Starting phenix.real_space_refine
on Sat Aug 23 10:43:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hfy_34728/08_2025/8hfy_34728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hfy_34728/08_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_34728/08_2025/8hfy_34728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hfy_34728/08_2025/8hfy_34728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hfy_34728/08_2025/8hfy_34728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hfy_34728/08_2025/8hfy_34728.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.94, per 1000 atoms: 0.30
  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: 0.58
  Conformation dependent library (CDL) restraints added in 320.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  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: 0.23
  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: 0.99

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:             6.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.990
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.770
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 161 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.009   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 378 

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

*********************** 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  : 0.269 
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: 0.8132 (t0)
REVERT: A  152 MET cc_start: 0.9148 (mmm) cc_final: 0.8650 (mmt)
REVERT: A  153 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7968 (mt-10)
  outliers start: 10
  outliers final: 3
  residues processed: 130
  average time/residue: 0.0956
  time to fit residues: 16.0787
Evaluate side-chains
  77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.120954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090713 restraints weight = 11889.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.77
r_work: 0.3113 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   6763  Z= 0.214
  Angle     :  0.674  10.928   9191  Z= 0.334
  Chirality :  0.045   0.218    979
  Planarity :  0.005   0.057   1166
  Dihedral  : 13.837 109.753   1061
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.78 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.30), residues: 785
  helix:  1.37 (0.27), residues: 395
  sheet:  0.34 (0.80), residues: 45
  loop : -1.34 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 177 
 TYR   0.015   0.002   TYR B 423 
 PHE   0.019   0.002   PHE A 369 
 TRP   0.014   0.001   TRP A 168 
 HIS   0.008   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 6748)
  covalent geometry    : angle       0.65394 ( 9156)
  SS BOND              : bond        0.00207 (    4)
  SS BOND              : angle       0.35838 (    8)
  hydrogen bonds       : bond        0.06118 (  297)
  hydrogen bonds       : angle       4.55080 (  843)
  metal coordination   : bond        0.00414 (    2)
  link_BETA1-4         : bond        0.00604 (    3)
  link_BETA1-4         : angle       3.71046 (    9)
  link_NAG-ASN         : bond        0.00315 (    6)
  link_NAG-ASN         : angle       2.72340 (   18)

*********************** 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
  87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7618 (t0) cc_final: 0.7271 (t0)
REVERT: A  552 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7982 (mp-120)
  outliers start: 16
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0847
  time to fit residues: 10.1665
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  : 0.265 
-------------------------------------------------------------------------------
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  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 16 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.121867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091912 restraints weight = 11875.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.78
r_work: 0.3129 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1923

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= 0.148
  Angle     :  0.591   7.390   9191  Z= 0.292
  Chirality :  0.043   0.235    979
  Planarity :  0.005   0.051   1166
  Dihedral  : 12.028 109.973   1061
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.21 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.30), residues: 785
  helix:  1.29 (0.27), residues: 397
  sheet:  0.35 (0.80), residues: 45
  loop : -1.25 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.014   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6748)
  covalent geometry    : angle       0.56729 ( 9156)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       0.30241 (    8)
  hydrogen bonds       : bond        0.05399 (  297)
  hydrogen bonds       : angle       4.45007 (  843)
  metal coordination   : bond        0.00211 (    2)
  link_BETA1-4         : bond        0.00776 (    3)
  link_BETA1-4         : angle       3.68464 (    9)
  link_NAG-ASN         : bond        0.00370 (    6)
  link_NAG-ASN         : angle       2.79654 (   18)

*********************** 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
  77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7611 (t0) cc_final: 0.7279 (t0)
REVERT: B  469 SER cc_start: 0.8342 (m) cc_final: 0.7976 (p)
REVERT: A  408 MET cc_start: 0.9139 (mmt) cc_final: 0.8840 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0803
  time to fit residues: 8.7052
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  : 0.275 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.122696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.092837 restraints weight = 11923.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.78
r_work: 0.3161 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2096

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= 0.122
  Angle     :  0.539   8.708   9191  Z= 0.267
  Chirality :  0.042   0.235    979
  Planarity :  0.004   0.054   1166
  Dihedral  : 10.555 107.658   1060
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.36 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.30), residues: 785
  helix:  1.44 (0.27), residues: 385
  sheet:  0.41 (0.80), residues: 45
  loop : -1.16 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6748)
  covalent geometry    : angle       0.51851 ( 9156)
  SS BOND              : bond        0.00152 (    4)
  SS BOND              : angle       0.29336 (    8)
  hydrogen bonds       : bond        0.04757 (  297)
  hydrogen bonds       : angle       4.37526 (  843)
  metal coordination   : bond        0.00155 (    2)
  link_BETA1-4         : bond        0.00967 (    3)
  link_BETA1-4         : angle       3.70610 (    9)
  link_NAG-ASN         : bond        0.00231 (    6)
  link_NAG-ASN         : angle       2.11695 (   18)

*********************** 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
  74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7593 (t0) cc_final: 0.7300 (t0)
REVERT: B  469 SER cc_start: 0.8346 (m) cc_final: 0.8062 (p)
REVERT: A  408 MET cc_start: 0.9144 (mmt) cc_final: 0.8885 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0817
  time to fit residues: 8.5181
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  : 0.286 
-------------------------------------------------------------------------------
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  195 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.120832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.090893 restraints weight = 12092.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.79
r_work: 0.3139 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2218

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= 0.164
  Angle     :  0.566   8.260   9191  Z= 0.283
  Chirality :  0.043   0.170    979
  Planarity :  0.004   0.058   1166
  Dihedral  :  9.610 104.581   1060
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.50 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.30), residues: 785
  helix:  1.42 (0.27), residues: 390
  sheet:  0.65 (0.82), residues: 44
  loop : -1.12 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.016   0.001   PHE A 369 
 TRP   0.016   0.001   TRP A 168 
 HIS   0.005   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6748)
  covalent geometry    : angle       0.54697 ( 9156)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       0.31127 (    8)
  hydrogen bonds       : bond        0.05304 (  297)
  hydrogen bonds       : angle       4.35526 (  843)
  metal coordination   : bond        0.00267 (    2)
  link_BETA1-4         : bond        0.00986 (    3)
  link_BETA1-4         : angle       3.60837 (    9)
  link_NAG-ASN         : bond        0.00273 (    6)
  link_NAG-ASN         : angle       2.25991 (   18)

*********************** 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  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7531 (t0) cc_final: 0.7259 (t0)
REVERT: B  469 SER cc_start: 0.8320 (m) cc_final: 0.8038 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0771
  time to fit residues: 8.4196
Evaluate side-chains
  73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  195 ASN
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 30 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.121555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091841 restraints weight = 11932.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.76
r_work: 0.3156 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2285

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= 0.139
  Angle     :  0.541   8.047   9191  Z= 0.270
  Chirality :  0.042   0.169    979
  Planarity :  0.005   0.085   1166
  Dihedral  :  9.183 103.378   1060
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.22 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.30), residues: 785
  helix:  1.49 (0.27), residues: 384
  sheet:  0.69 (0.82), residues: 44
  loop : -1.08 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 600 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.013   0.001   PHE A 369 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6748)
  covalent geometry    : angle       0.52305 ( 9156)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.28691 (    8)
  hydrogen bonds       : bond        0.04936 (  297)
  hydrogen bonds       : angle       4.30878 (  843)
  metal coordination   : bond        0.00206 (    2)
  link_BETA1-4         : bond        0.01003 (    3)
  link_BETA1-4         : angle       3.41224 (    9)
  link_NAG-ASN         : bond        0.00286 (    6)
  link_NAG-ASN         : angle       2.14522 (   18)

*********************** 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
  76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7538 (t0) cc_final: 0.7274 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0715
  time to fit residues: 7.4044
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  : 0.262 
-------------------------------------------------------------------------------
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  471 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.120992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.090933 restraints weight = 11975.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.66
r_work: 0.3080 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2367

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= 0.122
  Angle     :  0.527   8.213   9191  Z= 0.264
  Chirality :  0.041   0.169    979
  Planarity :  0.005   0.069   1166
  Dihedral  :  8.486 101.865   1058
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.07 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.30), residues: 785
  helix:  1.60 (0.27), residues: 382
  sheet:  0.69 (0.81), residues: 44
  loop : -1.07 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 600 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.011   0.001   PHE A 369 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6748)
  covalent geometry    : angle       0.51192 ( 9156)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.27401 (    8)
  hydrogen bonds       : bond        0.04625 (  297)
  hydrogen bonds       : angle       4.25890 (  843)
  metal coordination   : bond        0.00133 (    2)
  link_BETA1-4         : bond        0.00900 (    3)
  link_BETA1-4         : angle       2.97806 (    9)
  link_NAG-ASN         : bond        0.00254 (    6)
  link_NAG-ASN         : angle       2.05723 (   18)

*********************** 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
  77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7525 (t0) cc_final: 0.7285 (t0)
REVERT: B  375 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6729 (t80)
REVERT: A  151 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8539 (mp)
REVERT: A  365 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.8002 (p)
REVERT: A  408 MET cc_start: 0.9134 (mmt) cc_final: 0.8822 (mmt)
  outliers start: 11
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0792
  time to fit residues: 8.6157
Evaluate side-chains
  73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  151 ILE
Chi-restraints excluded: chain A residue  195 ASN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.0470
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.121445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.091623 restraints weight = 11917.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.64
r_work: 0.3097 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6763  Z= 0.115
  Angle     :  0.514   8.474   9191  Z= 0.258
  Chirality :  0.040   0.168    979
  Planarity :  0.005   0.064   1166
  Dihedral  :  7.859  99.425   1056
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.22 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.30), residues: 785
  helix:  1.68 (0.27), residues: 382
  sheet:  0.77 (0.81), residues: 44
  loop : -1.03 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.023   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 369 
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6748)
  covalent geometry    : angle       0.50120 ( 9156)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.25557 (    8)
  hydrogen bonds       : bond        0.04423 (  297)
  hydrogen bonds       : angle       4.23109 (  843)
  metal coordination   : bond        0.00127 (    2)
  link_BETA1-4         : bond        0.00836 (    3)
  link_BETA1-4         : angle       2.53798 (    9)
  link_NAG-ASN         : bond        0.00261 (    6)
  link_NAG-ASN         : angle       1.99425 (   18)

*********************** 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 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7468 (t0) cc_final: 0.7255 (t0)
REVERT: B  375 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6614 (t80)
REVERT: B  396 TYR cc_start: 0.8471 (m-10) cc_final: 0.8194 (m-10)
REVERT: A  151 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8542 (mp)
REVERT: A  153 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8260 (mt-10)
REVERT: A  365 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (p)
REVERT: A  408 MET cc_start: 0.9132 (mmt) cc_final: 0.8892 (mmt)
  outliers start: 11
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0789
  time to fit residues: 8.5087
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  : 0.261 
-------------------------------------------------------------------------------
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  151 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0770
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.5516

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.121928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.092095 restraints weight = 11990.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.65
r_work: 0.3109 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6763  Z= 0.112
  Angle     :  0.511   8.701   9191  Z= 0.255
  Chirality :  0.040   0.166    979
  Planarity :  0.005   0.081   1166
  Dihedral  :  7.508  96.864   1056
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.51 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.30), residues: 785
  helix:  1.83 (0.27), residues: 376
  sheet:  0.73 (0.79), residues: 44
  loop : -1.03 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6748)
  covalent geometry    : angle       0.49905 ( 9156)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.27869 (    8)
  hydrogen bonds       : bond        0.04299 (  297)
  hydrogen bonds       : angle       4.20314 (  843)
  metal coordination   : bond        0.00130 (    2)
  link_BETA1-4         : bond        0.00709 (    3)
  link_BETA1-4         : angle       2.20014 (    9)
  link_NAG-ASN         : bond        0.00260 (    6)
  link_NAG-ASN         : angle       1.98270 (   18)

*********************** 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
  78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7499 (t0) cc_final: 0.7276 (t0)
REVERT: B  375 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6607 (t80)
REVERT: A  151 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8488 (mp)
REVERT: A  153 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8250 (mt-10)
REVERT: A  365 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7960 (p)
REVERT: A  408 MET cc_start: 0.9128 (mmt) cc_final: 0.8846 (mmt)
  outliers start: 11
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0784
  time to fit residues: 8.6218
Evaluate side-chains
  75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 CYS
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  151 ILE
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 40 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.122346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.092599 restraints weight = 11936.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.59
r_work: 0.3116 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2570

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= 0.113
  Angle     :  0.521   8.820   9191  Z= 0.263
  Chirality :  0.041   0.168    979
  Planarity :  0.005   0.081   1166
  Dihedral  :  7.375  95.305   1056
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.08 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.30), residues: 785
  helix:  1.75 (0.27), residues: 377
  sheet:  0.78 (0.80), residues: 44
  loop : -1.04 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 369 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6748)
  covalent geometry    : angle       0.51014 ( 9156)
  SS BOND              : bond        0.00120 (    4)
  SS BOND              : angle       0.26970 (    8)
  hydrogen bonds       : bond        0.04357 (  297)
  hydrogen bonds       : angle       4.22260 (  843)
  metal coordination   : bond        0.00131 (    2)
  link_BETA1-4         : bond        0.00667 (    3)
  link_BETA1-4         : angle       2.15067 (    9)
  link_NAG-ASN         : bond        0.00260 (    6)
  link_NAG-ASN         : angle       1.99209 (   18)

********************** 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
  75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: B  370 ASN cc_start: 0.7506 (t0) cc_final: 0.7283 (t0)
REVERT: B  375 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6564 (t80)
REVERT: A  151 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (mp)
REVERT: A  153 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8221 (mt-10)
REVERT: A  365 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7931 (p)
REVERT: A  408 MET cc_start: 0.9131 (mmt) cc_final: 0.8850 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0769
  time to fit residues: 8.0753
Evaluate side-chains
  75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 CYS
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  151 ILE
Chi-restraints excluded: chain A residue  195 ASN
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 74 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.120822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.090848 restraints weight = 11874.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.63
r_work: 0.3088 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6763  Z= 0.134
  Angle     :  0.531   8.973   9191  Z= 0.268
  Chirality :  0.041   0.169    979
  Planarity :  0.005   0.079   1166
  Dihedral  :  7.310  92.641   1056
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.08 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.30), residues: 785
  helix:  1.69 (0.27), residues: 377
  sheet:  0.76 (0.79), residues: 44
  loop : -1.07 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 600 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.013   0.001   PHE A 369 
 TRP   0.012   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6748)
  covalent geometry    : angle       0.51916 ( 9156)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       0.29177 (    8)
  hydrogen bonds       : bond        0.04718 (  297)
  hydrogen bonds       : angle       4.26169 (  843)
  metal coordination   : bond        0.00220 (    2)
  link_BETA1-4         : bond        0.00628 (    3)
  link_BETA1-4         : angle       2.11185 (    9)
  link_NAG-ASN         : bond        0.00257 (    6)
  link_NAG-ASN         : angle       2.15569 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1685.84 seconds
wall clock time: 29 minutes 38.77 seconds (1778.77 seconds total)