Starting phenix.real_space_refine
on Thu Jul 24 17:18:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_31544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_31544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_31544.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_31544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2025/7fdi_31544.cif"
  }
  resolution = 3.12
  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=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 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: 7.38, per 1000 atoms: 1.15
  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: 1.44
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 0.80
  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: 2.35

  Time building geometry restraints manager: 1.74 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:             1.970
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     23.470
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.420
-------------------------------------------------------------------------------
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 : 15.52
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (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
 TRP   0.082   0.003   TRP A 478 
 HIS   0.003   0.001   HIS E 493 
 PHE   0.034   0.002   PHE E 347 
 TYR   0.021   0.002   TYR E 495 
 ARG   0.002   0.000   ARG A 582 

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

*********************** 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  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.6717 (t80) cc_final: 0.6351 (t80)
REVERT: A  156 LEU cc_start: 0.8303 (mp) cc_final: 0.7829 (tt)
REVERT: A  480 MET cc_start: 0.5235 (ptm) cc_final: 0.5000 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1741
  time to fit residues: 20.8332
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  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0470
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0070
   overall best weight:    0.4096

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.147542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.122395 restraints weight = 11816.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.72
r_work: 0.3639 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6598  Z= 0.122
  Angle     :  0.602  11.100   8991  Z= 0.304
  Chirality :  0.043   0.188    955
  Planarity :  0.005   0.053   1157
  Dihedral  :  7.035  58.753    960
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.14 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.31), residues: 785
  helix:  0.91 (0.26), residues: 399
  sheet:  0.43 (0.78), residues: 49
  loop : -0.26 (0.37), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.005   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00164 (    5)
  link_NAG-ASN         : angle       2.28549 (   15)
  hydrogen bonds       : bond        0.04444 (  324)
  hydrogen bonds       : angle       4.93255 (  908)
  SS BOND              : bond        0.00588 (    7)
  SS BOND              : angle       2.00071 (   14)
  covalent geometry    : bond        0.00257 ( 6586)
  covalent geometry    : angle       0.59078 ( 8962)

*********************** 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
  85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.6857 (t80) cc_final: 0.6314 (t80)
REVERT: E  457 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.7758 (ttt180)
  outliers start: 4
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1750
  time to fit residues: 20.4381
Evaluate side-chains
  70 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
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 23 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.143538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.118778 restraints weight = 12570.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.55
r_work: 0.3600 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1475

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= 0.138
  Angle     :  0.589  11.682   8991  Z= 0.294
  Chirality :  0.042   0.171    955
  Planarity :  0.005   0.047   1157
  Dihedral  :  5.469  55.247    960
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  6.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.31), residues: 785
  helix:  1.01 (0.26), residues: 398
  sheet:  0.58 (0.78), residues: 50
  loop : -0.15 (0.37), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00263 (    5)
  link_NAG-ASN         : angle       2.23412 (   15)
  hydrogen bonds       : bond        0.04343 (  324)
  hydrogen bonds       : angle       4.80964 (  908)
  SS BOND              : bond        0.00387 (    7)
  SS BOND              : angle       1.74329 (   14)
  covalent geometry    : bond        0.00302 ( 6586)
  covalent geometry    : angle       0.57904 ( 8962)

*********************** 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
  80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.6934 (t80) cc_final: 0.6315 (t80)
REVERT: A  376 MET cc_start: 0.8477 (tpp) cc_final: 0.8179 (mmm)
REVERT: A  408 MET cc_start: 0.8543 (mmt) cc_final: 0.8287 (mmt)
REVERT: A  435 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7618 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 77
  average time/residue: 0.1648
  time to fit residues: 18.0751
Evaluate side-chains
  74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 HIS
E 501 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.144171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.119744 restraints weight = 9888.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.48
r_work: 0.3610 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6598  Z= 0.136
  Angle     :  0.581  12.279   8991  Z= 0.289
  Chirality :  0.042   0.170    955
  Planarity :  0.004   0.048   1157
  Dihedral  :  4.984  42.366    960
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.27 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.31), residues: 785
  helix:  1.08 (0.26), residues: 397
  sheet:  0.50 (0.78), residues: 50
  loop : -0.01 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    5)
  link_NAG-ASN         : angle       2.23331 (   15)
  hydrogen bonds       : bond        0.04228 (  324)
  hydrogen bonds       : angle       4.73255 (  908)
  SS BOND              : bond        0.00373 (    7)
  SS BOND              : angle       1.57990 (   14)
  covalent geometry    : bond        0.00299 ( 6586)
  covalent geometry    : angle       0.57134 ( 8962)

*********************** 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
  82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.7072 (t80) cc_final: 0.6415 (t80)
REVERT: A  376 MET cc_start: 0.8456 (tpp) cc_final: 0.8184 (mmm)
REVERT: A  408 MET cc_start: 0.8542 (mmt) cc_final: 0.8291 (mmt)
REVERT: A  435 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7714 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1541
  time to fit residues: 17.6161
Evaluate side-chains
  76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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
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 15 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0170
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0170
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6062

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** 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 = 0.4106 r_free = 0.4106 target = 0.148442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.123059 restraints weight = 17457.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 3.88
r_work: 0.3582 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6598  Z= 0.118
  Angle     :  0.574  12.754   8991  Z= 0.283
  Chirality :  0.041   0.156    955
  Planarity :  0.004   0.048   1157
  Dihedral  :  4.735  40.729    960
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.45 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.31), residues: 785
  helix:  1.09 (0.26), residues: 400
  sheet:  0.51 (0.77), residues: 50
  loop :  0.05 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 478 
 HIS   0.003   0.001   HIS E 493 
 PHE   0.012   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    5)
  link_NAG-ASN         : angle       2.01173 (   15)
  hydrogen bonds       : bond        0.04054 (  324)
  hydrogen bonds       : angle       4.62612 (  908)
  SS BOND              : bond        0.00343 (    7)
  SS BOND              : angle       1.41842 (   14)
  covalent geometry    : bond        0.00255 ( 6586)
  covalent geometry    : angle       0.56599 ( 8962)

*********************** 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
  80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.7106 (t80) cc_final: 0.6385 (t80)
REVERT: A  435 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7687 (mp0)
REVERT: E  457 ARG cc_start: 0.8127 (ttt-90) cc_final: 0.7753 (ttt180)
  outliers start: 5
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1636
  time to fit residues: 18.1612
Evaluate side-chains
  74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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
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 72 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
A 194 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 = 0.4077 r_free = 0.4077 target = 0.145507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.120215 restraints weight = 12013.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.75
r_work: 0.3613 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2035

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= 0.125
  Angle     :  0.574  12.757   8991  Z= 0.283
  Chirality :  0.042   0.160    955
  Planarity :  0.004   0.046   1157
  Dihedral  :  4.685  40.006    960
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.01 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.31), residues: 785
  helix:  1.10 (0.26), residues: 399
  sheet:  0.45 (0.77), residues: 50
  loop :  0.14 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.003   0.001   HIS E 493 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    5)
  link_NAG-ASN         : angle       2.00652 (   15)
  hydrogen bonds       : bond        0.04036 (  324)
  hydrogen bonds       : angle       4.61295 (  908)
  SS BOND              : bond        0.00334 (    7)
  SS BOND              : angle       1.37555 (   14)
  covalent geometry    : bond        0.00273 ( 6586)
  covalent geometry    : angle       0.56659 ( 8962)

*********************** 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
  75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6839 (mm-30)
REVERT: A  435 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7618 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1604
  time to fit residues: 16.9774
Evaluate side-chains
  73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0970
   chunk 44 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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 = 0.4098 r_free = 0.4098 target = 0.147362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.122297 restraints weight = 19163.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 4.09
r_work: 0.3586 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
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 = 0.37   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: 0.7695
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6598  Z= 0.108
  Angle     :  0.558  12.872   8991  Z= 0.274
  Chirality :  0.041   0.144    955
  Planarity :  0.004   0.042   1157
  Dihedral  :  4.487  38.122    960
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.31 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.31), residues: 785
  helix:  1.14 (0.26), residues: 400
  sheet:  0.53 (0.78), residues: 50
  loop :  0.17 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    5)
  link_NAG-ASN         : angle       1.81233 (   15)
  hydrogen bonds       : bond        0.03890 (  324)
  hydrogen bonds       : angle       4.53003 (  908)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       1.30134 (   14)
  covalent geometry    : bond        0.00231 ( 6586)
  covalent geometry    : angle       0.55112 ( 8962)

*********************** 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
  83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6811 (mm-30)
REVERT: A  249 MET cc_start: 0.7726 (tpp) cc_final: 0.7296 (tpp)
REVERT: A  429 GLN cc_start: 0.6861 (tp-100) cc_final: 0.6586 (tp-100)
REVERT: A  435 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7709 (mp0)
REVERT: A  557 MET cc_start: 0.8817 (tmm) cc_final: 0.8485 (tmm)
REVERT: E  457 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7767 (ttt180)
  outliers start: 6
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1716
  time to fit residues: 19.5337
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  : 0.775 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.145081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.120275 restraints weight = 12014.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.52
r_work: 0.3624 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6598  Z= 0.134
  Angle     :  0.577  12.372   8991  Z= 0.284
  Chirality :  0.042   0.157    955
  Planarity :  0.004   0.042   1157
  Dihedral  :  4.631  39.837    960
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.60 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.31), residues: 785
  helix:  1.15 (0.26), residues: 401
  sheet:  0.42 (0.77), residues: 50
  loop :  0.18 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.002   0.001   HIS E 493 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.004   0.000   ARG E 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00236 (    5)
  link_NAG-ASN         : angle       1.97798 (   15)
  hydrogen bonds       : bond        0.04047 (  324)
  hydrogen bonds       : angle       4.56693 (  908)
  SS BOND              : bond        0.00327 (    7)
  SS BOND              : angle       1.33830 (   14)
  covalent geometry    : bond        0.00298 ( 6586)
  covalent geometry    : angle       0.56960 ( 8962)

*********************** 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
  77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6880 (mm-30)
REVERT: A  249 MET cc_start: 0.7918 (tpp) cc_final: 0.7484 (tpp)
REVERT: A  435 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7770 (mp0)
REVERT: E  346 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6454 (ptt180)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1595
  time to fit residues: 17.1522
Evaluate side-chains
  76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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 17 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0020
   chunk 33 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.8790

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.145066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.120962 restraints weight = 13855.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.87
r_work: 0.3616 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6598  Z= 0.133
  Angle     :  0.574  12.334   8991  Z= 0.283
  Chirality :  0.042   0.157    955
  Planarity :  0.004   0.044   1157
  Dihedral  :  4.646  40.308    960
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.31), residues: 785
  helix:  1.14 (0.26), residues: 401
  sheet:  0.39 (0.76), residues: 50
  loop :  0.20 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.002   0.001   HIS E 493 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    5)
  link_NAG-ASN         : angle       1.97165 (   15)
  hydrogen bonds       : bond        0.04035 (  324)
  hydrogen bonds       : angle       4.56315 (  908)
  SS BOND              : bond        0.00312 (    7)
  SS BOND              : angle       1.32447 (   14)
  covalent geometry    : bond        0.00294 ( 6586)
  covalent geometry    : angle       0.56717 ( 8962)

*********************** 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
  80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6858 (mm-30)
REVERT: A  156 LEU cc_start: 0.8822 (mp) cc_final: 0.8112 (tt)
REVERT: A  249 MET cc_start: 0.7726 (tpp) cc_final: 0.7329 (tpp)
REVERT: A  429 GLN cc_start: 0.6678 (tp-100) cc_final: 0.6419 (tp-100)
REVERT: A  435 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7654 (mp0)
REVERT: E  346 ARG cc_start: 0.7175 (mtm180) cc_final: 0.6419 (ptt180)
  outliers start: 7
  outliers final: 5
  residues processed: 77
  average time/residue: 0.1688
  time to fit residues: 18.1384
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  : 0.700 
-------------------------------------------------------------------------------
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 11 optimal weight:    0.0870
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0040
   chunk 76 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.7974

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.145487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.121563 restraints weight = 12510.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.83
r_work: 0.3620 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6598  Z= 0.128
  Angle     :  0.577  12.176   8991  Z= 0.284
  Chirality :  0.042   0.155    955
  Planarity :  0.004   0.040   1157
  Dihedral  :  4.627  39.838    960
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.04 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.31), residues: 785
  helix:  1.15 (0.26), residues: 401
  sheet:  0.35 (0.76), residues: 50
  loop :  0.22 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 271 
 HIS   0.002   0.001   HIS E 493 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00222 (    5)
  link_NAG-ASN         : angle       1.95364 (   15)
  hydrogen bonds       : bond        0.04021 (  324)
  hydrogen bonds       : angle       4.55404 (  908)
  SS BOND              : bond        0.00313 (    7)
  SS BOND              : angle       1.30401 (   14)
  covalent geometry    : bond        0.00284 ( 6586)
  covalent geometry    : angle       0.57030 ( 8962)

********************** 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
  79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6866 (mm-30)
REVERT: A  156 LEU cc_start: 0.8803 (mp) cc_final: 0.8104 (tt)
REVERT: A  249 MET cc_start: 0.7710 (tpp) cc_final: 0.7316 (tpp)
REVERT: A  429 GLN cc_start: 0.6639 (tp-100) cc_final: 0.6365 (tp-100)
REVERT: A  435 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7664 (mp0)
REVERT: E  346 ARG cc_start: 0.7172 (mtm180) cc_final: 0.6431 (ptt180)
  outliers start: 7
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1953
  time to fit residues: 21.1728
Evaluate side-chains
  78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
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 2 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0570
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.146792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.122426 restraints weight = 14362.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.88
r_work: 0.3634 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2347

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= 0.115
  Angle     :  0.566  12.210   8991  Z= 0.277
  Chirality :  0.041   0.156    955
  Planarity :  0.004   0.039   1157
  Dihedral  :  4.492  38.139    960
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.19 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.05 (0.31), residues: 785
  helix:  1.20 (0.26), residues: 400
  sheet:  0.35 (0.77), residues: 50
  loop :  0.29 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 271 
 HIS   0.002   0.001   HIS E 493 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    5)
  link_NAG-ASN         : angle       1.81844 (   15)
  hydrogen bonds       : bond        0.03895 (  324)
  hydrogen bonds       : angle       4.50266 (  908)
  SS BOND              : bond        0.00311 (    7)
  SS BOND              : angle       1.26913 (   14)
  covalent geometry    : bond        0.00250 ( 6586)
  covalent geometry    : angle       0.56021 ( 8962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4714.78 seconds
wall clock time: 83 minutes 12.39 seconds (4992.39 seconds total)