Starting phenix.real_space_refine
on Sat May 10 02:16:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p2z_17380/05_2025/8p2z_17380.cif"
  }
  resolution = 3.5
  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=   0.002 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     Cl      1      4.86       5
     C    3073      2.51       5
     N     712      2.21       5
     O     824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4641
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 199
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "C"
      Number of atoms: 4404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4404
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 20, 'TRANS': 552}
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 37
          Unusual residues: {'NAG': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.58, per 1000 atoms: 0.77
  Number of scatterers: 4641
  At special positions: 0
  Unit cell: (61.0785, 72.297, 103.46, 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)
     Cl      1     17.00
     S      31     16.00
     O     824      8.00
     N     712      7.00
     C    3073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 126 " - pdb=" SG  CYS C 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 309 " - pdb=" SG  CYS C 358 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 701 " - " ASN C 131 "
      " NAG C 702 " - " ASN C 357 "
  Time building additional restraints: 1.38
  Conformation dependent library (CDL) restraints added in 589.4 milliseconds
  

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1116

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 1 sheets defined
      82.9% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 740 through 768
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 24 through 29
      removed outlier: 3.569A  pdb=" N   VAL C  28 " --> pdb=" O   GLY C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 38
      removed outlier: 3.834A  pdb=" N   TYR C  33 " --> pdb=" O   TRP C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 54
      Proline residue:  C  46  - end of helix
      removed outlier: 3.666A  pdb=" N   VAL C  53 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 70
      removed outlier: 3.610A  pdb=" N   LEU C  58 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
      removed outlier: 4.030A  pdb=" N   SER C  81 " --> pdb=" O   TRP C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 84
      No H-bonds generated for 'chain 'C' and resid 82 through 84'
    Processing helix  chain 'C' and resid 85 through 115
      removed outlier: 3.645A  pdb=" N   VAL C  89 " --> pdb=" O   SER C  85 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL C  92 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER C  95 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ASN C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   VAL C 104 " --> pdb=" O   MET C 100 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ILE C 105 " --> pdb=" O   TYR C 101 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN C 106 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 142
    Processing helix  chain 'C' and resid 143 through 151
    Processing helix  chain 'C' and resid 167 through 188
      removed outlier: 3.536A  pdb=" N   GLY C 188 " --> pdb=" O   CYS C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 3.658A  pdb=" N   TYR C 197 " --> pdb=" O   GLY C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 215
    Processing helix  chain 'C' and resid 219 through 229
      removed outlier: 4.129A  pdb=" N   GLY C 223 " --> pdb=" O   GLY C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 253
      removed outlier: 3.758A  pdb=" N   TRP C 241 " --> pdb=" O   ASN C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 265
      removed outlier: 3.697A  pdb=" N   ALA C 261 " --> pdb=" O   GLY C 257 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR C 265 " --> pdb=" O   ALA C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 322
      removed outlier: 3.663A  pdb=" N   HIS C 275 " --> pdb=" O   ASN C 271 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE C 277 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR C 320 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 331
      No H-bonds generated for 'chain 'C' and resid 329 through 331'
    Processing helix  chain 'C' and resid 332 through 344
    Processing helix  chain 'C' and resid 344 through 352
      removed outlier: 3.813A  pdb=" N   TYR C 348 " --> pdb=" O   TYR C 344 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU C 350 " --> pdb=" O   SER C 346 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   MET C 351 " --> pdb=" O   LYS C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 367
    Processing helix  chain 'C' and resid 372 through 384
    Processing helix  chain 'C' and resid 387 through 421
      removed outlier: 3.570A  pdb=" N   TRP C 391 " --> pdb=" O   VAL C 387 " (cutoff:3.500A)
      Proline residue:  C 417  - end of helix
    Processing helix  chain 'C' and resid 421 through 426
    Processing helix  chain 'C' and resid 429 through 445
    Processing helix  chain 'C' and resid 446 through 450
      removed outlier: 3.842A  pdb=" N   MET C 450 " --> pdb=" O   VAL C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 464
      removed outlier: 3.795A  pdb=" N   TRP C 456 " --> pdb=" O   ALA C 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 467 through 482
    Processing helix  chain 'C' and resid 485 through 498
    Processing helix  chain 'C' and resid 502 through 511
    Processing helix  chain 'C' and resid 511 through 532
    Processing helix  chain 'C' and resid 552 through 582
      removed outlier: 3.640A  pdb=" N   LEU C 556 " --> pdb=" O   PRO C 552 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA C 557 " --> pdb=" O   ALA C 553 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL C 558 " --> pdb=" O   TYR C 554 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL C 563 " --> pdb=" O   ILE C 559 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   SER C 566 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE C 570 " --> pdb=" O   SER C 566 " (cutoff:3.500A)
      Proline residue:  C 571  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 535 through 540

    335 hydrogen bonds defined for protein.
    999 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: 1.21

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 990
        1.33 -     1.45: 1152
        1.45 -     1.57: 2573
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 4764
  Sorted by residual:
  bond pdb=" C   YCP C 703 "
       pdb=" O   YCP C 703 "
    ideal  model  delta    sigma   weight residual
    1.231  1.305 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" CD  YCP C 703 "
       pdb=" CE  YCP C 703 "
    ideal  model  delta    sigma   weight residual
    1.535  1.500  0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C   YCP C 703 "
       pdb=" OXT YCP C 703 "
    ideal  model  delta    sigma   weight residual
    1.246  1.214  0.032 2.00e-02 2.50e+03 2.64e+00
  bond pdb=" CB  PRO C 353 "
       pdb=" CG  PRO C 353 "
    ideal  model  delta    sigma   weight residual
    1.492  1.573 -0.081 5.00e-02 4.00e+02 2.61e+00
  bond pdb=" C1  NAG C 702 "
       pdb=" O5  NAG C 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.34e+00
  ... (remaining 4759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6354
        1.64 -     3.28: 131
        3.28 -     4.92: 17
        4.92 -     6.57: 5
        6.57 -     8.21: 4
  Bond angle restraints: 6511
  Sorted by residual:
  angle pdb=" CA  PRO C 353 "
        pdb=" N   PRO C 353 "
        pdb=" CD  PRO C 353 "
      ideal   model   delta    sigma   weight residual
     112.00  103.84    8.16 1.40e+00 5.10e-01 3.40e+01
  angle pdb=" CA  YCP C 703 "
        pdb=" C   YCP C 703 "
        pdb=" O   YCP C 703 "
      ideal   model   delta    sigma   weight residual
     120.80  112.59    8.21 1.70e+00 3.46e-01 2.33e+01
  angle pdb=" N   LEU C  84 "
        pdb=" CA  LEU C  84 "
        pdb=" C   LEU C  84 "
      ideal   model   delta    sigma   weight residual
     114.12  110.16    3.96 1.39e+00 5.18e-01 8.10e+00
  angle pdb=" CB  MET C 407 "
        pdb=" CG  MET C 407 "
        pdb=" SD  MET C 407 "
      ideal   model   delta    sigma   weight residual
     112.70  105.37    7.33 3.00e+00 1.11e-01 5.97e+00
  angle pdb=" CA  LEU C  84 "
        pdb=" CB  LEU C  84 "
        pdb=" CG  LEU C  84 "
      ideal   model   delta    sigma   weight residual
     116.30  124.06   -7.76 3.50e+00 8.16e-02 4.91e+00
  ... (remaining 6506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.06: 2462
       18.06 -    36.12: 220
       36.12 -    54.18: 53
       54.18 -    72.24: 6
       72.24 -    90.30: 4
  Dihedral angle restraints: 2745
    sinusoidal: 994
      harmonic: 1751
  Sorted by residual:
  dihedral pdb=" CA  YCP C 703 "
           pdb=" N   YCP C 703 "
           pdb=" CE  YCP C 703 "
           pdb=" CD  YCP C 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
      28.56  -61.74   90.30     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU C 267 "
           pdb=" CG  GLU C 267 "
           pdb=" CD  GLU C 267 "
           pdb=" OE1 GLU C 267 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.41  -87.41     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CA  GLY C 511 "
           pdb=" C   GLY C 511 "
           pdb=" N   VAL C 512 "
           pdb=" CA  VAL C 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.49  -15.51     0      5.00e+00 4.00e-02 9.62e+00
  ... (remaining 2742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 647
       0.057 -    0.114: 115
       0.114 -    0.171: 1
       0.171 -    0.228: 0
       0.228 -    0.285: 1
  Chirality restraints: 764
  Sorted by residual:
  chirality pdb=" C1  NAG C 701 "
            pdb=" ND2 ASN C 131 "
            pdb=" C2  NAG C 701 "
            pdb=" O5  NAG C 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  VAL C 368 "
            pdb=" N   VAL C 368 "
            pdb=" C   VAL C 368 "
            pdb=" CB  VAL C 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  PRO C  32 "
            pdb=" N   PRO C  32 "
            pdb=" C   PRO C  32 "
            pdb=" CB  PRO C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.04e-01
  ... (remaining 761 not shown)

  Planarity restraints: 796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 352 "    0.094 5.00e-02 4.00e+02   1.38e-01 3.03e+01
        pdb=" N   PRO C 353 "   -0.238 5.00e-02 4.00e+02
        pdb=" CA  PRO C 353 "    0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO C 353 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 365 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" CG  ASP C 365 "   -0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 365 "    0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 365 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  98 "    0.008 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   LEU C  98 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LEU C  98 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER C  99 "    0.009 2.00e-02 2.50e+03
  ... (remaining 793 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 766
        2.76 -     3.29: 4580
        3.29 -     3.83: 8090
        3.83 -     4.36: 8712
        4.36 -     4.90: 15637
  Nonbonded interactions: 37785
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 298 "
            pdb=" O   LEU C 364 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" ND2 ASN C  27 "
            pdb=" OD1 ASN C 283 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   ASP C 540 "
            pdb=" N   GLY C 544 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OH  TYR C 204 "
            pdb=" OG1 THR C 286 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" ND2 ASN C  27 "
            pdb=" OG  SER C 287 "
     model   vdw
     2.271 3.120
  ... (remaining 37780 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 group one per residue
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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.350
  Find NCS groups from input model:        0.040
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
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      :  0.004   0.081   4768  Z= 0.174
  Angle     :  0.630   8.207   6521  Z= 0.354
  Chirality :  0.040   0.285    764
  Planarity :  0.006   0.138    794
  Dihedral  : 14.807  90.304   1623
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 17.65 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.35), residues: 598
  helix:  1.64 (0.25), residues: 437
  sheet: -0.24 (1.30), residues: 14
  loop : -1.33 (0.48), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 178 
 HIS   0.001   0.000   HIS C 218 
 PHE   0.013   0.001   PHE C 295 
 TYR   0.021   0.001   TYR C  21 
 ARG   0.002   0.000   ARG C  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00385 (    2)
  link_NAG-ASN         : angle       3.60369 (    6)
  hydrogen bonds       : bond        0.14653 (  335)
  hydrogen bonds       : angle       6.22227 (  999)
  SS BOND              : bond        0.00186 (    2)
  SS BOND              : angle       0.72159 (    4)
  covalent geometry    : bond        0.00378 ( 4764)
  covalent geometry    : angle       0.62028 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.583 
Fit side-chains
REVERT: C  100 MET cc_start: 0.8359 (mtp) cc_final: 0.8139 (ttp)
REVERT: C  271 ASN cc_start: 0.5772 (m-40) cc_final: 0.5402 (m-40)
REVERT: C  407 MET cc_start: 0.9006 (tpp) cc_final: 0.8389 (mmm)
REVERT: C  416 THR cc_start: 0.8660 (m) cc_final: 0.8331 (p)
REVERT: C  568 MET cc_start: 0.7106 (ttm) cc_final: 0.6613 (ttt)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1916
  time to fit residues: 17.6826
Evaluate side-chains
  64 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  447 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN
C 247 GLN
C 461 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.158936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.132448 restraints weight = 5588.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.136150 restraints weight = 3259.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.138536 restraints weight = 2338.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4768  Z= 0.176
  Angle     :  0.568   7.098   6521  Z= 0.290
  Chirality :  0.042   0.291    764
  Planarity :  0.004   0.077    794
  Dihedral  :  6.243  80.480    691
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.71 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.34), residues: 598
  helix:  1.95 (0.24), residues: 442
  sheet:  0.53 (1.35), residues: 12
  loop : -1.29 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 178 
 HIS   0.002   0.001   HIS C 115 
 PHE   0.018   0.001   PHE C 295 
 TYR   0.015   0.001   TYR C 463 
 ARG   0.003   0.001   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00437 (    2)
  link_NAG-ASN         : angle       3.47567 (    6)
  hydrogen bonds       : bond        0.04905 (  335)
  hydrogen bonds       : angle       4.36677 (  999)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.70617 (    4)
  covalent geometry    : bond        0.00412 ( 4764)
  covalent geometry    : angle       0.55792 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.504 
Fit side-chains
REVERT: C   70 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7468 (mmm-85)
REVERT: C   71 GLN cc_start: 0.7825 (tt0) cc_final: 0.7539 (tt0)
REVERT: C  271 ASN cc_start: 0.5965 (m-40) cc_final: 0.5619 (m-40)
REVERT: C  365 ASP cc_start: 0.8493 (m-30) cc_final: 0.8276 (m-30)
REVERT: C  416 THR cc_start: 0.8566 (m) cc_final: 0.8272 (p)
REVERT: C  508 MET cc_start: 0.7352 (mmm) cc_final: 0.6819 (mmm)
REVERT: C  521 PHE cc_start: 0.8219 (m-10) cc_final: 0.7955 (m-10)
REVERT: C  568 MET cc_start: 0.7159 (ttm) cc_final: 0.6686 (ttt)
  outliers start: 13
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1703
  time to fit residues: 15.9961
Evaluate side-chains
  68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  447 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0870
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0970
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.2956

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

Flipped N/Q/H residues before XYZ refinement:
C  67 GLN
C 103 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.163116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.137001 restraints weight = 5606.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.140709 restraints weight = 3254.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.143203 restraints weight = 2326.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4768  Z= 0.107
  Angle     :  0.476   6.321   6521  Z= 0.240
  Chirality :  0.039   0.267    764
  Planarity :  0.004   0.062    794
  Dihedral  :  5.839  77.244    691
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.97 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.34), residues: 598
  helix:  2.23 (0.24), residues: 446
  sheet:  0.45 (1.25), residues: 12
  loop : -0.99 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 275 
 PHE   0.011   0.001   PHE C 250 
 TYR   0.013   0.001   TYR C  21 
 ARG   0.006   0.001   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00451 (    2)
  link_NAG-ASN         : angle       3.19820 (    6)
  hydrogen bonds       : bond        0.04052 (  335)
  hydrogen bonds       : angle       3.98335 (  999)
  SS BOND              : bond        0.00481 (    2)
  SS BOND              : angle       0.60277 (    4)
  covalent geometry    : bond        0.00223 ( 4764)
  covalent geometry    : angle       0.46634 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: C  365 ASP cc_start: 0.8447 (m-30) cc_final: 0.8205 (m-30)
REVERT: C  387 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7125 (p)
REVERT: C  508 MET cc_start: 0.7176 (mmm) cc_final: 0.6631 (mmm)
REVERT: C  568 MET cc_start: 0.7196 (ttm) cc_final: 0.6782 (ttt)
  outliers start: 9
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1290
  time to fit residues: 12.2378
Evaluate side-chains
  63 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 146 GLN
C 271 ASN
C 543 GLN
C 545 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.160363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.133507 restraints weight = 5719.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.137273 restraints weight = 3360.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.139710 restraints weight = 2418.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4768  Z= 0.150
  Angle     :  0.520   6.122   6521  Z= 0.261
  Chirality :  0.041   0.272    764
  Planarity :  0.004   0.053    794
  Dihedral  :  5.897  77.005    690
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.76 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.34), residues: 598
  helix:  2.27 (0.24), residues: 437
  sheet:  0.62 (1.27), residues: 12
  loop : -0.93 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 111 
 HIS   0.002   0.001   HIS C 115 
 PHE   0.017   0.001   PHE C 295 
 TYR   0.014   0.001   TYR C  21 
 ARG   0.004   0.001   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       3.08039 (    6)
  hydrogen bonds       : bond        0.04385 (  335)
  hydrogen bonds       : angle       4.01638 (  999)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.74436 (    4)
  covalent geometry    : bond        0.00351 ( 4764)
  covalent geometry    : angle       0.51137 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7378 (mmm-85)
REVERT: C  183 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (tp)
REVERT: C  365 ASP cc_start: 0.8399 (m-30) cc_final: 0.8048 (m-30)
REVERT: C  508 MET cc_start: 0.7242 (mmm) cc_final: 0.6581 (mmm)
REVERT: C  521 PHE cc_start: 0.8252 (m-10) cc_final: 0.7976 (m-10)
REVERT: C  568 MET cc_start: 0.7237 (ttm) cc_final: 0.6848 (ttt)
  outliers start: 17
  outliers final: 12
  residues processed: 73
  average time/residue: 0.1672
  time to fit residues: 15.7503
Evaluate side-chains
  69 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    0.1980
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.159962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.133143 restraints weight = 5721.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.136975 restraints weight = 3273.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.139262 restraints weight = 2329.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.126
  Angle     :  0.493   5.788   6521  Z= 0.248
  Chirality :  0.040   0.260    764
  Planarity :  0.003   0.049    794
  Dihedral  :  5.829  76.617    690
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.97 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.34), residues: 598
  helix:  2.37 (0.24), residues: 438
  sheet:  0.69 (1.30), residues: 12
  loop : -0.82 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.012   0.001   PHE C 295 
 TYR   0.013   0.001   TYR C  21 
 ARG   0.002   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00401 (    2)
  link_NAG-ASN         : angle       2.95269 (    6)
  hydrogen bonds       : bond        0.04121 (  335)
  hydrogen bonds       : angle       3.92179 (  999)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.60012 (    4)
  covalent geometry    : bond        0.00289 ( 4764)
  covalent geometry    : angle       0.48533 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7400 (mtp180)
REVERT: C  183 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7667 (tp)
REVERT: C  365 ASP cc_start: 0.8369 (m-30) cc_final: 0.8082 (m-30)
REVERT: C  387 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7308 (p)
REVERT: C  508 MET cc_start: 0.7278 (mmm) cc_final: 0.6640 (mmm)
REVERT: C  521 PHE cc_start: 0.8233 (m-10) cc_final: 0.7979 (m-10)
REVERT: C  568 MET cc_start: 0.7210 (ttm) cc_final: 0.6798 (ttt)
  outliers start: 16
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1759
  time to fit residues: 15.6344
Evaluate side-chains
  68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  569 CYS
Chi-restraints excluded: chain C residue  575 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0970
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.162110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.135190 restraints weight = 5636.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.139063 restraints weight = 3246.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.141318 restraints weight = 2312.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.119
  Angle     :  0.490   5.904   6521  Z= 0.246
  Chirality :  0.040   0.252    764
  Planarity :  0.003   0.046    794
  Dihedral  :  5.784  76.559    690
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.02 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.34), residues: 598
  helix:  2.45 (0.23), residues: 438
  sheet:  0.61 (1.30), residues: 12
  loop : -0.77 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.011   0.001   PHE C 295 
 TYR   0.013   0.001   TYR C 101 
 ARG   0.002   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    2)
  link_NAG-ASN         : angle       2.82953 (    6)
  hydrogen bonds       : bond        0.04039 (  335)
  hydrogen bonds       : angle       3.86046 (  999)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.57986 (    4)
  covalent geometry    : bond        0.00269 ( 4764)
  covalent geometry    : angle       0.48285 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.454 
Fit side-chains
REVERT: C   70 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7441 (mtp180)
REVERT: C   84 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8063 (tt)
REVERT: C  183 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (tp)
REVERT: C  271 ASN cc_start: 0.6234 (m-40) cc_final: 0.6002 (m-40)
REVERT: C  365 ASP cc_start: 0.8357 (m-30) cc_final: 0.8077 (m-30)
REVERT: C  387 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7281 (p)
REVERT: C  508 MET cc_start: 0.7271 (mmm) cc_final: 0.6660 (mmm)
REVERT: C  521 PHE cc_start: 0.8233 (m-10) cc_final: 0.7923 (m-10)
REVERT: C  568 MET cc_start: 0.7211 (ttm) cc_final: 0.6829 (ttt)
  outliers start: 16
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1628
  time to fit residues: 14.8486
Evaluate side-chains
  70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0060
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
C 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.159837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.133726 restraints weight = 5655.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.137307 restraints weight = 3281.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.139773 restraints weight = 2363.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.123
  Angle     :  0.491   5.777   6521  Z= 0.247
  Chirality :  0.040   0.245    764
  Planarity :  0.003   0.045    794
  Dihedral  :  5.764  76.536    690
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.81 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.34), residues: 598
  helix:  2.48 (0.23), residues: 438
  sheet:  0.56 (1.31), residues: 12
  loop : -0.77 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.012   0.001   PHE C 295 
 TYR   0.012   0.001   TYR C  21 
 ARG   0.001   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    2)
  link_NAG-ASN         : angle       2.72272 (    6)
  hydrogen bonds       : bond        0.04040 (  335)
  hydrogen bonds       : angle       3.84486 (  999)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.58828 (    4)
  covalent geometry    : bond        0.00281 ( 4764)
  covalent geometry    : angle       0.48456 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7446 (mtp180)
REVERT: C   84 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: C  183 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7665 (tp)
REVERT: C  365 ASP cc_start: 0.8310 (m-30) cc_final: 0.7992 (m-30)
REVERT: C  387 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7283 (p)
REVERT: C  508 MET cc_start: 0.7269 (mmm) cc_final: 0.6670 (mmm)
REVERT: C  515 LEU cc_start: 0.7718 (mm) cc_final: 0.7492 (mm)
REVERT: C  521 PHE cc_start: 0.8229 (m-10) cc_final: 0.7902 (m-10)
REVERT: C  568 MET cc_start: 0.7170 (ttm) cc_final: 0.6852 (ttt)
  outliers start: 16
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1617
  time to fit residues: 15.6636
Evaluate side-chains
  73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   71 GLN
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
C 271 ASN
C 543 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.158991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.132719 restraints weight = 5627.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.136461 restraints weight = 3290.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.138606 restraints weight = 2357.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.113
  Angle     :  0.487   5.740   6521  Z= 0.244
  Chirality :  0.039   0.240    764
  Planarity :  0.003   0.043    794
  Dihedral  :  5.730  76.443    690
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.81 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.34), residues: 598
  helix:  2.52 (0.23), residues: 440
  sheet:  0.57 (1.32), residues: 12
  loop : -0.73 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.011   0.001   PHE C 250 
 TYR   0.012   0.001   TYR C 101 
 ARG   0.001   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00377 (    2)
  link_NAG-ASN         : angle       2.66428 (    6)
  hydrogen bonds       : bond        0.03934 (  335)
  hydrogen bonds       : angle       3.82150 (  999)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       0.54156 (    4)
  covalent geometry    : bond        0.00254 ( 4764)
  covalent geometry    : angle       0.48046 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7305 (mtp180)
REVERT: C   84 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7838 (tt)
REVERT: C  183 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7598 (tp)
REVERT: C  365 ASP cc_start: 0.8320 (m-30) cc_final: 0.7987 (m-30)
REVERT: C  387 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7278 (p)
REVERT: C  508 MET cc_start: 0.7246 (mmm) cc_final: 0.6654 (mmm)
REVERT: C  515 LEU cc_start: 0.7716 (mm) cc_final: 0.7497 (mm)
REVERT: C  521 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7875 (m-10)
REVERT: C  568 MET cc_start: 0.7177 (ttm) cc_final: 0.6870 (ttt)
  outliers start: 17
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1730
  time to fit residues: 16.6942
Evaluate side-chains
  77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   71 GLN
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  561 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
C 271 ASN
C 543 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.159403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.133104 restraints weight = 5716.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.136794 restraints weight = 3339.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.139020 restraints weight = 2400.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4768  Z= 0.131
  Angle     :  0.499   5.777   6521  Z= 0.250
  Chirality :  0.040   0.242    764
  Planarity :  0.003   0.043    794
  Dihedral  :  5.759  76.610    690
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.60 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.34), residues: 598
  helix:  2.50 (0.23), residues: 439
  sheet:  0.64 (1.32), residues: 12
  loop : -0.77 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.012   0.001   PHE C 295 
 TYR   0.012   0.001   TYR C  21 
 ARG   0.002   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00365 (    2)
  link_NAG-ASN         : angle       2.65724 (    6)
  hydrogen bonds       : bond        0.04069 (  335)
  hydrogen bonds       : angle       3.84421 (  999)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.57532 (    4)
  covalent geometry    : bond        0.00304 ( 4764)
  covalent geometry    : angle       0.49255 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7319 (mtp180)
REVERT: C   84 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7840 (tt)
REVERT: C  183 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7672 (tp)
REVERT: C  365 ASP cc_start: 0.8316 (m-30) cc_final: 0.7972 (m-30)
REVERT: C  387 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7265 (p)
REVERT: C  508 MET cc_start: 0.7273 (mmm) cc_final: 0.6678 (mmm)
REVERT: C  515 LEU cc_start: 0.7756 (mm) cc_final: 0.7532 (mm)
REVERT: C  521 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7838 (m-10)
REVERT: C  568 MET cc_start: 0.7209 (ttm) cc_final: 0.6910 (ttt)
  outliers start: 17
  outliers final: 12
  residues processed: 73
  average time/residue: 0.1753
  time to fit residues: 16.5252
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   71 GLN
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0570
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
C 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.161617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.134976 restraints weight = 5633.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.138711 restraints weight = 3233.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.141228 restraints weight = 2310.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4768  Z= 0.123
  Angle     :  0.496   5.777   6521  Z= 0.249
  Chirality :  0.040   0.238    764
  Planarity :  0.003   0.042    794
  Dihedral  :  5.741  76.434    690
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.60 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.34), residues: 598
  helix:  2.53 (0.23), residues: 439
  sheet:  0.66 (1.31), residues: 12
  loop : -0.74 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.011   0.001   PHE C 295 
 TYR   0.012   0.001   TYR C  21 
 ARG   0.002   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (    2)
  link_NAG-ASN         : angle       2.63727 (    6)
  hydrogen bonds       : bond        0.04025 (  335)
  hydrogen bonds       : angle       3.83364 (  999)
  SS BOND              : bond        0.00125 (    2)
  SS BOND              : angle       0.56351 (    4)
  covalent geometry    : bond        0.00281 ( 4764)
  covalent geometry    : angle       0.49009 ( 6511)

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: C   70 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7267 (mtp180)
REVERT: C   84 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: C  183 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7634 (tp)
REVERT: C  365 ASP cc_start: 0.8305 (m-30) cc_final: 0.7946 (m-30)
REVERT: C  387 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7250 (p)
REVERT: C  508 MET cc_start: 0.7166 (mmm) cc_final: 0.6540 (mmm)
REVERT: C  515 LEU cc_start: 0.7947 (mm) cc_final: 0.7722 (mm)
REVERT: C  521 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7816 (m-10)
REVERT: C  568 MET cc_start: 0.7180 (ttm) cc_final: 0.6867 (ttt)
  outliers start: 18
  outliers final: 12
  residues processed: 74
  average time/residue: 0.1687
  time to fit residues: 16.1253
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
C 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.160821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.133846 restraints weight = 5719.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.137613 restraints weight = 3284.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.140104 restraints weight = 2339.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4768  Z= 0.132
  Angle     :  0.497   5.846   6521  Z= 0.250
  Chirality :  0.040   0.237    764
  Planarity :  0.003   0.042    794
  Dihedral  :  5.773  76.485    690
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.02 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.34), residues: 598
  helix:  2.51 (0.23), residues: 438
  sheet:  0.70 (1.31), residues: 12
  loop : -0.72 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 178 
 HIS   0.001   0.000   HIS C 115 
 PHE   0.012   0.001   PHE C 295 
 TYR   0.012   0.001   TYR C  21 
 ARG   0.002   0.000   ARG C 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00358 (    2)
  link_NAG-ASN         : angle       2.62004 (    6)
  hydrogen bonds       : bond        0.04115 (  335)
  hydrogen bonds       : angle       3.84050 (  999)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.60305 (    4)
  covalent geometry    : bond        0.00307 ( 4764)
  covalent geometry    : angle       0.49110 ( 6511)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1659.07 seconds
wall clock time: 29 minutes 43.97 seconds (1783.97 seconds total)