Starting phenix.real_space_refine
on Tue Feb 11 17:14:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqu_15590/02_2025/8aqu_15590.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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      37      5.16       5
     C    4049      2.51       5
     N    1062      2.21       5
     O    1192      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6340
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4744
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 557}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1554
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.83, per 1000 atoms: 0.76
  Number of scatterers: 6340
  At special positions: 0
  Unit cell: (96.4503, 81.9309, 113.044, 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      37     16.00
     O    1192      8.00
     N    1062      7.00
     C    4049      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B 526 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      49.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.512A  pdb=" N   ALA A  25 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASP A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 88
      removed outlier: 4.859A  pdb=" N   SER A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LEU A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 9.568A  pdb=" N   GLN A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 9.949A  pdb=" N   GLU A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ILE A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 5.539A  pdb=" N   LYS A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ARG A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 128
      removed outlier: 4.652A  pdb=" N   GLN A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ASN A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE A 119 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ASN A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   THR A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.872A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   THR A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   SER A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 4.471A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   TRP A 163 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TRP A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 4.636A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ALA A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ARG A 192 " --> pdb=" O   ASN A 188 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   ALA A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.727A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 3.634A  pdb=" N   TYR A 279 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      No H-bonds generated for 'chain 'A' and resid 275 through 282'
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.977A  pdb=" N   ASN A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A 300 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.723A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLN A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.943A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 393
      removed outlier: 4.011A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ALA A 386 " --> pdb=" O   ASP A 382 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ARG A 387 " --> pdb=" O   MET A 383 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   GLN A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      Proline residue:  A 389  - end of helix
      removed outlier: 5.879A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 419
      removed outlier: 3.839A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      Proline residue:  A 415  - end of helix
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.607A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL A 447 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
      removed outlier: 3.865A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   GLY A 466 " --> pdb=" O   MET A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.268A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
      removed outlier: 4.980A  pdb=" N   SER A 502 " --> pdb=" O   CYS A 498 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   LEU A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   PHE A 504 " --> pdb=" O   PRO A 500 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   HIS A 505 " --> pdb=" O   ALA A 501 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   VAL A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.529A  pdb=" N   ARG A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 575
      removed outlier: 4.000A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   LEU A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ASN A 562 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   SER A 563 " --> pdb=" O   SER A 559 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLU A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      Proline residue:  A 565  - end of helix
      removed outlier: 6.348A  pdb=" N   LYS A 568 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 574 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      removed outlier: 3.949A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
      removed outlier: 5.375A  pdb=" N   ASP A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   LEU A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN A 599 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.865A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 4.425A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 370'
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 416 through 421
      removed outlier: 4.236A  pdb=" N   ASP B 420 " --> pdb=" O   GLY B 416 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   TYR B 421 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 416 through 421'

    177 hydrogen bonds defined for protein.
    531 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: 1.30

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2039
        1.35 -     1.47: 1681
        1.47 -     1.59: 2737
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 6515
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.468 -0.062 2.00e-02 2.50e+03 9.63e+00
  bond pdb=" C   ASP A 499 "
       pdb=" N   PRO A 500 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.038 2.34e-02 1.83e+03 2.58e+00
  bond pdb=" C1  NAG B 526 "
       pdb=" O5  NAG B 526 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.440 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" C2  NAG B 526 "
       pdb=" N2  NAG B 526 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.59e+00
  ... (remaining 6510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 8592
        1.60 -     3.20: 211
        3.20 -     4.79: 35
        4.79 -     6.39: 8
        6.39 -     7.99: 1
  Bond angle restraints: 8847
  Sorted by residual:
  angle pdb=" C   ALA A 107 "
        pdb=" CA  ALA A 107 "
        pdb=" CB  ALA A 107 "
      ideal   model   delta    sigma   weight residual
     115.89  110.49    5.40 1.32e+00 5.74e-01 1.67e+01
  angle pdb=" N   GLU A 471 "
        pdb=" CA  GLU A 471 "
        pdb=" C   GLU A 471 "
      ideal   model   delta    sigma   weight residual
     114.56  109.81    4.75 1.27e+00 6.20e-01 1.40e+01
  angle pdb=" N   VAL A 318 "
        pdb=" CA  VAL A 318 "
        pdb=" C   VAL A 318 "
      ideal   model   delta    sigma   weight residual
     111.81  109.20    2.61 8.60e-01 1.35e+00 9.24e+00
  angle pdb=" C   THR A  55 "
        pdb=" N   GLU A  56 "
        pdb=" CA  GLU A  56 "
      ideal   model   delta    sigma   weight residual
     121.54  127.16   -5.62 1.91e+00 2.74e-01 8.65e+00
  angle pdb=" C   ARG B 457 "
        pdb=" N   LYS B 458 "
        pdb=" CA  LYS B 458 "
      ideal   model   delta    sigma   weight residual
     121.54  127.07   -5.53 1.91e+00 2.74e-01 8.39e+00
  ... (remaining 8842 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.87: 3621
       22.87 -    45.74: 232
       45.74 -    68.61: 22
       68.61 -    91.48: 12
       91.48 -   114.35: 17
  Dihedral angle restraints: 3904
    sinusoidal: 1614
      harmonic: 2290
  Sorted by residual:
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -29.20  -56.80     1      1.00e+01 1.00e-02 4.34e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C1  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   51.39 -114.35     1      3.00e+01 1.11e-03 1.51e+01
  dihedral pdb=" C3  NAG C   2 "
           pdb=" C1  NAG C   2 "
           pdb=" C2  NAG C   2 "
           pdb=" O5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   55.41 -110.96     1      3.00e+01 1.11e-03 1.45e+01
  ... (remaining 3901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 592
       0.035 -    0.070: 253
       0.070 -    0.105: 76
       0.105 -    0.139: 9
       0.139 -    0.174: 2
  Chirality restraints: 932
  Sorted by residual:
  chirality pdb=" C2  NAG B 526 "
            pdb=" C1  NAG B 526 "
            pdb=" C3  NAG B 526 "
            pdb=" N2  NAG B 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  PRO B 337 "
            pdb=" N   PRO B 337 "
            pdb=" C   PRO B 337 "
            pdb=" CB  PRO B 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 929 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 336 "    0.048 5.00e-02 4.00e+02   7.30e-02 8.53e+00
        pdb=" N   PRO B 337 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B 337 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 337 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  56 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   GLU A  56 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLU A  56 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A  57 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 134 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 135 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 135 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 135 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1190
        2.77 -     3.30: 6104
        3.30 -     3.84: 9943
        3.84 -     4.37: 11280
        4.37 -     4.90: 19334
  Nonbonded interactions: 47851
  Sorted by model distance:
  nonbonded pdb=" O   SER A  77 "
            pdb=" NE2 GLN A  81 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   ARG A 273 "
            pdb=" OG1 THR A 445 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   ASN A  53 "
            pdb=" ND2 ASN A  58 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OD1 ASP A 382 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NH1 ARG B 454 "
            pdb=" O   ASP B 467 "
     model   vdw
     2.311 3.120
  ... (remaining 47846 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.510
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     17.920
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6515  Z= 0.182
  Angle     :  0.616   7.988   8847  Z= 0.340
  Chirality :  0.040   0.174    932
  Planarity :  0.005   0.073   1145
  Dihedral  : 16.844 114.347   2414
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.31), residues: 773
  helix:  0.63 (0.33), residues: 274
  sheet: -2.59 (0.83), residues: 37
  loop : -1.94 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 461 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.017   0.001   PHE B 497 
 TYR   0.015   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 355 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  439 LEU cc_start: 0.6302 (pp) cc_final: 0.6079 (mp)
REVERT: A  455 MET cc_start: 0.7447 (ppp) cc_final: 0.7055 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1896
  time to fit residues: 32.1850
Evaluate side-chains
  89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0020
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 265 HIS
A 345 HIS
A 388 GLN
A 442 GLN
A 526 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.236370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.203569 restraints weight = 9212.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4414 rms_B_bonded: 3.48
r_work: 0.4113 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6515  Z= 0.174
  Angle     :  0.616   9.679   8847  Z= 0.300
  Chirality :  0.043   0.234    932
  Planarity :  0.005   0.074   1145
  Dihedral  : 11.467 106.092    915
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.91 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.31), residues: 773
  helix:  0.23 (0.31), residues: 295
  sheet: -2.28 (0.84), residues: 36
  loop : -1.95 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.017   0.001   PHE A 452 
 TYR   0.039   0.002   TYR A 535 
 ARG   0.005   0.000   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6733 (tt0)
REVERT: A  236 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.3915 (mt)
REVERT: A  270 MET cc_start: 0.2586 (tpt) cc_final: 0.2024 (tpt)
REVERT: A  455 MET cc_start: 0.7512 (ppp) cc_final: 0.7171 (ppp)
  outliers start: 7
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1753
  time to fit residues: 22.2974
Evaluate side-chains
  86 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.225529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.192519 restraints weight = 9395.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.4289 rms_B_bonded: 4.68
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6515  Z= 0.316
  Angle     :  0.689   9.872   8847  Z= 0.345
  Chirality :  0.044   0.258    932
  Planarity :  0.005   0.070   1145
  Dihedral  :  8.191  89.762    914
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.44 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 12.72 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.30), residues: 773
  helix: -0.21 (0.30), residues: 300
  sheet: -2.31 (0.74), residues: 47
  loop : -2.27 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.016   0.002   PHE B 347 
 TYR   0.022   0.002   TYR B 453 
 ARG   0.004   0.001   ARG B 509 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 TYR cc_start: 0.2515 (OUTLIER) cc_final: 0.2029 (m-80)
REVERT: A  229 THR cc_start: 0.2448 (t) cc_final: 0.1876 (m)
REVERT: A  236 LEU cc_start: 0.4363 (OUTLIER) cc_final: 0.3873 (mt)
REVERT: A  270 MET cc_start: 0.2113 (tpt) cc_final: 0.1769 (tpt)
REVERT: A  455 MET cc_start: 0.6988 (ppp) cc_final: 0.6517 (ppp)
  outliers start: 22
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1553
  time to fit residues: 22.3377
Evaluate side-chains
  94 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  330 ASN
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0570
   chunk 24 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
A 397 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.227873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.193634 restraints weight = 9385.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 4.04
r_work: 0.3996 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6515  Z= 0.176
  Angle     :  0.611   9.708   8847  Z= 0.298
  Chirality :  0.042   0.248    932
  Planarity :  0.005   0.065   1145
  Dihedral  :  7.683  86.881    914
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.05 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.30), residues: 773
  helix: -0.02 (0.31), residues: 300
  sheet: -2.03 (0.73), residues: 49
  loop : -2.17 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.008   0.001   PHE A 369 
 TYR   0.015   0.001   TYR A 535 
 ARG   0.002   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  229 THR cc_start: 0.2055 (t) cc_final: 0.1265 (m)
REVERT: A  236 LEU cc_start: 0.4592 (OUTLIER) cc_final: 0.4097 (mt)
REVERT: A  270 MET cc_start: 0.2020 (tpt) cc_final: 0.1568 (tpt)
REVERT: A  455 MET cc_start: 0.6999 (ppp) cc_final: 0.6453 (ppp)
REVERT: B  418 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7758 (tt)
  outliers start: 21
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1588
  time to fit residues: 21.5120
Evaluate side-chains
  90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0060
   chunk 63 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    1.2600

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

Flipped N/Q/H residues before XYZ refinement:
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.222034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.187532 restraints weight = 9326.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 3.64
r_work: 0.3962 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6515  Z= 0.255
  Angle     :  0.646   9.859   8847  Z= 0.322
  Chirality :  0.043   0.254    932
  Planarity :  0.005   0.062   1145
  Dihedral  :  7.385  79.431    914
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.09 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.30), residues: 773
  helix: -0.10 (0.31), residues: 305
  sheet: -2.02 (0.74), residues: 49
  loop : -2.22 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.013   0.002   PHE A 603 
 TYR   0.016   0.002   TYR B 453 
 ARG   0.003   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  236 LEU cc_start: 0.4626 (OUTLIER) cc_final: 0.4157 (mt)
REVERT: A  241 HIS cc_start: 0.3440 (m90) cc_final: 0.3234 (t-170)
REVERT: A  270 MET cc_start: 0.2019 (tpt) cc_final: 0.1685 (tpt)
REVERT: A  455 MET cc_start: 0.6837 (ppp) cc_final: 0.6282 (ppp)
REVERT: A  579 MET cc_start: 0.6993 (mtm) cc_final: 0.6764 (mtt)
REVERT: B  380 TYR cc_start: 0.7258 (m-80) cc_final: 0.6945 (m-80)
REVERT: B  418 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7775 (tt)
  outliers start: 27
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1526
  time to fit residues: 23.2950
Evaluate side-chains
  91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0970
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0470
   overall best weight:    0.3454

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.227437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.193532 restraints weight = 9332.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.4309 rms_B_bonded: 3.92
r_work: 0.3998 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6515  Z= 0.161
  Angle     :  0.603   9.742   8847  Z= 0.296
  Chirality :  0.041   0.249    932
  Planarity :  0.005   0.060   1145
  Dihedral  :  7.086  75.863    914
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.42 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.31), residues: 773
  helix:  0.11 (0.31), residues: 306
  sheet: -1.85 (0.73), residues: 49
  loop : -2.11 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.009   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 535 
 ARG   0.002   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  236 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4154 (mt)
REVERT: A  270 MET cc_start: 0.2118 (tpt) cc_final: 0.1714 (tpt)
REVERT: A  455 MET cc_start: 0.6764 (ppp) cc_final: 0.6221 (ppp)
REVERT: A  592 PHE cc_start: 0.5527 (OUTLIER) cc_final: 0.4773 (t80)
REVERT: B  418 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7671 (tt)
  outliers start: 20
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1454
  time to fit residues: 19.7676
Evaluate side-chains
  90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0370
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0170
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.227204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.193199 restraints weight = 9312.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 3.96
r_work: 0.3997 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6515  Z= 0.161
  Angle     :  0.600   9.742   8847  Z= 0.293
  Chirality :  0.041   0.248    932
  Planarity :  0.005   0.059   1145
  Dihedral  :  6.828  72.720    914
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.05 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.31), residues: 773
  helix:  0.14 (0.31), residues: 310
  sheet: -1.93 (0.75), residues: 47
  loop : -2.07 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 459 
 HIS   0.011   0.001   HIS A 241 
 PHE   0.010   0.001   PHE A 369 
 TYR   0.009   0.001   TYR B 380 
 ARG   0.002   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  152 MET cc_start: 0.0406 (ttt) cc_final: -0.0583 (ptp)
REVERT: A  158 TYR cc_start: 0.2697 (m-80) cc_final: 0.2425 (m-10)
REVERT: A  236 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.4030 (mt)
REVERT: A  270 MET cc_start: 0.2098 (tpt) cc_final: 0.1734 (tpt)
REVERT: A  455 MET cc_start: 0.6784 (ppp) cc_final: 0.6245 (ppp)
REVERT: A  592 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.4754 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1453
  time to fit residues: 19.4480
Evaluate side-chains
  88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0020
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.227019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.192964 restraints weight = 9283.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.4286 rms_B_bonded: 3.97
r_work: 0.3972 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6515  Z= 0.173
  Angle     :  0.611  10.377   8847  Z= 0.295
  Chirality :  0.041   0.251    932
  Planarity :  0.005   0.058   1145
  Dihedral  :  6.573  67.563    914
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.60 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.31), residues: 773
  helix:  0.18 (0.31), residues: 306
  sheet: -2.00 (0.75), residues: 47
  loop : -2.07 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.010   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A  152 MET cc_start: 0.0450 (ttt) cc_final: -0.0562 (ptp)
REVERT: A  158 TYR cc_start: 0.3031 (m-80) cc_final: 0.2770 (m-10)
REVERT: A  236 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.3976 (mt)
REVERT: A  270 MET cc_start: 0.2016 (tpt) cc_final: 0.1638 (tpt)
REVERT: A  455 MET cc_start: 0.6818 (ppp) cc_final: 0.6237 (ppp)
REVERT: A  592 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.4715 (t80)
REVERT: B  418 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7669 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1634
  time to fit residues: 21.4990
Evaluate side-chains
  90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0970
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.226387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.192168 restraints weight = 9347.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 3.96
r_work: 0.3968 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6515  Z= 0.179
  Angle     :  0.631  13.780   8847  Z= 0.302
  Chirality :  0.041   0.249    932
  Planarity :  0.005   0.057   1145
  Dihedral  :  6.294  60.884    914
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.60 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.31), residues: 773
  helix:  0.16 (0.31), residues: 309
  sheet: -1.95 (0.76), residues: 47
  loop : -2.07 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.010   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A  41 
 ARG   0.002   0.000   ARG B 454 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  152 MET cc_start: 0.0348 (ttt) cc_final: -0.0597 (ptp)
REVERT: A  158 TYR cc_start: 0.3389 (m-80) cc_final: 0.3158 (m-10)
REVERT: A  236 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3972 (mt)
REVERT: A  270 MET cc_start: 0.1975 (tpt) cc_final: 0.1619 (tpt)
REVERT: A  455 MET cc_start: 0.6880 (ppp) cc_final: 0.6302 (ppp)
REVERT: A  592 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.4745 (t80)
REVERT: B  418 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7676 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1445
  time to fit residues: 19.1458
Evaluate side-chains
  87 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0570
   chunk 52 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0030
   chunk 43 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4308

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.227474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.193488 restraints weight = 9378.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 3.97
r_work: 0.3995 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6515  Z= 0.160
  Angle     :  0.623  11.564   8847  Z= 0.297
  Chirality :  0.041   0.249    932
  Planarity :  0.005   0.057   1145
  Dihedral  :  6.010  55.633    914
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.46 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.31), residues: 773
  helix:  0.12 (0.30), residues: 320
  sheet: -1.91 (0.76), residues: 47
  loop : -2.10 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.009   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B 457 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.0325 (ttt) cc_final: -0.0623 (ptp)
REVERT: A  183 TYR cc_start: 0.6198 (t80) cc_final: 0.5920 (t80)
REVERT: A  236 LEU cc_start: 0.4288 (OUTLIER) cc_final: 0.3970 (mt)
REVERT: A  270 MET cc_start: 0.2053 (tpt) cc_final: 0.1695 (tpt)
REVERT: A  455 MET cc_start: 0.6855 (ppp) cc_final: 0.6264 (ppp)
REVERT: A  592 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.4746 (t80)
REVERT: B  418 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7621 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 94
  average time/residue: 0.1549
  time to fit residues: 20.6348
Evaluate side-chains
  93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  330 ASN
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  499 ASP
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0040
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.227917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.194012 restraints weight = 9427.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4299 rms_B_bonded: 4.02
r_work: 0.3981 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   6515  Z= 0.205
  Angle     :  1.033  59.186   8847  Z= 0.577
  Chirality :  0.044   0.472    932
  Planarity :  0.005   0.057   1145
  Dihedral  :  6.110  55.653    914
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.90 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.31), residues: 773
  helix:  0.17 (0.31), residues: 314
  sheet: -1.91 (0.76), residues: 47
  loop : -2.07 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.009   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A  41 
 ARG   0.003   0.000   ARG B 454 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3696.14 seconds
wall clock time: 66 minutes 32.01 seconds (3992.01 seconds total)