues: 1378
  helix:  0.45 (0.79), residues: 49
  sheet: -0.15 (0.21), residues: 568
  loop : -2.56 (0.20), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.014   0.001   TYR A 846 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.011   0.001   TRP A 748 
 HIS   0.008   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10974)
  covalent geometry    : angle       0.57284 (14858)
  SS BOND              : bond        0.00310 (    3)
  SS BOND              : angle       1.82020 (    6)
  hydrogen bonds       : bond        0.02850 (  332)
  hydrogen bonds       : angle       5.39045 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8716 (tptm) cc_final: 0.8454 (tptm)
REVERT: A  343 MET cc_start: 0.9180 (mmp) cc_final: 0.8855 (mmp)
REVERT: A  632 LEU cc_start: 0.9171 (tt) cc_final: 0.8431 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0765
  time to fit residues: 7.5477
Evaluate side-chains
  47 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 132 optimal weight:    8.9990
   chunk 107 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0980
   chunk 1 optimal weight:    0.0670
   chunk 78 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   overall best weight:    1.8322

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 890 GLN
B 209 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.055283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.043657 restraints weight = 63052.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044799 restraints weight = 36302.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.045576 restraints weight = 24828.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.046086 restraints weight = 19142.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.046457 restraints weight = 16008.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10977  Z= 0.146
  Angle     :  0.585   8.651  14864  Z= 0.312
  Chirality :  0.042   0.150   1560
  Planarity :  0.004   0.045   1970
  Dihedral  :  4.925  42.146   1539
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.81 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.22), residues: 1378
  helix:  0.39 (0.79), residues: 49
  sheet: -0.14 (0.22), residues: 561
  loop : -2.49 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.012   0.001   TYR A 846 
 PHE   0.012   0.001   PHE B 152 
 TRP   0.010   0.001   TRP A 548 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10974)
  covalent geometry    : angle       0.58412 (14858)
  SS BOND              : bond        0.00296 (    3)
  SS BOND              : angle       1.96373 (    6)
  hydrogen bonds       : bond        0.02942 (  332)
  hydrogen bonds       : angle       5.46850 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8714 (tptm) cc_final: 0.8489 (tptm)
REVERT: A  632 LEU cc_start: 0.9209 (tt) cc_final: 0.8448 (mp)
REVERT: B  361 VAL cc_start: 0.8937 (t) cc_final: 0.8737 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0752
  time to fit residues: 7.2659
Evaluate side-chains
  45 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 122 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 118 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 787 GLN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.042501 restraints weight = 63722.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.043638 restraints weight = 36841.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.044390 restraints weight = 25278.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.044910 restraints weight = 19508.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.045209 restraints weight = 16325.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10977  Z= 0.210
  Angle     :  0.636   9.669  14864  Z= 0.340
  Chirality :  0.043   0.154   1560
  Planarity :  0.004   0.046   1970
  Dihedral  :  5.244  42.781   1539
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.54 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.22), residues: 1378
  helix:  0.24 (0.78), residues: 49
  sheet: -0.29 (0.22), residues: 552
  loop : -2.44 (0.21), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 341 
 TYR   0.016   0.002   TYR A 846 
 PHE   0.012   0.002   PHE A 338 
 TRP   0.013   0.002   TRP A 312 
 HIS   0.007   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (10974)
  covalent geometry    : angle       0.63443 (14858)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       2.59593 (    6)
  hydrogen bonds       : bond        0.03319 (  332)
  hydrogen bonds       : angle       5.71966 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  283 LYS cc_start: 0.8704 (tptm) cc_final: 0.8481 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0777
  time to fit residues: 7.2100
Evaluate side-chains
  43 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 890 GLN
B  53 GLN
B 209 HIS
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.054122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.042578 restraints weight = 63560.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.043692 restraints weight = 36762.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.044454 restraints weight = 25279.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.044972 restraints weight = 19487.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.045172 restraints weight = 16365.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10977  Z= 0.202
  Angle     :  0.637   9.615  14864  Z= 0.338
  Chirality :  0.043   0.153   1560
  Planarity :  0.004   0.046   1970
  Dihedral  :  5.289  43.185   1539
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.54 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.22), residues: 1378
  helix:  0.19 (0.78), residues: 49
  sheet: -0.40 (0.21), residues: 563
  loop : -2.42 (0.21), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.013   0.002   TYR A  82 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.014   0.001   TRP A 312 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (10974)
  covalent geometry    : angle       0.63423 (14858)
  SS BOND              : bond        0.00484 (    3)
  SS BOND              : angle       2.76141 (    6)
  hydrogen bonds       : bond        0.03283 (  332)
  hydrogen bonds       : angle       5.75672 (  900)

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

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

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2756 Ramachandran restraints generated.
    1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  809 MET cc_start: 0.8640 (ttm) cc_final: 0.8410 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0796
  time to fit residues: 7.1658
Evaluate side-chains
  43 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 24 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 133 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 129 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 ASN
A 890 GLN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.055467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.043756 restraints weight = 63195.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.044944 restraints weight = 35927.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.045719 restraints weight = 24341.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.046278 restraints weight = 18684.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.046586 restraints weight = 15464.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10977  Z= 0.114
  Angle     :  0.592   9.400  14864  Z= 0.311
  Chirality :  0.043   0.152   1560
  Planarity :  0.004   0.045   1970
  Dihedral  :  4.964  42.078   1539
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.65 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.22), residues: 1378
  helix: -0.04 (0.74), residues: 55
  sheet: -0.25 (0.22), residues: 560
  loop : -2.37 (0.21), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.016   0.001   TYR B 124 
 PHE   0.008   0.001   PHE A 860 
 TRP   0.014   0.001   TRP A 548 
 HIS   0.006   0.001   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10974)
  covalent geometry    : angle       0.59079 (14858)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       1.77388 (    6)
  hydrogen bonds       : bond        0.02889 (  332)
  hydrogen bonds       : angle       5.46942 (  900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1598.15 seconds
wall clock time: 28 minutes 29.17 seconds (1709.17 seconds total)