Starting phenix.real_space_refine
on Tue Mar  3 15:08:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdi_31544/03_2026/7fdi_31544.map"
  }
  resolution = 3.12
  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=   0.003
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      36      5.16       5
     C    4097      2.51       5
     N    1058      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6403
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4802
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 594, 4795
          Classifications: {'peptide': 594}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 32
      Conformer: "B"
        Number of residues, atoms: 594, 4795
          Classifications: {'peptide': 594}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 32
          bond proxies already assigned to first conformer: 4922
    Chain: "E"
      Number of atoms: 1531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1531
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      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: 2.28, per 1000 atoms: 0.36
  Number of scatterers: 6403
  At special positions: 0
  Unit cell: (113.36, 88.4, 79.04, 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      36     16.00
     O    1212      8.00
     N    1058      7.00
     C    4097      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 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
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 402.8 milliseconds
  

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 7 sheets defined
      58.5% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.647A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 82
      removed outlier: 3.908A  pdb=" N   MET A  82 " --> pdb=" O   THR A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.609A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.529A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.699A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.836A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.556A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 4.198A  pdb=" N   ILE A 256 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.552A  pdb=" N   GLN A 300 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.567A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.540A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.881A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 3.732A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   THR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.625A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU A 483 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.265A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.668A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.808A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.859A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 371
    Processing helix  chain 'E' and resid 385 through 390
    Processing helix  chain 'E' and resid 406 through 410
    Processing helix  chain 'E' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.457A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.552A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362
      removed outlier: 6.691A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453
    Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474

    324 hydrogen bonds defined for protein.
    908 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: 0.94

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2055
        1.35 -     1.47: 1740
        1.47 -     1.59: 2735
        1.59 -     1.71: 0
        1.71 -     1.84: 56
  Bond restraints: 6586
  Sorted by residual:
  bond pdb=" CB  TRP A 478 "
       pdb=" CG  TRP A 478 "
    ideal  model  delta    sigma   weight residual
    1.498  1.452  0.046 3.10e-02 1.04e+03 2.20e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  bond pdb=" CG  MET A 455 "
       pdb=" SD  MET A 455 "
    ideal  model  delta    sigma   weight residual
    1.803  1.773  0.030 2.50e-02 1.60e+03 1.48e+00
  bond pdb=" CB  CYS A 530 "
       pdb=" SG  CYS A 530 "
    ideal  model  delta    sigma   weight residual
    1.808  1.769  0.039 3.30e-02 9.18e+02 1.38e+00
  ... (remaining 6581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8711
        1.70 -     3.39: 214
        3.39 -     5.09: 31
        5.09 -     6.78: 4
        6.78 -     8.48: 2
  Bond angle restraints: 8962
  Sorted by residual:
  angle pdb=" C   LEU A 529 "
        pdb=" N   CYS A 530 "
        pdb=" CA  CYS A 530 "
      ideal   model   delta    sigma   weight residual
     122.65  118.39    4.26 1.66e+00 3.63e-01 6.58e+00
  angle pdb=" CB  MET A 152 "
        pdb=" CG  MET A 152 "
        pdb=" SD  MET A 152 "
      ideal   model   delta    sigma   weight residual
     112.70  120.23   -7.53 3.00e+00 1.11e-01 6.30e+00
  angle pdb=" N   LYS A 234 "
        pdb=" CA  LYS A 234 "
        pdb=" C   LYS A 234 "
      ideal   model   delta    sigma   weight residual
     109.81  115.33   -5.52 2.21e+00 2.05e-01 6.25e+00
  angle pdb=" CA  LEU A 266 "
        pdb=" CB  LEU A 266 "
        pdb=" CG  LEU A 266 "
      ideal   model   delta    sigma   weight residual
     116.30  124.78   -8.48 3.50e+00 8.16e-02 5.87e+00
  angle pdb=" CA  GLU A 435 "
        pdb=" CB  GLU A 435 "
        pdb=" CG  GLU A 435 "
      ideal   model   delta    sigma   weight residual
     114.10  118.90   -4.80 2.00e+00 2.50e-01 5.77e+00
  ... (remaining 8957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.93: 3647
       21.93 -    43.86: 243
       43.86 -    65.78: 21
       65.78 -    87.71: 16
       87.71 -   109.64: 9
  Dihedral angle restraints: 3936
    sinusoidal: 1622
      harmonic: 2314
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.03  -68.97     1      1.00e+01 1.00e-02 6.15e+01
  dihedral pdb=" CA  CYS A 530 "
           pdb=" C   CYS A 530 "
           pdb=" N   GLN A 531 "
           pdb=" CA  GLN A 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.60   30.40     0      5.00e+00 4.00e-02 3.70e+01
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.31   25.69     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 3933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 753
       0.054 -    0.108: 181
       0.108 -    0.162: 18
       0.162 -    0.216: 2
       0.216 -    0.269: 1
  Chirality restraints: 955
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CA  CYS A 530 "
            pdb=" N   CYS A 530 "
            pdb=" C   CYS A 530 "
            pdb=" CB  CYS A 530 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.26e-01
  chirality pdb=" CB  ILE A 468 "
            pdb=" CA  ILE A 468 "
            pdb=" CG1 ILE A 468 "
            pdb=" CG2 ILE A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.79e-01
  ... (remaining 952 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 478 "    0.040 2.00e-02 2.50e+03   3.06e-02 2.34e+01
        pdb=" CG  TRP A 478 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 478 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 478 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 478 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 478 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 478 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 478 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 478 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 478 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 252 "    0.046 5.00e-02 4.00e+02   6.98e-02 7.80e+00
        pdb=" N   PRO A 253 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 347 "   -0.016 2.00e-02 2.50e+03   1.48e-02 3.84e+00
        pdb=" CG  PHE E 347 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 347 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 347 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 347 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 347 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 347 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 127
        2.67 -     3.23: 6444
        3.23 -     3.78: 10606
        3.78 -     4.34: 14672
        4.34 -     4.90: 23636
  Nonbonded interactions: 55485
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" NH1 ARG A 460 "
            pdb=" O   TYR A 510 "
     model   vdw
     2.133 3.120
  nonbonded pdb=" O   ASN E 439 "
            pdb=" OG  SER E 443 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR E 500 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.208 3.120
  ... (remaining 55480 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.340
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.790
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
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      :  0.005   0.046   6598  Z= 0.220
  Angle     :  0.662   8.479   8991  Z= 0.349
  Chirality :  0.046   0.269    955
  Planarity :  0.005   0.070   1157
  Dihedral  : 15.545 109.641   2431
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.19 (0.30), residues: 785
  helix:  0.41 (0.25), residues: 397
  sheet:  0.28 (0.79), residues: 48
  loop : -0.74 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 582 
 TYR   0.021   0.002   TYR E 495 
 PHE   0.034   0.002   PHE E 347 
 TRP   0.082   0.003   TRP A 478 
 HIS   0.003   0.001   HIS E 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 6586)
  covalent geometry    : angle       0.64306 ( 8962)
  SS BOND              : bond        0.00530 (    7)
  SS BOND              : angle       2.41379 (   14)
  hydrogen bonds       : bond        0.13468 (  324)
  hydrogen bonds       : angle       6.36841 (  908)
  link_NAG-ASN         : bond        0.00348 (    5)
  link_NAG-ASN         : angle       3.21182 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.6717 (t80) cc_final: 0.6350 (t80)
REVERT: A  156 LEU cc_start: 0.8305 (mp) cc_final: 0.7830 (tt)
REVERT: A  480 MET cc_start: 0.5237 (ptm) cc_final: 0.4998 (ptt)
REVERT: A  557 MET cc_start: 0.8818 (tmm) cc_final: 0.8514 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0679
  time to fit residues: 8.2344
Evaluate side-chains
  68 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 239 HIS
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 501 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.145148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.120514 restraints weight = 17544.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 3.31
r_work: 0.3583 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6598  Z= 0.149
  Angle     :  0.626  11.013   8991  Z= 0.316
  Chirality :  0.044   0.209    955
  Planarity :  0.005   0.054   1157
  Dihedral  :  7.523  59.235    960
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.28 %
    Favored  : 95.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.38 (0.31), residues: 785
  helix:  0.82 (0.25), residues: 399
  sheet:  0.47 (0.78), residues: 50
  loop : -0.37 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 177 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.052   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6586)
  covalent geometry    : angle       0.61291 ( 8962)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       2.05496 (   14)
  hydrogen bonds       : bond        0.04708 (  324)
  hydrogen bonds       : angle       5.04212 (  908)
  link_NAG-ASN         : bond        0.00234 (    5)
  link_NAG-ASN         : angle       2.55887 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.6903 (t80) cc_final: 0.6373 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 0.0574
  time to fit residues: 6.7839
Evaluate side-chains
  69 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.144425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.119116 restraints weight = 9856.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.28
r_work: 0.3630 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3499 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6598  Z= 0.124
  Angle     :  0.583  11.583   8991  Z= 0.290
  Chirality :  0.042   0.163    955
  Planarity :  0.004   0.047   1157
  Dihedral  :  5.453  54.618    960
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.09 %
    Favored  : 92.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.68 (0.31), residues: 785
  helix:  1.05 (0.26), residues: 398
  sheet:  0.58 (0.78), residues: 50
  loop : -0.18 (0.37), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 460 
 TYR   0.021   0.001   TYR A 385 
 PHE   0.016   0.001   PHE A 369 
 TRP   0.029   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6586)
  covalent geometry    : angle       0.57330 ( 8962)
  SS BOND              : bond        0.00407 (    7)
  SS BOND              : angle       1.74257 (   14)
  hydrogen bonds       : bond        0.04248 (  324)
  hydrogen bonds       : angle       4.75656 (  908)
  link_NAG-ASN         : bond        0.00245 (    5)
  link_NAG-ASN         : angle       2.18108 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.7009 (t80) cc_final: 0.6354 (t80)
REVERT: A  408 MET cc_start: 0.8560 (mmt) cc_final: 0.8306 (mmt)
REVERT: A  435 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7636 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 77
  average time/residue: 0.0619
  time to fit residues: 6.8843
Evaluate side-chains
  76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 373 HIS
E 501 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.143394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.118955 restraints weight = 14808.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 3.03
r_work: 0.3581 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6598  Z= 0.142
  Angle     :  0.588  12.231   8991  Z= 0.290
  Chirality :  0.042   0.173    955
  Planarity :  0.004   0.050   1157
  Dihedral  :  5.023  43.308    960
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  8.27 %
    Favored  : 90.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.81 (0.31), residues: 785
  helix:  1.11 (0.26), residues: 397
  sheet:  0.60 (0.78), residues: 49
  loop : -0.05 (0.37), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.021   0.001   TYR A 385 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.023   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6586)
  covalent geometry    : angle       0.57810 ( 8962)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       1.60278 (   14)
  hydrogen bonds       : bond        0.04239 (  324)
  hydrogen bonds       : angle       4.72307 (  908)
  link_NAG-ASN         : bond        0.00246 (    5)
  link_NAG-ASN         : angle       2.28584 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.7003 (t80) cc_final: 0.6343 (t80)
REVERT: A  376 MET cc_start: 0.8420 (tpp) cc_final: 0.8130 (mmm)
REVERT: A  408 MET cc_start: 0.8471 (mmt) cc_final: 0.8186 (mmt)
REVERT: A  435 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7602 (mp0)
REVERT: E  346 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6213 (ptt180)
  outliers start: 6
  outliers final: 4
  residues processed: 83
  average time/residue: 0.0650
  time to fit residues: 7.5376
Evaluate side-chains
  78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0010
   chunk 64 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.148475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.123564 restraints weight = 12430.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.56
r_work: 0.3657 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6598  Z= 0.116
  Angle     :  0.566  12.507   8991  Z= 0.280
  Chirality :  0.041   0.155    955
  Planarity :  0.004   0.047   1157
  Dihedral  :  4.743  40.812    960
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.16 %
    Favored  : 89.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.86 (0.31), residues: 785
  helix:  1.14 (0.26), residues: 400
  sheet:  0.49 (0.78), residues: 50
  loop :  0.02 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.011   0.001   PHE A 369 
 TRP   0.040   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6586)
  covalent geometry    : angle       0.55845 ( 8962)
  SS BOND              : bond        0.00355 (    7)
  SS BOND              : angle       1.43426 (   14)
  hydrogen bonds       : bond        0.04032 (  324)
  hydrogen bonds       : angle       4.62351 (  908)
  link_NAG-ASN         : bond        0.00217 (    5)
  link_NAG-ASN         : angle       2.00432 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.7170 (t80) cc_final: 0.6444 (t80)
REVERT: A  435 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7770 (mp0)
REVERT: E  457 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7835 (ttt180)
  outliers start: 6
  outliers final: 4
  residues processed: 79
  average time/residue: 0.0598
  time to fit residues: 6.8698
Evaluate side-chains
  77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 55 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0060
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.148541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.123066 restraints weight = 17402.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 3.72
r_work: 0.3596 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6598  Z= 0.119
  Angle     :  0.576  12.817   8991  Z= 0.283
  Chirality :  0.041   0.155    955
  Planarity :  0.004   0.045   1157
  Dihedral  :  4.654  39.778    960
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.45 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.93 (0.31), residues: 785
  helix:  1.16 (0.26), residues: 399
  sheet:  0.47 (0.77), residues: 50
  loop :  0.11 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 369 
 TRP   0.037   0.002   TRP A 165 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6586)
  covalent geometry    : angle       0.56899 ( 8962)
  SS BOND              : bond        0.00338 (    7)
  SS BOND              : angle       1.38281 (   14)
  hydrogen bonds       : bond        0.03991 (  324)
  hydrogen bonds       : angle       4.58177 (  908)
  link_NAG-ASN         : bond        0.00215 (    5)
  link_NAG-ASN         : angle       1.96301 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6886 (mm-30)
REVERT: A  435 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7707 (mp0)
REVERT: E  346 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6382 (ptt180)
REVERT: E  457 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7714 (ttt180)
  outliers start: 6
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0658
  time to fit residues: 7.2233
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.144761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.120436 restraints weight = 14332.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.96
r_work: 0.3604 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6598  Z= 0.137
  Angle     :  0.576  12.675   8991  Z= 0.285
  Chirality :  0.042   0.158    955
  Planarity :  0.004   0.044   1157
  Dihedral  :  4.715  40.584    960
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.60 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.90 (0.31), residues: 785
  helix:  1.14 (0.26), residues: 400
  sheet:  0.42 (0.77), residues: 50
  loop :  0.11 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.025   0.002   TYR A 243 
 PHE   0.013   0.001   PHE A 369 
 TRP   0.053   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6586)
  covalent geometry    : angle       0.56785 ( 8962)
  SS BOND              : bond        0.00334 (    7)
  SS BOND              : angle       1.40156 (   14)
  hydrogen bonds       : bond        0.04088 (  324)
  hydrogen bonds       : angle       4.60414 (  908)
  link_NAG-ASN         : bond        0.00234 (    5)
  link_NAG-ASN         : angle       2.04411 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6841 (mm-30)
REVERT: A  156 LEU cc_start: 0.8830 (mp) cc_final: 0.8111 (tt)
REVERT: A  429 GLN cc_start: 0.6703 (tp-100) cc_final: 0.6435 (tp-100)
REVERT: A  435 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7611 (mp0)
REVERT: E  346 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6414 (ptt180)
REVERT: E  457 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7681 (ttt180)
  outliers start: 7
  outliers final: 5
  residues processed: 76
  average time/residue: 0.0692
  time to fit residues: 7.3458
Evaluate side-chains
  77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 12 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
E 501 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.146638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.121446 restraints weight = 17562.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 3.85
r_work: 0.3572 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6598  Z= 0.114
  Angle     :  0.563  12.984   8991  Z= 0.277
  Chirality :  0.041   0.150    955
  Planarity :  0.004   0.041   1157
  Dihedral  :  4.540  38.707    960
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.90 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.00 (0.31), residues: 785
  helix:  1.20 (0.26), residues: 400
  sheet:  0.41 (0.76), residues: 50
  loop :  0.19 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 369 
 TRP   0.044   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6586)
  covalent geometry    : angle       0.55610 ( 8962)
  SS BOND              : bond        0.00321 (    7)
  SS BOND              : angle       1.31000 (   14)
  hydrogen bonds       : bond        0.03938 (  324)
  hydrogen bonds       : angle       4.52247 (  908)
  link_NAG-ASN         : bond        0.00211 (    5)
  link_NAG-ASN         : angle       1.86471 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6908 (mm-30)
REVERT: A  156 LEU cc_start: 0.8812 (mp) cc_final: 0.8110 (tt)
REVERT: A  429 GLN cc_start: 0.6655 (tp-100) cc_final: 0.6372 (tp-100)
REVERT: A  435 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7697 (mp0)
REVERT: A  557 MET cc_start: 0.8814 (tmm) cc_final: 0.8481 (tmm)
REVERT: E  346 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6348 (ptt180)
REVERT: E  457 ARG cc_start: 0.8128 (ttt-90) cc_final: 0.7744 (ttt180)
  outliers start: 6
  outliers final: 4
  residues processed: 81
  average time/residue: 0.0715
  time to fit residues: 7.9788
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 54 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.146134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122239 restraints weight = 12529.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.86
r_work: 0.3626 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6598  Z= 0.123
  Angle     :  0.571  12.920   8991  Z= 0.282
  Chirality :  0.041   0.151    955
  Planarity :  0.004   0.039   1157
  Dihedral  :  4.547  38.857    960
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.90 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.00 (0.31), residues: 785
  helix:  1.20 (0.26), residues: 400
  sheet:  0.29 (0.76), residues: 50
  loop :  0.22 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.013   0.001   PHE E 392 
 TRP   0.040   0.002   TRP A 478 
 HIS   0.003   0.001   HIS E 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6586)
  covalent geometry    : angle       0.56461 ( 8962)
  SS BOND              : bond        0.00314 (    7)
  SS BOND              : angle       1.28739 (   14)
  hydrogen bonds       : bond        0.03972 (  324)
  hydrogen bonds       : angle       4.48374 (  908)
  link_NAG-ASN         : bond        0.00221 (    5)
  link_NAG-ASN         : angle       1.88248 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6883 (mm-30)
REVERT: A  156 LEU cc_start: 0.8807 (mp) cc_final: 0.8115 (tt)
REVERT: A  435 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7660 (mp0)
REVERT: E  346 ARG cc_start: 0.7128 (mtm180) cc_final: 0.6388 (ptt180)
REVERT: E  457 ARG cc_start: 0.8039 (ttt-90) cc_final: 0.7641 (ttt180)
  outliers start: 7
  outliers final: 5
  residues processed: 78
  average time/residue: 0.0776
  time to fit residues: 8.2236
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 30 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 586 ASN
E 501 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.123094 restraints weight = 12449.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 2.86
r_work: 0.3642 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3648 r_free = 0.3648    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6598  Z= 0.116
  Angle     :  0.574  12.824   8991  Z= 0.283
  Chirality :  0.041   0.145    955
  Planarity :  0.004   0.039   1157
  Dihedral  :  4.475  38.149    960
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.90 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.03 (0.31), residues: 785
  helix:  1.22 (0.26), residues: 400
  sheet:  0.31 (0.76), residues: 50
  loop :  0.24 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.012   0.001   PHE E 392 
 TRP   0.038   0.002   TRP A 478 
 HIS   0.003   0.001   HIS E 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6586)
  covalent geometry    : angle       0.56795 ( 8962)
  SS BOND              : bond        0.00317 (    7)
  SS BOND              : angle       1.26722 (   14)
  hydrogen bonds       : bond        0.03896 (  324)
  hydrogen bonds       : angle       4.45268 (  908)
  link_NAG-ASN         : bond        0.00212 (    5)
  link_NAG-ASN         : angle       1.81487 (   15)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6826 (mm-30)
REVERT: A  156 LEU cc_start: 0.8793 (mp) cc_final: 0.8104 (tt)
REVERT: A  429 GLN cc_start: 0.6575 (tp-100) cc_final: 0.6324 (tp-100)
REVERT: A  435 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7657 (mp0)
REVERT: E  346 ARG cc_start: 0.6999 (mtm180) cc_final: 0.6356 (ptt180)
REVERT: E  457 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7651 (ttt180)
  outliers start: 7
  outliers final: 5
  residues processed: 80
  average time/residue: 0.0756
  time to fit residues: 8.2542
Evaluate side-chains
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
E 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.121815 restraints weight = 17690.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 3.93
r_work: 0.3580 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6598  Z= 0.118
  Angle     :  0.578  12.763   8991  Z= 0.285
  Chirality :  0.041   0.150    955
  Planarity :  0.004   0.038   1157
  Dihedral  :  4.432  37.625    960
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.49 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.04 (0.31), residues: 785
  helix:  1.22 (0.26), residues: 400
  sheet:  0.29 (0.76), residues: 50
  loop :  0.25 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 369 
 TRP   0.039   0.002   TRP A 478 
 HIS   0.003   0.001   HIS E 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6586)
  covalent geometry    : angle       0.57175 ( 8962)
  SS BOND              : bond        0.00313 (    7)
  SS BOND              : angle       1.26480 (   14)
  hydrogen bonds       : bond        0.03883 (  324)
  hydrogen bonds       : angle       4.44023 (  908)
  link_NAG-ASN         : bond        0.00224 (    5)
  link_NAG-ASN         : angle       1.79935 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.13 seconds
wall clock time: 30 minutes 23.82 seconds (1823.82 seconds total)