Starting phenix.real_space_refine
on Tue Jun 10 09:56:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hfy_34728/06_2025/8hfy_34728.cif"
  }
  resolution = 3.21
  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=   0.001 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      38      5.16       5
     C    4195      2.51       5
     N    1075      2.21       5
     O    1259      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6568
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 4886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4886
          Classifications: {'peptide': 595}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen chiralities: 7
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.54, per 1000 atoms: 0.84
  Number of scatterers: 6568
  At special positions: 0
  Unit cell: (85, 88.4, 120.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      38     16.00
     O    1259      8.00
     N    1075      7.00
     C    4195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A 432 "
      " NAG A 702 " - " ASN A 299 "
      " NAG A 703 " - " ASN A  91 "
      " NAG B 601 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  54 "
      " NAG D   1 " - " ASN A 546 "
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 848.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 704 "
        pdb="ZN    ZN A 704 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 704 " - pdb=" NE2 HIS A 378 "


  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:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      54.9% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'B' and resid 367 through 371
      removed outlier: 3.749A  pdb=" N   ASN B 370 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 409
      removed outlier: 4.090A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.508A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'A' and resid 21 through 54
      removed outlier: 3.677A  pdb=" N   HIS A  35 " --> pdb=" O   GLU A  31 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP A  39 " --> pdb=" O   HIS A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 82
      removed outlier: 3.724A  pdb=" N   LYS A  82 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 103
      removed outlier: 3.559A  pdb=" N   GLN A 103 " --> pdb=" O   LYS A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 4.243A  pdb=" N   VAL A 108 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 130
      removed outlier: 3.585A  pdb=" N   LYS A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 139
      removed outlier: 3.831A  pdb=" N   GLN A 139 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 139'
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.705A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.959A  pdb=" N   GLU A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.647A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   MET A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS A 224 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 4.110A  pdb=" N   ASP A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    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
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.948A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.909A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.687A  pdb=" N   ARG A 393 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 4.136A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.504A  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 448
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.194A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 484
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 516 through 533
      removed outlier: 3.575A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS A 530 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.047A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLN A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   MET A 557 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.723A  pdb=" N   ILE 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
      removed outlier: 3.626A  pdb=" N   THR A 593 " --> pdb=" O   GLU A 589 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 134
    Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.114A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.368A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.69

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2075
        1.34 -     1.46: 1522
        1.46 -     1.58: 3091
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6748
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.479 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.475 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.557 -0.038 2.00e-02 2.50e+03 3.55e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.44e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.444 -0.031 2.00e-02 2.50e+03 2.33e+00
  ... (remaining 6743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8936
        1.56 -     3.13: 179
        3.13 -     4.69: 32
        4.69 -     6.25: 7
        6.25 -     7.82: 2
  Bond angle restraints: 9156
  Sorted by residual:
  angle pdb=" N   ILE A  55 "
        pdb=" CA  ILE A  55 "
        pdb=" C   ILE A  55 "
      ideal   model   delta    sigma   weight residual
     106.55  110.56   -4.01 1.45e+00 4.76e-01 7.66e+00
  angle pdb=" C   PHE B 375 "
        pdb=" N   THR B 376 "
        pdb=" CA  THR B 376 "
      ideal   model   delta    sigma   weight residual
     122.41  118.51    3.90 1.47e+00 4.63e-01 7.04e+00
  angle pdb=" C1  NAG D   1 "
        pdb=" O5  NAG D   1 "
        pdb=" C5  NAG D   1 "
      ideal   model   delta    sigma   weight residual
     113.21  121.03   -7.82 3.00e+00 1.11e-01 6.79e+00
  angle pdb=" C   ALA A 384 "
        pdb=" N   TYR A 385 "
        pdb=" CA  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     122.65  118.46    4.19 1.66e+00 3.63e-01 6.36e+00
  angle pdb=" N   GLY A 537 "
        pdb=" CA  GLY A 537 "
        pdb=" C   GLY A 537 "
      ideal   model   delta    sigma   weight residual
     110.46  113.97   -3.51 1.43e+00 4.89e-01 6.04e+00
  ... (remaining 9151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.82: 3926
       24.82 -    49.64: 135
       49.64 -    74.46: 18
       74.46 -    99.28: 14
       99.28 -   124.10: 15
  Dihedral angle restraints: 4108
    sinusoidal: 1778
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" C2  NAG A 701 "
           pdb=" C1  NAG A 701 "
           pdb=" O5  NAG A 701 "
           pdb=" C5  NAG A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   61.14 -124.10     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  173.99  114.72     1      3.00e+01 1.11e-03 1.51e+01
  dihedral pdb=" C3  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -65.53  113.15     1      3.00e+01 1.11e-03 1.49e+01
  ... (remaining 4105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 812
       0.053 -    0.107: 146
       0.107 -    0.160: 19
       0.160 -    0.214: 1
       0.214 -    0.267: 1
  Chirality restraints: 979
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.36   -0.04 2.00e-02 2.50e+03 4.58e+00
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.48e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 372 "   -0.032 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO B 373 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 444 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   LEU A 444 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LEU A 444 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR A 445 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.62e+00
        pdb=" N   PRO A 146 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 68
        2.64 -     3.21: 5868
        3.21 -     3.77: 9628
        3.77 -     4.34: 13493
        4.34 -     4.90: 22737
  Nonbonded interactions: 51794
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 704 "
     model   vdw
     2.081 2.230
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR A  42 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP A 382 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.257 3.040
  ... (remaining 51789 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.820
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   6763  Z= 0.161
  Angle     :  0.565   7.817   9191  Z= 0.290
  Chirality :  0.042   0.267    979
  Planarity :  0.004   0.049   1166
  Dihedral  : 15.549 124.095   2600
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  6.47 %
    Favored  : 92.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.29 (0.30), residues: 785
  helix:  1.41 (0.27), residues: 392
  sheet:  0.52 (0.80), residues: 44
  loop : -1.30 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    6)
  link_NAG-ASN         : angle       1.90321 (   18)
  link_BETA1-4         : bond        0.00615 (    3)
  link_BETA1-4         : angle       2.40347 (    9)
  hydrogen bonds       : bond        0.14669 (  297)
  hydrogen bonds       : angle       5.28726 (  843)
  metal coordination   : bond        0.00402 (    2)
  SS BOND              : bond        0.00106 (    4)
  SS BOND              : angle       0.73216 (    8)
  covalent geometry    : bond        0.00316 ( 6748)
  covalent geometry    : angle       0.55418 ( 9156)

*********************** 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
  132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7229 (t0) cc_final: 0.6988 (t0)
REVERT: A  149 ASP cc_start: 0.8409 (t0) cc_final: 0.8204 (t0)
REVERT: A  152 MET cc_start: 0.9148 (mmm) cc_final: 0.8644 (mmt)
  outliers start: 10
  outliers final: 3
  residues processed: 130
  average time/residue: 0.2133
  time to fit residues: 35.5208
Evaluate side-chains
  76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain A residue   21 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0870
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.2282

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.121796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091628 restraints weight = 11769.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.75
r_work: 0.3128 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6763  Z= 0.182
  Angle     :  0.647  10.860   9191  Z= 0.319
  Chirality :  0.044   0.219    979
  Planarity :  0.005   0.055   1166
  Dihedral  : 13.761 109.555   1061
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.63 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.27 (0.30), residues: 785
  helix:  1.39 (0.27), residues: 396
  sheet:  0.34 (0.80), residues: 45
  loop : -1.33 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.007   0.001   HIS B 519 
 PHE   0.017   0.002   PHE A 369 
 TYR   0.017   0.002   TYR B 365 
 ARG   0.004   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00307 (    6)
  link_NAG-ASN         : angle       2.66644 (   18)
  link_BETA1-4         : bond        0.00635 (    3)
  link_BETA1-4         : angle       3.68442 (    9)
  hydrogen bonds       : bond        0.05810 (  297)
  hydrogen bonds       : angle       4.50243 (  843)
  metal coordination   : bond        0.00347 (    2)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.38014 (    8)
  covalent geometry    : bond        0.00423 ( 6748)
  covalent geometry    : angle       0.62717 ( 9156)

*********************** 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
  86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7598 (t0) cc_final: 0.7252 (t0)
REVERT: B  469 SER cc_start: 0.8363 (m) cc_final: 0.8045 (p)
REVERT: A  552 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8029 (mp-120)
  outliers start: 15
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1846
  time to fit residues: 21.8315
Evaluate side-chains
  73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  576 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 14 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.126287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.096000 restraints weight = 11811.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.76
r_work: 0.3179 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6763  Z= 0.130
  Angle     :  0.573   7.381   9191  Z= 0.282
  Chirality :  0.042   0.237    979
  Planarity :  0.005   0.050   1166
  Dihedral  : 12.011 110.055   1060
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.78 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.34 (0.30), residues: 785
  helix:  1.46 (0.27), residues: 386
  sheet:  0.32 (0.80), residues: 45
  loop : -1.20 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    6)
  link_NAG-ASN         : angle       2.69033 (   18)
  link_BETA1-4         : bond        0.00813 (    3)
  link_BETA1-4         : angle       3.66855 (    9)
  hydrogen bonds       : bond        0.05150 (  297)
  hydrogen bonds       : angle       4.40941 (  843)
  metal coordination   : bond        0.00159 (    2)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       0.29832 (    8)
  covalent geometry    : bond        0.00284 ( 6748)
  covalent geometry    : angle       0.55011 ( 9156)

*********************** 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 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.7561 (mp0) cc_final: 0.7287 (mp0)
REVERT: B  370 ASN cc_start: 0.7651 (t0) cc_final: 0.7315 (t0)
REVERT: B  469 SER cc_start: 0.8406 (m) cc_final: 0.8033 (p)
REVERT: A  332 MET cc_start: 0.8631 (ttm) cc_final: 0.8419 (ttt)
REVERT: A  408 MET cc_start: 0.9152 (mmt) cc_final: 0.8870 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.1688
  time to fit residues: 18.7799
Evaluate side-chains
  71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  576 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.120501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090551 restraints weight = 12016.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.77
r_work: 0.3114 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6763  Z= 0.188
  Angle     :  0.596   8.777   9191  Z= 0.297
  Chirality :  0.044   0.231    979
  Planarity :  0.005   0.062   1166
  Dihedral  : 10.416 106.334   1060
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.36 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.28 (0.30), residues: 785
  helix:  1.31 (0.27), residues: 397
  sheet:  0.68 (0.80), residues: 45
  loop : -1.26 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.006   0.001   HIS B 519 
 PHE   0.018   0.002   PHE A 369 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00324 (    6)
  link_NAG-ASN         : angle       2.48312 (   18)
  link_BETA1-4         : bond        0.01070 (    3)
  link_BETA1-4         : angle       3.79776 (    9)
  hydrogen bonds       : bond        0.05636 (  297)
  hydrogen bonds       : angle       4.41774 (  843)
  metal coordination   : bond        0.00327 (    2)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       0.32466 (    8)
  covalent geometry    : bond        0.00442 ( 6748)
  covalent geometry    : angle       0.57418 ( 9156)

*********************** 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
  78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.7571 (mp0) cc_final: 0.7311 (mp0)
REVERT: B  370 ASN cc_start: 0.7640 (t0) cc_final: 0.7335 (t0)
REVERT: B  469 SER cc_start: 0.8363 (m) cc_final: 0.7999 (p)
REVERT: A  332 MET cc_start: 0.8696 (ttm) cc_final: 0.8463 (ttt)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1535
  time to fit residues: 17.1303
Evaluate side-chains
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  576 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.121666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091901 restraints weight = 11958.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.78
r_work: 0.3151 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6763  Z= 0.129
  Angle     :  0.537   8.164   9191  Z= 0.267
  Chirality :  0.041   0.166    979
  Planarity :  0.004   0.051   1166
  Dihedral  :  9.656 105.315   1060
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.21 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.37 (0.30), residues: 785
  helix:  1.43 (0.27), residues: 385
  sheet:  0.73 (0.80), residues: 45
  loop : -1.19 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 519 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.013   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    6)
  link_NAG-ASN         : angle       2.14481 (   18)
  link_BETA1-4         : bond        0.00957 (    3)
  link_BETA1-4         : angle       3.59973 (    9)
  hydrogen bonds       : bond        0.04914 (  297)
  hydrogen bonds       : angle       4.33304 (  843)
  metal coordination   : bond        0.00152 (    2)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.29389 (    8)
  covalent geometry    : bond        0.00288 ( 6748)
  covalent geometry    : angle       0.51782 ( 9156)

*********************** 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
  78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7544 (t0) cc_final: 0.7272 (t0)
REVERT: A  332 MET cc_start: 0.8678 (ttm) cc_final: 0.8467 (ttt)
REVERT: A  408 MET cc_start: 0.9127 (mmt) cc_final: 0.8849 (mmt)
  outliers start: 13
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1588
  time to fit residues: 17.4784
Evaluate side-chains
  71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  576 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.121854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092089 restraints weight = 11828.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.76
r_work: 0.3145 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6763  Z= 0.136
  Angle     :  0.542   8.033   9191  Z= 0.269
  Chirality :  0.041   0.148    979
  Planarity :  0.005   0.085   1166
  Dihedral  :  9.177 103.460   1060
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.22 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.45 (0.30), residues: 785
  helix:  1.48 (0.27), residues: 385
  sheet:  0.80 (0.82), residues: 45
  loop : -1.12 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 519 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    6)
  link_NAG-ASN         : angle       2.13063 (   18)
  link_BETA1-4         : bond        0.00986 (    3)
  link_BETA1-4         : angle       3.45548 (    9)
  hydrogen bonds       : bond        0.04897 (  297)
  hydrogen bonds       : angle       4.27519 (  843)
  metal coordination   : bond        0.00215 (    2)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.29744 (    8)
  covalent geometry    : bond        0.00310 ( 6748)
  covalent geometry    : angle       0.52386 ( 9156)

*********************** 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
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7551 (t0) cc_final: 0.7276 (t0)
REVERT: A  332 MET cc_start: 0.8678 (ttm) cc_final: 0.8463 (ttt)
REVERT: A  408 MET cc_start: 0.9127 (mmt) cc_final: 0.8805 (mmt)
  outliers start: 9
  outliers final: 6
  residues processed: 72
  average time/residue: 0.1583
  time to fit residues: 16.4964
Evaluate side-chains
  67 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0270
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   overall best weight:    1.0242

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.120483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089806 restraints weight = 12033.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.84
r_work: 0.3092 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6763  Z= 0.153
  Angle     :  0.549   8.229   9191  Z= 0.275
  Chirality :  0.042   0.152    979
  Planarity :  0.005   0.070   1166
  Dihedral  :  8.506 101.478   1056
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.65 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.44 (0.30), residues: 785
  helix:  1.45 (0.27), residues: 391
  sheet:  0.76 (0.80), residues: 45
  loop : -1.14 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.005   0.001   HIS B 519 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00278 (    6)
  link_NAG-ASN         : angle       2.21874 (   18)
  link_BETA1-4         : bond        0.00846 (    3)
  link_BETA1-4         : angle       3.06528 (    9)
  hydrogen bonds       : bond        0.05089 (  297)
  hydrogen bonds       : angle       4.27990 (  843)
  metal coordination   : bond        0.00266 (    2)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.28885 (    8)
  covalent geometry    : bond        0.00355 ( 6748)
  covalent geometry    : angle       0.53257 ( 9156)

*********************** 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
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.725 
Fit side-chains
REVERT: B  370 ASN cc_start: 0.7543 (t0) cc_final: 0.7280 (t0)
REVERT: B  375 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6824 (t80)
REVERT: A  332 MET cc_start: 0.8735 (ttm) cc_final: 0.8507 (ttt)
  outliers start: 11
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2052
  time to fit residues: 21.3267
Evaluate side-chains
  66 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.121532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090940 restraints weight = 12047.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.85
r_work: 0.3116 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6763  Z= 0.115
  Angle     :  0.525   8.326   9191  Z= 0.264
  Chirality :  0.041   0.145    979
  Planarity :  0.004   0.064   1166
  Dihedral  :  8.158 100.830   1056
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.65 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.44 (0.30), residues: 785
  helix:  1.45 (0.27), residues: 385
  sheet:  0.80 (0.80), residues: 45
  loop : -1.10 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    6)
  link_NAG-ASN         : angle       2.06545 (   18)
  link_BETA1-4         : bond        0.00831 (    3)
  link_BETA1-4         : angle       2.74581 (    9)
  hydrogen bonds       : bond        0.04684 (  297)
  hydrogen bonds       : angle       4.27890 (  843)
  metal coordination   : bond        0.00123 (    2)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.28287 (    8)
  covalent geometry    : bond        0.00253 ( 6748)
  covalent geometry    : angle       0.51020 ( 9156)

*********************** 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
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.759 
Fit side-chains
REVERT: B  370 ASN cc_start: 0.7504 (t0) cc_final: 0.7259 (t0)
REVERT: B  375 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6747 (t80)
REVERT: B  396 TYR cc_start: 0.8518 (m-10) cc_final: 0.8295 (m-10)
REVERT: A  332 MET cc_start: 0.8698 (ttm) cc_final: 0.8482 (ttt)
REVERT: A  365 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (p)
REVERT: A  408 MET cc_start: 0.9122 (mmt) cc_final: 0.8875 (mmt)
  outliers start: 9
  outliers final: 5
  residues processed: 72
  average time/residue: 0.2469
  time to fit residues: 26.4845
Evaluate side-chains
  67 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.119987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.089309 restraints weight = 12151.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.84
r_work: 0.3086 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6763  Z= 0.180
  Angle     :  0.578   8.731   9191  Z= 0.294
  Chirality :  0.042   0.154    979
  Planarity :  0.005   0.064   1166
  Dihedral  :  8.034  98.821   1056
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.94 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.37 (0.30), residues: 785
  helix:  1.49 (0.27), residues: 384
  sheet:  0.77 (0.79), residues: 45
  loop : -1.26 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.006   0.001   HIS B 519 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.002   0.000   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    6)
  link_NAG-ASN         : angle       2.29762 (   18)
  link_BETA1-4         : bond        0.00735 (    3)
  link_BETA1-4         : angle       2.58460 (    9)
  hydrogen bonds       : bond        0.05327 (  297)
  hydrogen bonds       : angle       4.35111 (  843)
  metal coordination   : bond        0.00372 (    2)
  SS BOND              : bond        0.00197 (    4)
  SS BOND              : angle       0.33774 (    8)
  covalent geometry    : bond        0.00422 ( 6748)
  covalent geometry    : angle       0.56396 ( 9156)

*********************** 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
  71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.710 
Fit side-chains
REVERT: B  370 ASN cc_start: 0.7521 (t0) cc_final: 0.7280 (t0)
REVERT: B  375 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6806 (t80)
REVERT: A  332 MET cc_start: 0.8776 (ttm) cc_final: 0.8549 (ttt)
REVERT: A  365 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8115 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 0.2085
  time to fit residues: 20.9552
Evaluate side-chains
  69 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.121505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090954 restraints weight = 12171.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.85
r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6763  Z= 0.130
  Angle     :  0.537   8.609   9191  Z= 0.273
  Chirality :  0.041   0.147    979
  Planarity :  0.005   0.062   1166
  Dihedral  :  7.716  97.642   1056
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.65 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.43 (0.30), residues: 785
  helix:  1.57 (0.27), residues: 378
  sheet:  0.74 (0.78), residues: 45
  loop : -1.21 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 519 
 PHE   0.012   0.001   PHE A 369 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.004   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00284 (    6)
  link_NAG-ASN         : angle       2.13678 (   18)
  link_BETA1-4         : bond        0.00706 (    3)
  link_BETA1-4         : angle       2.27013 (    9)
  hydrogen bonds       : bond        0.04783 (  297)
  hydrogen bonds       : angle       4.33002 (  843)
  metal coordination   : bond        0.00139 (    2)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       0.31447 (    8)
  covalent geometry    : bond        0.00293 ( 6748)
  covalent geometry    : angle       0.52487 ( 9156)

********************** 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
  74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.896 
Fit side-chains
REVERT: B  370 ASN cc_start: 0.7499 (t0) cc_final: 0.7271 (t0)
REVERT: B  375 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6693 (t80)
REVERT: A  332 MET cc_start: 0.8724 (ttm) cc_final: 0.8510 (ttt)
REVERT: A  365 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (p)
REVERT: A  408 MET cc_start: 0.9125 (mmt) cc_final: 0.8869 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1901
  time to fit residues: 19.8209
Evaluate side-chains
  72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  375 PHE
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  532 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    0.1980
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.121607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.091608 restraints weight = 12011.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.66
r_work: 0.3092 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6763  Z= 0.115
  Angle     :  0.531   8.766   9191  Z= 0.269
  Chirality :  0.040   0.148    979
  Planarity :  0.005   0.062   1166
  Dihedral  :  7.472  95.680   1056
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.37 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.30), residues: 785
  helix:  1.62 (0.27), residues: 378
  sheet:  0.83 (0.77), residues: 45
  loop : -1.17 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.006   0.000   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00258 (    6)
  link_NAG-ASN         : angle       2.08257 (   18)
  link_BETA1-4         : bond        0.00653 (    3)
  link_BETA1-4         : angle       2.08441 (    9)
  hydrogen bonds       : bond        0.04536 (  297)
  hydrogen bonds       : angle       4.30175 (  843)
  metal coordination   : bond        0.00113 (    2)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       0.29065 (    8)
  covalent geometry    : bond        0.00258 ( 6748)
  covalent geometry    : angle       0.51969 ( 9156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4554.91 seconds
wall clock time: 82 minutes 18.80 seconds (4938.80 seconds total)