Starting phenix.real_space_refine
on Fri Jul 25 20:32:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v12_42878/07_2025/8v12_42878.cif"
  }
  resolution = 3.81
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5231      2.51       5
     N    1243      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7960
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 979, 7918
          Classifications: {'peptide': 979}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 953}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 107
          Planarities with less than four sites: {'TYR:plan': 2, 'HIS%COO:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 72
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Unusual residues: {'CLR': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.05, per 1000 atoms: 0.76
  Number of scatterers: 7960
  At special positions: 0
  Unit cell: (89.88, 97.37, 127.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1442      8.00
     N    1243      7.00
     C    5231      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 A1502 " - " ASN A 165 "
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      70.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 35
      removed outlier: 3.706A  pdb=" N   ARG A  35 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 52
      removed outlier: 3.764A  pdb=" N   PHE A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 57
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 71 through 85
    Processing helix  chain 'A' and resid 103 through 120
    Processing helix  chain 'A' and resid 125 through 127
      No H-bonds generated for 'chain 'A' and resid 125 through 127'
    Processing helix  chain 'A' and resid 141 through 162
    Processing helix  chain 'A' and resid 294 through 299
      removed outlier: 3.767A  pdb=" N   TYR A 298 " --> pdb=" O   ASN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 320 through 325
      removed outlier: 3.593A  pdb=" N   VAL A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 333 through 337
      removed outlier: 3.572A  pdb=" N   ALA A 337 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 350 through 353
    Processing helix  chain 'A' and resid 355 through 359
    Processing helix  chain 'A' and resid 364 through 368
    Processing helix  chain 'A' and resid 369 through 373
      removed outlier: 3.510A  pdb=" N   GLY A 372 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 402
    Processing helix  chain 'A' and resid 435 through 452
    Processing helix  chain 'A' and resid 455 through 460
      removed outlier: 3.667A  pdb=" N   ILE A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 491
    Processing helix  chain 'A' and resid 493 through 516
    Processing helix  chain 'A' and resid 524 through 550
      removed outlier: 3.699A  pdb=" N   ALA A 528 " --> pdb=" O   LYS A 524 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   PHE A 536 " --> pdb=" O   ILE A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 559 through 582
      removed outlier: 3.620A  pdb=" N   ASP A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 619
      removed outlier: 3.803A  pdb=" N   ALA A 600 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   LEU A 601 " --> pdb=" O   LYS A 597 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ALA A 602 " --> pdb=" O   ASP A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 660
      removed outlier: 3.574A  pdb=" N   LEU A 647 " --> pdb=" O   VAL A 643 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   LEU A 648 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 673
    Processing helix  chain 'A' and resid 722 through 736
    Processing helix  chain 'A' and resid 1057 through 1067
    Processing helix  chain 'A' and resid 1067 through 1074
    Processing helix  chain 'A' and resid 1074 through 1099
    Processing helix  chain 'A' and resid 1113 through 1126
    Processing helix  chain 'A' and resid 1139 through 1150
    Processing helix  chain 'A' and resid 1184 through 1201
    Processing helix  chain 'A' and resid 1209 through 1218
      removed outlier: 3.612A  pdb=" N   PHE A1213 " --> pdb=" O   ASN A1209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1224
      removed outlier: 4.045A  pdb=" N   LYS A1224 " --> pdb=" O   SER A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1240
    Processing helix  chain 'A' and resid 1241 through 1247
    Processing helix  chain 'A' and resid 1272 through 1287
    Processing helix  chain 'A' and resid 1289 through 1293
      removed outlier: 3.606A  pdb=" N   HIS A1292 " --> pdb=" O   LEU A1289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1302 through 1333
      removed outlier: 5.199A  pdb=" N   ILE A1313 " --> pdb=" O   ASP A1309 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   GLU A1314 " --> pdb=" O   GLU A1310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1337 through 1362
    Processing helix  chain 'A' and resid 1367 through 1395
      removed outlier: 3.579A  pdb=" N   VAL A1375 " --> pdb=" O   MET A1371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1399 through 1428
      removed outlier: 5.952A  pdb=" N   GLY A1413 " --> pdb=" O   HIS A1409 " (cutoff:3.500A)
      Proline residue:  A1414  - end of helix
      removed outlier: 4.474A  pdb=" N   THR A1428 " --> pdb=" O   PHE A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1431
      No H-bonds generated for 'chain 'A' and resid 1429 through 1431'
    Processing helix  chain 'A' and resid 1434 through 1457
      removed outlier: 3.537A  pdb=" N   VAL A1438 " --> pdb=" O   LYS A1434 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE A1440 " --> pdb=" O   PHE A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1457 through 1467
    Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.632A  pdb=" N   ALA A 420 " --> pdb=" O   MET A 406 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   MET A 406 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 304
      removed outlier: 4.051A  pdb=" N   ALA A1260 " --> pdb=" O   VAL A1252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 304
      removed outlier: 4.051A  pdb=" N   ALA A1260 " --> pdb=" O   VAL A1252 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 390
      removed outlier: 4.023A  pdb=" N   TYR A 388 " --> pdb=" O   MET A 397 " (cutoff:3.500A)

    516 hydrogen bonds defined for protein.
    1488 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.97

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2420
        1.34 -     1.46: 1864
        1.46 -     1.58: 3797
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 8147
  Sorted by residual:
  bond pdb=" N   THR A 117 "
       pdb=" CA  THR A 117 "
    ideal  model  delta    sigma   weight residual
    1.459  1.443  0.017 1.19e-02 7.06e+03 1.92e+00
  bond pdb=" CA  THR A 117 "
       pdb=" C   THR A 117 "
    ideal  model  delta    sigma   weight residual
    1.524  1.507  0.017 1.27e-02 6.20e+03 1.74e+00
  bond pdb=" CA  TYR A 449 "
       pdb=" C   TYR A 449 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.30e-02 5.92e+03 1.58e+00
  bond pdb=" CA  ASP A 448 "
       pdb=" C   ASP A 448 "
    ideal  model  delta    sigma   weight residual
    1.523  1.508  0.016 1.30e-02 5.92e+03 1.46e+00
  bond pdb=" N   VAL A  95 "
       pdb=" CA  VAL A  95 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.018 1.57e-02 4.06e+03 1.38e+00
  ... (remaining 8142 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 10797
        1.48 -     2.96: 195
        2.96 -     4.43: 21
        4.43 -     5.91: 5
        5.91 -     7.39: 2
  Bond angle restraints: 11020
  Sorted by residual:
  angle pdb=" N   LYS A 112 "
        pdb=" CA  LYS A 112 "
        pdb=" C   LYS A 112 "
      ideal   model   delta    sigma   weight residual
     111.07  106.73    4.34 1.07e+00 8.73e-01 1.65e+01
  angle pdb=" N   THR A 117 "
        pdb=" CA  THR A 117 "
        pdb=" C   THR A 117 "
      ideal   model   delta    sigma   weight residual
     111.07  107.85    3.22 1.07e+00 8.73e-01 9.06e+00
  angle pdb=" N   ASP A 448 "
        pdb=" CA  ASP A 448 "
        pdb=" C   ASP A 448 "
      ideal   model   delta    sigma   weight residual
     111.28  108.25    3.03 1.09e+00 8.42e-01 7.71e+00
  angle pdb=" N   THR A 645 "
        pdb=" CA  THR A 645 "
        pdb=" C   THR A 645 "
      ideal   model   delta    sigma   weight residual
     112.93  109.47    3.46 1.33e+00 5.65e-01 6.78e+00
  angle pdb=" N   LEU A 446 "
        pdb=" CA  LEU A 446 "
        pdb=" C   LEU A 446 "
      ideal   model   delta    sigma   weight residual
     111.07  113.78   -2.71 1.07e+00 8.73e-01 6.40e+00
  ... (remaining 11015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.41: 4680
       21.41 -    42.82: 171
       42.82 -    64.24: 15
       64.24 -    85.65: 1
       85.65 -   107.06: 8
  Dihedral angle restraints: 4875
    sinusoidal: 1980
      harmonic: 2895
  Sorted by residual:
  dihedral pdb=" C1  NAG A1502 "
           pdb=" C2  NAG A1502 "
           pdb=" C3  NAG A1502 "
           pdb=" O3  NAG A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -68.03 -107.06     1      3.00e+01 1.11e-03 1.38e+01
  dihedral pdb=" C1  NAG A1502 "
           pdb=" C2  NAG A1502 "
           pdb=" C3  NAG A1502 "
           pdb=" C4  NAG A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.39   54.21 -106.60     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" N2  NAG A1502 "
           pdb=" C2  NAG A1502 "
           pdb=" C3  NAG A1502 "
           pdb=" O3  NAG A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.25  168.21 -105.96     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 4872 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 859
       0.029 -    0.059: 240
       0.059 -    0.088: 112
       0.088 -    0.118: 39
       0.118 -    0.147: 4
  Chirality restraints: 1254
  Sorted by residual:
  chirality pdb=" CA  ILE A 309 "
            pdb=" N   ILE A 309 "
            pdb=" C   ILE A 309 "
            pdb=" CB  ILE A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" C1  NAG A1502 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1502 "
            pdb=" O5  NAG A1502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  ILE A 380 "
            pdb=" N   ILE A 380 "
            pdb=" C   ILE A 380 "
            pdb=" CB  ILE A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1251 not shown)

  Planarity restraints: 1362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1143 "   -0.008 2.00e-02 2.50e+03   1.56e-02 2.45e+00
        pdb=" C   ILE A1143 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A1143 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A1144 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 574 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.13e+00
        pdb=" C   VAL A 574 "    0.025 2.00e-02 2.50e+03
        pdb=" O   VAL A 574 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 575 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 565 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   ILE A 565 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ILE A 565 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 566 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1359 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 568
        2.74 -     3.28: 9077
        3.28 -     3.82: 14585
        3.82 -     4.36: 16918
        4.36 -     4.90: 27637
  Nonbonded interactions: 68785
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  64 "
            pdb=" OG  SER A  68 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   ASN A1367 "
            pdb=" OG  SER A1370 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG1 THR A 478 "
            pdb=" OG  SER A 481 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP A 123 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER A 155 "
            pdb=" O   TYR A 306 "
     model   vdw
     2.284 3.040
  ... (remaining 68780 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             3.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
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      :  0.002   0.030   8148  Z= 0.141
  Angle     :  0.503   7.389  11023  Z= 0.315
  Chirality :  0.036   0.147   1254
  Planarity :  0.003   0.034   1361
  Dihedral  : 11.584 107.060   3007
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  7.26 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  2.07 (0.27), residues: 967
  helix:  2.38 (0.21), residues: 609
  sheet: -1.76 (0.78), residues: 36
  loop : -0.20 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1423 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.012   0.001   PHE A 646 
 TYR   0.013   0.001   TYR A 521 
 ARG   0.002   0.000   ARG A1117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00517 (    1)
  link_NAG-ASN         : angle       1.96969 (    3)
  hydrogen bonds       : bond        0.12871 (  513)
  hydrogen bonds       : angle       5.76106 ( 1488)
  covalent geometry    : bond        0.00232 ( 8147)
  covalent geometry    : angle       0.50177 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 317
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 THR cc_start: 0.7362 (p) cc_final: 0.6963 (m)
REVERT: A  169 PHE cc_start: 0.6826 (m-10) cc_final: 0.5672 (m-80)
REVERT: A  352 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7998 (pp)
REVERT: A  727 ILE cc_start: 0.8567 (tp) cc_final: 0.8099 (tt)
REVERT: A  728 HIS cc_start: 0.6987 (t70) cc_final: 0.6455 (t-170)
REVERT: A 1420 LEU cc_start: 0.7708 (mt) cc_final: 0.7259 (mt)
  outliers start: 24
  outliers final: 4
  residues processed: 334
  average time/residue: 0.1855
  time to fit residues: 85.2316
Evaluate side-chains
  206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 201
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue 1312 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 344 GLN
A 433 HIS
A 514 ASN
A 588 ASN
A 593 GLN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1144 ASN
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1409 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.084912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.071400 restraints weight = 32664.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.073528 restraints weight = 19535.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.075049 restraints weight = 13706.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8148  Z= 0.156
  Angle     :  0.664   8.210  11023  Z= 0.345
  Chirality :  0.047   0.285   1254
  Planarity :  0.004   0.044   1361
  Dihedral  :  8.282  77.632   1152
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 14.51 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.80 (0.26), residues: 967
  helix:  2.08 (0.20), residues: 610
  sheet: -1.60 (0.80), residues: 42
  loop : -0.11 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1237 
 HIS   0.010   0.002   HIS A   8 
 PHE   0.021   0.002   PHE A1454 
 TYR   0.019   0.002   TYR A 442 
 ARG   0.006   0.001   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00762 (    1)
  link_NAG-ASN         : angle       2.53776 (    3)
  hydrogen bonds       : bond        0.04975 (  513)
  hydrogen bonds       : angle       4.98057 ( 1488)
  covalent geometry    : bond        0.00335 ( 8147)
  covalent geometry    : angle       0.66272 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 226
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9035 (mmmt)
REVERT: A  169 PHE cc_start: 0.8020 (m-10) cc_final: 0.6844 (m-80)
REVERT: A  334 LEU cc_start: 0.8827 (mm) cc_final: 0.8600 (mm)
REVERT: A  352 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8959 (pp)
REVERT: A  424 MET cc_start: 0.8434 (tpp) cc_final: 0.8163 (tpp)
REVERT: A  452 PHE cc_start: 0.9444 (m-10) cc_final: 0.9118 (m-80)
REVERT: A  573 PHE cc_start: 0.8805 (m-80) cc_final: 0.8309 (m-80)
REVERT: A  724 TYR cc_start: 0.8830 (m-80) cc_final: 0.8624 (m-80)
REVERT: A  726 TRP cc_start: 0.8802 (t60) cc_final: 0.8474 (t60)
REVERT: A  728 HIS cc_start: 0.8570 (t70) cc_final: 0.8181 (t70)
REVERT: A 1099 MET cc_start: 0.5412 (ptp) cc_final: 0.5079 (tpp)
REVERT: A 1191 LEU cc_start: 0.9203 (mt) cc_final: 0.8996 (mt)
REVERT: A 1232 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8844 (mm-30)
REVERT: A 1296 MET cc_start: 0.8871 (mmm) cc_final: 0.7534 (mmm)
REVERT: A 1356 PHE cc_start: 0.8507 (t80) cc_final: 0.8097 (t80)
REVERT: A 1384 HIS cc_start: 0.9100 (m90) cc_final: 0.8634 (m90)
REVERT: A 1396 MET cc_start: 0.7224 (tpt) cc_final: 0.6813 (mmm)
REVERT: A 1420 LEU cc_start: 0.9299 (mt) cc_final: 0.8963 (mt)
  outliers start: 37
  outliers final: 12
  residues processed: 248
  average time/residue: 0.1985
  time to fit residues: 69.3385
Evaluate side-chains
  198 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 185
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1435 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0000
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   chunk 84 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 ASN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.085590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071715 restraints weight = 33718.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.073878 restraints weight = 20114.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.075436 restraints weight = 14095.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8148  Z= 0.143
  Angle     :  0.676  12.894  11023  Z= 0.344
  Chirality :  0.046   0.261   1254
  Planarity :  0.004   0.049   1361
  Dihedral  :  6.926  74.914   1144
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.23 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.64 (0.26), residues: 967
  helix:  1.91 (0.20), residues: 611
  sheet: -1.76 (1.09), residues: 27
  loop : -0.14 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1423 
 HIS   0.007   0.001   HIS A   8 
 PHE   0.039   0.001   PHE A1424 
 TYR   0.017   0.002   TYR A  75 
 ARG   0.004   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00781 (    1)
  link_NAG-ASN         : angle       2.60258 (    3)
  hydrogen bonds       : bond        0.04675 (  513)
  hydrogen bonds       : angle       4.84353 ( 1488)
  covalent geometry    : bond        0.00302 ( 8147)
  covalent geometry    : angle       0.67431 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 204
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 LYS cc_start: 0.9339 (mttm) cc_final: 0.9038 (mttm)
REVERT: A  169 PHE cc_start: 0.8238 (m-10) cc_final: 0.7030 (m-80)
REVERT: A  334 LEU cc_start: 0.8788 (mm) cc_final: 0.8543 (mm)
REVERT: A  352 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8971 (pp)
REVERT: A  424 MET cc_start: 0.8527 (tpp) cc_final: 0.8261 (tpp)
REVERT: A  594 MET cc_start: 0.8698 (mmt) cc_final: 0.8397 (mmm)
REVERT: A  642 MET cc_start: 0.8567 (mtp) cc_final: 0.8344 (ttm)
REVERT: A  724 TYR cc_start: 0.8829 (m-80) cc_final: 0.8594 (m-80)
REVERT: A  728 HIS cc_start: 0.8576 (t70) cc_final: 0.8249 (t-170)
REVERT: A 1088 ILE cc_start: 0.9590 (mm) cc_final: 0.9363 (mm)
REVERT: A 1099 MET cc_start: 0.5416 (ptp) cc_final: 0.4920 (tpt)
REVERT: A 1232 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8845 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (t80)
REVERT: A 1281 LYS cc_start: 0.9488 (mttt) cc_final: 0.9183 (mttp)
REVERT: A 1296 MET cc_start: 0.8848 (mmm) cc_final: 0.7639 (mmm)
REVERT: A 1317 LEU cc_start: 0.9030 (tt) cc_final: 0.8820 (pp)
REVERT: A 1319 ASN cc_start: 0.9035 (m-40) cc_final: 0.8764 (m110)
REVERT: A 1328 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8860 (mm)
REVERT: A 1356 PHE cc_start: 0.8454 (t80) cc_final: 0.8214 (t80)
REVERT: A 1384 HIS cc_start: 0.9091 (m90) cc_final: 0.8374 (m90)
REVERT: A 1396 MET cc_start: 0.7392 (tpt) cc_final: 0.6880 (mmm)
REVERT: A 1420 LEU cc_start: 0.9302 (mt) cc_final: 0.9079 (mt)
  outliers start: 32
  outliers final: 18
  residues processed: 226
  average time/residue: 0.2282
  time to fit residues: 74.3333
Evaluate side-chains
  208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1254 LEU
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1382 ILE
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0770
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1300 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.085968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.071669 restraints weight = 33845.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.073806 restraints weight = 20718.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.075316 restraints weight = 14824.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8148  Z= 0.138
  Angle     :  0.664  13.530  11023  Z= 0.333
  Chirality :  0.045   0.258   1254
  Planarity :  0.004   0.048   1361
  Dihedral  :  6.194  75.079   1144
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 17.69 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.66 (0.27), residues: 967
  helix:  1.89 (0.20), residues: 612
  sheet: -1.74 (1.08), residues: 27
  loop : -0.09 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1279 
 HIS   0.004   0.001   HIS A 475 
 PHE   0.045   0.002   PHE A1424 
 TYR   0.013   0.002   TYR A1265 
 ARG   0.004   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00743 (    1)
  link_NAG-ASN         : angle       2.80694 (    3)
  hydrogen bonds       : bond        0.04441 (  513)
  hydrogen bonds       : angle       4.79992 ( 1488)
  covalent geometry    : bond        0.00297 ( 8147)
  covalent geometry    : angle       0.66284 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 198
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9077 (pp) cc_final: 0.8662 (mm)
REVERT: A   60 GLU cc_start: 0.6984 (tp30) cc_final: 0.6649 (tp30)
REVERT: A   94 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (tt)
REVERT: A  169 PHE cc_start: 0.8109 (m-10) cc_final: 0.6993 (m-80)
REVERT: A  334 LEU cc_start: 0.8787 (mm) cc_final: 0.8542 (mm)
REVERT: A  352 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8949 (pp)
REVERT: A  424 MET cc_start: 0.8524 (tpp) cc_final: 0.8270 (tpp)
REVERT: A  458 ILE cc_start: 0.8387 (tp) cc_final: 0.7904 (tp)
REVERT: A  594 MET cc_start: 0.8694 (mmt) cc_final: 0.8367 (mmm)
REVERT: A  642 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8223 (ttm)
REVERT: A  724 TYR cc_start: 0.8875 (m-80) cc_final: 0.8466 (m-80)
REVERT: A  728 HIS cc_start: 0.8719 (t70) cc_final: 0.8294 (t-170)
REVERT: A 1088 ILE cc_start: 0.9616 (mm) cc_final: 0.9372 (mm)
REVERT: A 1099 MET cc_start: 0.5661 (ptp) cc_final: 0.5150 (tpt)
REVERT: A 1232 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8855 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (t80)
REVERT: A 1296 MET cc_start: 0.8745 (mmm) cc_final: 0.7581 (mmm)
REVERT: A 1317 LEU cc_start: 0.9028 (tt) cc_final: 0.8783 (pp)
REVERT: A 1319 ASN cc_start: 0.9054 (m-40) cc_final: 0.8793 (m110)
REVERT: A 1328 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8913 (mm)
REVERT: A 1384 HIS cc_start: 0.9099 (m90) cc_final: 0.8564 (m90)
REVERT: A 1396 MET cc_start: 0.7302 (tpt) cc_final: 0.6784 (mmm)
REVERT: A 1458 PHE cc_start: 0.8896 (t80) cc_final: 0.8660 (t80)
  outliers start: 39
  outliers final: 23
  residues processed: 221
  average time/residue: 0.1699
  time to fit residues: 53.5561
Evaluate side-chains
  209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 181
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1276 SER
Chi-restraints excluded: chain A residue 1280 LEU
Chi-restraints excluded: chain A residue 1304 ILE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1382 ILE
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 95 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.086070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.071801 restraints weight = 33573.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.073938 restraints weight = 20551.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.075452 restraints weight = 14715.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8148  Z= 0.138
  Angle     :  0.688  16.537  11023  Z= 0.340
  Chirality :  0.046   0.335   1254
  Planarity :  0.004   0.052   1361
  Dihedral  :  5.836  75.065   1144
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.27 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.70 (0.27), residues: 967
  helix:  1.91 (0.20), residues: 613
  sheet: -0.62 (0.97), residues: 36
  loop : -0.14 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 726 
 HIS   0.004   0.001   HIS A1417 
 PHE   0.044   0.002   PHE A1424 
 TYR   0.020   0.002   TYR A 408 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00742 (    1)
  link_NAG-ASN         : angle       2.90843 (    3)
  hydrogen bonds       : bond        0.04331 (  513)
  hydrogen bonds       : angle       4.79716 ( 1488)
  covalent geometry    : bond        0.00296 ( 8147)
  covalent geometry    : angle       0.68628 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.6946 (tp30) cc_final: 0.6559 (tp30)
REVERT: A   75 TYR cc_start: 0.7663 (m-80) cc_final: 0.7457 (m-80)
REVERT: A   82 ASN cc_start: 0.9184 (m-40) cc_final: 0.8908 (m-40)
REVERT: A   96 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: A  169 PHE cc_start: 0.8118 (m-10) cc_final: 0.7009 (m-80)
REVERT: A  334 LEU cc_start: 0.8787 (mm) cc_final: 0.8556 (mm)
REVERT: A  352 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8930 (pp)
REVERT: A  424 MET cc_start: 0.8655 (tpp) cc_final: 0.8371 (tpp)
REVERT: A  594 MET cc_start: 0.8720 (mmt) cc_final: 0.8363 (mmm)
REVERT: A  596 LEU cc_start: 0.9054 (tp) cc_final: 0.8800 (tp)
REVERT: A  642 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8198 (ttm)
REVERT: A  724 TYR cc_start: 0.8819 (m-80) cc_final: 0.8242 (m-80)
REVERT: A  728 HIS cc_start: 0.8704 (t70) cc_final: 0.8276 (t-170)
REVERT: A 1088 ILE cc_start: 0.9626 (mm) cc_final: 0.9305 (mm)
REVERT: A 1099 MET cc_start: 0.5699 (ptp) cc_final: 0.5254 (tpt)
REVERT: A 1232 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8858 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8430 (t80)
REVERT: A 1317 LEU cc_start: 0.9018 (tt) cc_final: 0.8792 (pp)
REVERT: A 1319 ASN cc_start: 0.9018 (m-40) cc_final: 0.8745 (m110)
REVERT: A 1384 HIS cc_start: 0.9126 (m90) cc_final: 0.8768 (m90)
REVERT: A 1396 MET cc_start: 0.7312 (tpt) cc_final: 0.6781 (mmm)
REVERT: A 1458 PHE cc_start: 0.9000 (t80) cc_final: 0.8626 (t80)
  outliers start: 38
  outliers final: 22
  residues processed: 218
  average time/residue: 0.1728
  time to fit residues: 54.3940
Evaluate side-chains
  206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1280 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1382 ILE
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 92 optimal weight:    0.1980
   chunk 73 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.086588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.072536 restraints weight = 32878.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.074671 restraints weight = 19859.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.076181 restraints weight = 14087.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8148  Z= 0.138
  Angle     :  0.700  17.660  11023  Z= 0.345
  Chirality :  0.046   0.285   1254
  Planarity :  0.004   0.053   1361
  Dihedral  :  5.738  75.072   1144
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 16.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 20.52 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.60 (0.27), residues: 967
  helix:  1.87 (0.20), residues: 612
  sheet: -1.75 (1.09), residues: 27
  loop : -0.16 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 726 
 HIS   0.004   0.001   HIS A 475 
 PHE   0.045   0.002   PHE A1424 
 TYR   0.014   0.001   TYR A  28 
 ARG   0.007   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00719 (    1)
  link_NAG-ASN         : angle       3.38415 (    3)
  hydrogen bonds       : bond        0.04242 (  513)
  hydrogen bonds       : angle       4.75865 ( 1488)
  covalent geometry    : bond        0.00305 ( 8147)
  covalent geometry    : angle       0.69836 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 192
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9179 (mm) cc_final: 0.8784 (tp)
REVERT: A   60 GLU cc_start: 0.6891 (tp30) cc_final: 0.6528 (tp30)
REVERT: A   82 ASN cc_start: 0.9233 (m-40) cc_final: 0.8927 (m-40)
REVERT: A   94 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8693 (tt)
REVERT: A   96 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8048 (tm-30)
REVERT: A  103 LYS cc_start: 0.9131 (tppt) cc_final: 0.8538 (tppt)
REVERT: A  108 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8577 (mpp80)
REVERT: A  169 PHE cc_start: 0.8159 (m-10) cc_final: 0.7049 (m-80)
REVERT: A  352 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8941 (pp)
REVERT: A  424 MET cc_start: 0.8661 (tpp) cc_final: 0.8391 (tpp)
REVERT: A  594 MET cc_start: 0.8701 (mmt) cc_final: 0.8350 (mmm)
REVERT: A  596 LEU cc_start: 0.9080 (tp) cc_final: 0.8807 (tp)
REVERT: A  642 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8202 (ttm)
REVERT: A  724 TYR cc_start: 0.8933 (m-80) cc_final: 0.8385 (m-80)
REVERT: A  728 HIS cc_start: 0.8632 (t70) cc_final: 0.8197 (t-170)
REVERT: A 1088 ILE cc_start: 0.9572 (mm) cc_final: 0.9280 (mm)
REVERT: A 1099 MET cc_start: 0.5554 (ptp) cc_final: 0.5142 (tpt)
REVERT: A 1131 ASP cc_start: 0.7979 (m-30) cc_final: 0.7741 (m-30)
REVERT: A 1232 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8859 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8448 (t80)
REVERT: A 1317 LEU cc_start: 0.8990 (tt) cc_final: 0.8768 (pp)
REVERT: A 1384 HIS cc_start: 0.9147 (m90) cc_final: 0.8796 (m90)
REVERT: A 1396 MET cc_start: 0.7332 (tpt) cc_final: 0.6767 (mmm)
REVERT: A 1458 PHE cc_start: 0.9044 (t80) cc_final: 0.8626 (t80)
  outliers start: 40
  outliers final: 23
  residues processed: 217
  average time/residue: 0.1950
  time to fit residues: 60.1069
Evaluate side-chains
  205 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1280 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1382 ILE
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   chunk 76 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.087030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.072827 restraints weight = 33221.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.074979 restraints weight = 20232.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.076513 restraints weight = 14345.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8148  Z= 0.136
  Angle     :  0.729  18.369  11023  Z= 0.355
  Chirality :  0.046   0.324   1254
  Planarity :  0.004   0.057   1361
  Dihedral  :  5.513  75.167   1144
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.54 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.64 (0.27), residues: 967
  helix:  1.84 (0.20), residues: 614
  sheet: -1.03 (1.36), residues: 21
  loop : -0.12 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 726 
 HIS   0.004   0.001   HIS A 475 
 PHE   0.047   0.002   PHE A1424 
 TYR   0.013   0.001   TYR A  28 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00693 (    1)
  link_NAG-ASN         : angle       3.35362 (    3)
  hydrogen bonds       : bond        0.04173 (  513)
  hydrogen bonds       : angle       4.72633 ( 1488)
  covalent geometry    : bond        0.00300 ( 8147)
  covalent geometry    : angle       0.72650 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 185
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9175 (mm) cc_final: 0.8800 (tp)
REVERT: A   60 GLU cc_start: 0.6840 (tp30) cc_final: 0.6525 (tp30)
REVERT: A   82 ASN cc_start: 0.9241 (m-40) cc_final: 0.8934 (m-40)
REVERT: A   94 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8750 (tt)
REVERT: A  105 LYS cc_start: 0.9304 (ptpp) cc_final: 0.9013 (mmmt)
REVERT: A  169 PHE cc_start: 0.8173 (m-10) cc_final: 0.6976 (m-80)
REVERT: A  352 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8914 (pp)
REVERT: A  424 MET cc_start: 0.8765 (tpp) cc_final: 0.8470 (tpp)
REVERT: A  482 LEU cc_start: 0.9431 (pp) cc_final: 0.9180 (tp)
REVERT: A  594 MET cc_start: 0.8695 (mmt) cc_final: 0.8354 (mmm)
REVERT: A  596 LEU cc_start: 0.9065 (tp) cc_final: 0.8795 (tp)
REVERT: A  623 TYR cc_start: 0.7901 (t80) cc_final: 0.7380 (t80)
REVERT: A  642 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8209 (ttm)
REVERT: A  724 TYR cc_start: 0.8931 (m-80) cc_final: 0.8346 (m-80)
REVERT: A  728 HIS cc_start: 0.8723 (t70) cc_final: 0.8273 (t-170)
REVERT: A 1088 ILE cc_start: 0.9570 (mm) cc_final: 0.9268 (mm)
REVERT: A 1099 MET cc_start: 0.5444 (ptp) cc_final: 0.5024 (tpt)
REVERT: A 1188 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9159 (mp10)
REVERT: A 1232 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8824 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8467 (t80)
REVERT: A 1296 MET cc_start: 0.8710 (mmt) cc_final: 0.7839 (mmm)
REVERT: A 1297 VAL cc_start: 0.7018 (t) cc_final: 0.6769 (t)
REVERT: A 1317 LEU cc_start: 0.9000 (tt) cc_final: 0.8784 (pp)
REVERT: A 1319 ASN cc_start: 0.8976 (m-40) cc_final: 0.8723 (m110)
REVERT: A 1384 HIS cc_start: 0.9137 (m90) cc_final: 0.8777 (m90)
REVERT: A 1396 MET cc_start: 0.7251 (tpt) cc_final: 0.6657 (mmm)
REVERT: A 1458 PHE cc_start: 0.9009 (t80) cc_final: 0.8523 (t80)
  outliers start: 39
  outliers final: 26
  residues processed: 207
  average time/residue: 0.1671
  time to fit residues: 49.7452
Evaluate side-chains
  204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1280 LEU
Chi-restraints excluded: chain A residue 1304 ILE
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1371 MET
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1441 PHE
Chi-restraints excluded: chain A residue 1457 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0030
   chunk 27 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0770
   overall best weight:    0.4750

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.087569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.073401 restraints weight = 33317.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.075567 restraints weight = 20227.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.077102 restraints weight = 14347.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.5176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8148  Z= 0.132
  Angle     :  0.739  18.449  11023  Z= 0.359
  Chirality :  0.046   0.289   1254
  Planarity :  0.004   0.052   1361
  Dihedral  :  5.373  75.336   1144
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.22 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.62 (0.27), residues: 967
  helix:  1.82 (0.20), residues: 615
  sheet: -1.13 (1.13), residues: 27
  loop : -0.10 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 726 
 HIS   0.004   0.001   HIS A 475 
 PHE   0.049   0.002   PHE A1424 
 TYR   0.017   0.001   TYR A 408 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00662 (    1)
  link_NAG-ASN         : angle       3.21435 (    3)
  hydrogen bonds       : bond        0.04128 (  513)
  hydrogen bonds       : angle       4.69601 ( 1488)
  covalent geometry    : bond        0.00288 ( 8147)
  covalent geometry    : angle       0.73706 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9163 (mm) cc_final: 0.8792 (tp)
REVERT: A   60 GLU cc_start: 0.6668 (tp30) cc_final: 0.6380 (tp30)
REVERT: A   82 ASN cc_start: 0.9247 (m-40) cc_final: 0.8939 (m-40)
REVERT: A  169 PHE cc_start: 0.8162 (m-10) cc_final: 0.6962 (m-80)
REVERT: A  352 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8891 (pp)
REVERT: A  357 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8245 (m-80)
REVERT: A  424 MET cc_start: 0.8781 (tpp) cc_final: 0.8456 (tpp)
REVERT: A  482 LEU cc_start: 0.9451 (pp) cc_final: 0.9201 (tp)
REVERT: A  594 MET cc_start: 0.8631 (mmt) cc_final: 0.8270 (mmm)
REVERT: A  623 TYR cc_start: 0.7845 (t80) cc_final: 0.7510 (t80)
REVERT: A  642 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8216 (ttm)
REVERT: A  724 TYR cc_start: 0.8969 (m-80) cc_final: 0.8434 (m-80)
REVERT: A  728 HIS cc_start: 0.8736 (t70) cc_final: 0.8303 (t-170)
REVERT: A 1088 ILE cc_start: 0.9558 (mm) cc_final: 0.9249 (mm)
REVERT: A 1099 MET cc_start: 0.5387 (ptp) cc_final: 0.5015 (tpt)
REVERT: A 1188 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9154 (mp10)
REVERT: A 1232 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8816 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8492 (t80)
REVERT: A 1288 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8329 (mmmm)
REVERT: A 1317 LEU cc_start: 0.8981 (tt) cc_final: 0.8776 (pp)
REVERT: A 1319 ASN cc_start: 0.8962 (m-40) cc_final: 0.8714 (m110)
REVERT: A 1349 PHE cc_start: 0.8403 (t80) cc_final: 0.8131 (t80)
REVERT: A 1384 HIS cc_start: 0.9176 (m90) cc_final: 0.8826 (m90)
REVERT: A 1396 MET cc_start: 0.7255 (tpt) cc_final: 0.6636 (mmm)
REVERT: A 1423 TRP cc_start: 0.7526 (t60) cc_final: 0.7268 (t60)
REVERT: A 1458 PHE cc_start: 0.9019 (t80) cc_final: 0.8513 (t80)
  outliers start: 33
  outliers final: 25
  residues processed: 203
  average time/residue: 0.2241
  time to fit residues: 64.5381
Evaluate side-chains
  208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  357 TYR
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1304 ILE
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1371 MET
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1441 PHE
Chi-restraints excluded: chain A residue 1457 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 361 ASN
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 ASN
** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.083284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.069504 restraints weight = 34754.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.071591 restraints weight = 20881.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.073016 restraints weight = 14733.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8148  Z= 0.250
  Angle     :  0.798  17.913  11023  Z= 0.406
  Chirality :  0.049   0.311   1254
  Planarity :  0.004   0.049   1361
  Dihedral  :  5.471  74.569   1144
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.79 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.35 (0.27), residues: 967
  helix:  1.58 (0.20), residues: 623
  sheet: -0.92 (0.95), residues: 36
  loop : -0.18 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 726 
 HIS   0.005   0.001   HIS A1141 
 PHE   0.054   0.002   PHE A1380 
 TYR   0.024   0.002   TYR A 408 
 ARG   0.003   0.001   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (    1)
  link_NAG-ASN         : angle       3.48047 (    3)
  hydrogen bonds       : bond        0.04787 (  513)
  hydrogen bonds       : angle       4.99883 ( 1488)
  covalent geometry    : bond        0.00534 ( 8147)
  covalent geometry    : angle       0.79571 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 172
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.6856 (tp30) cc_final: 0.6528 (tp30)
REVERT: A   94 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8860 (tt)
REVERT: A  169 PHE cc_start: 0.8327 (m-10) cc_final: 0.7070 (m-80)
REVERT: A  352 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9032 (pp)
REVERT: A  397 MET cc_start: 0.8779 (ppp) cc_final: 0.8534 (ppp)
REVERT: A  424 MET cc_start: 0.8792 (tpp) cc_final: 0.8508 (tpp)
REVERT: A  429 LEU cc_start: 0.9359 (mp) cc_final: 0.9157 (mt)
REVERT: A  594 MET cc_start: 0.8685 (mmt) cc_final: 0.8325 (mmm)
REVERT: A  596 LEU cc_start: 0.9194 (tp) cc_final: 0.8961 (tp)
REVERT: A  623 TYR cc_start: 0.8069 (t80) cc_final: 0.7637 (t80)
REVERT: A  724 TYR cc_start: 0.9286 (m-80) cc_final: 0.8930 (m-80)
REVERT: A  728 HIS cc_start: 0.8785 (t70) cc_final: 0.8499 (t70)
REVERT: A 1088 ILE cc_start: 0.9612 (mm) cc_final: 0.9329 (mm)
REVERT: A 1099 MET cc_start: 0.5698 (ptp) cc_final: 0.5182 (tpt)
REVERT: A 1266 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8543 (t80)
REVERT: A 1317 LEU cc_start: 0.9046 (tt) cc_final: 0.8794 (pp)
REVERT: A 1319 ASN cc_start: 0.9041 (m-40) cc_final: 0.8831 (m110)
REVERT: A 1328 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8790 (mm)
REVERT: A 1384 HIS cc_start: 0.9127 (m90) cc_final: 0.8749 (m90)
REVERT: A 1396 MET cc_start: 0.7302 (tpt) cc_final: 0.6767 (mmm)
REVERT: A 1446 LEU cc_start: 0.9315 (mt) cc_final: 0.9115 (mt)
REVERT: A 1458 PHE cc_start: 0.9067 (t80) cc_final: 0.8518 (t80)
  outliers start: 38
  outliers final: 25
  residues processed: 194
  average time/residue: 0.2652
  time to fit residues: 74.8566
Evaluate side-chains
  191 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 1.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1371 MET
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1425 VAL
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    0.0000
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0570
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5702

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.086378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.072306 restraints weight = 33191.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.074417 restraints weight = 20381.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.075867 restraints weight = 14517.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.5437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8148  Z= 0.141
  Angle     :  0.797  18.911  11023  Z= 0.385
  Chirality :  0.048   0.347   1254
  Planarity :  0.004   0.044   1361
  Dihedral  :  5.277  74.635   1144
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.13 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.45 (0.27), residues: 967
  helix:  1.69 (0.20), residues: 605
  sheet: -0.70 (0.90), residues: 42
  loop : -0.11 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 726 
 HIS   0.005   0.001   HIS A 475 
 PHE   0.055   0.002   PHE A1424 
 TYR   0.016   0.001   TYR A 408 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00601 (    1)
  link_NAG-ASN         : angle       2.98048 (    3)
  hydrogen bonds       : bond        0.04398 (  513)
  hydrogen bonds       : angle       4.84550 ( 1488)
  covalent geometry    : bond        0.00307 ( 8147)
  covalent geometry    : angle       0.79576 (11020)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9144 (mm) cc_final: 0.8801 (tp)
REVERT: A   94 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8865 (tt)
REVERT: A  105 LYS cc_start: 0.9323 (pttm) cc_final: 0.8899 (mmmt)
REVERT: A  169 PHE cc_start: 0.8199 (m-10) cc_final: 0.6854 (m-80)
REVERT: A  397 MET cc_start: 0.8622 (ppp) cc_final: 0.8306 (ppp)
REVERT: A  482 LEU cc_start: 0.9453 (pp) cc_final: 0.9205 (tp)
REVERT: A  594 MET cc_start: 0.8617 (mmt) cc_final: 0.8196 (mmm)
REVERT: A  596 LEU cc_start: 0.9131 (tp) cc_final: 0.8827 (tp)
REVERT: A  623 TYR cc_start: 0.7968 (t80) cc_final: 0.7665 (t80)
REVERT: A  636 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: A  724 TYR cc_start: 0.9044 (m-80) cc_final: 0.8583 (m-80)
REVERT: A  728 HIS cc_start: 0.8909 (t70) cc_final: 0.8554 (t-170)
REVERT: A 1088 ILE cc_start: 0.9586 (mm) cc_final: 0.9296 (mm)
REVERT: A 1099 MET cc_start: 0.5607 (ptp) cc_final: 0.5186 (tpt)
REVERT: A 1232 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8814 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8524 (t80)
REVERT: A 1296 MET cc_start: 0.8682 (mmt) cc_final: 0.8107 (mmt)
REVERT: A 1317 LEU cc_start: 0.9004 (tt) cc_final: 0.8754 (pp)
REVERT: A 1319 ASN cc_start: 0.9021 (m-40) cc_final: 0.8793 (m110)
REVERT: A 1328 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8800 (mm)
REVERT: A 1384 HIS cc_start: 0.9129 (m90) cc_final: 0.8704 (m90)
REVERT: A 1396 MET cc_start: 0.7276 (tpt) cc_final: 0.6732 (mmm)
REVERT: A 1458 PHE cc_start: 0.9073 (t80) cc_final: 0.8542 (t80)
  outliers start: 31
  outliers final: 23
  residues processed: 196
  average time/residue: 0.2452
  time to fit residues: 71.7996
Evaluate side-chains
  197 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 170
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  599 SER
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1371 MET
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1425 VAL
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0050
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.086507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.072264 restraints weight = 33720.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.074393 restraints weight = 20612.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.075886 restraints weight = 14680.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.5596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8148  Z= 0.139
  Angle     :  0.790  19.114  11023  Z= 0.384
  Chirality :  0.048   0.341   1254
  Planarity :  0.004   0.045   1361
  Dihedral  :  5.121  74.703   1142
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.02 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.44 (0.27), residues: 967
  helix:  1.65 (0.20), residues: 610
  sheet: -0.67 (0.89), residues: 42
  loop : -0.08 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 726 
 HIS   0.005   0.001   HIS A 475 
 PHE   0.054   0.002   PHE A1424 
 TYR   0.028   0.001   TYR A 408 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00584 (    1)
  link_NAG-ASN         : angle       2.78173 (    3)
  hydrogen bonds       : bond        0.04360 (  513)
  hydrogen bonds       : angle       4.84520 ( 1488)
  covalent geometry    : bond        0.00302 ( 8147)
  covalent geometry    : angle       0.78861 (11020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3324.59 seconds
wall clock time: 62 minutes 27.32 seconds (3747.32 seconds total)