Starting phenix.real_space_refine
on Fri Oct 10 17:15:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v12_42878/10_2025/8v12_42878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v12_42878/10_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_42878/10_2025/8v12_42878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v12_42878/10_2025/8v12_42878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v12_42878/10_2025/8v12_42878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v12_42878/10_2025/8v12_42878.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS%COO:plan': 1}
          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: 2.15, per 1000 atoms: 0.27
  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: 0.88
  Conformation dependent library (CDL) restraints added in 236.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.36

  Time building geometry restraints manager: 1.08 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:             2.400
  Set stop_for_unknowns flag:              0.010
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.360
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.002   0.000   ARG A1117 
 TYR   0.013   0.001   TYR A 521 
 PHE   0.012   0.001   PHE A 646 
 TRP   0.008   0.001   TRP A1423 
 HIS   0.005   0.001   HIS A   8 

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

*********************** 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  : 0.249 
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: 0.7997 (pp)
REVERT: A  727 ILE cc_start: 0.8567 (tp) cc_final: 0.8098 (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: 0.0817
  time to fit residues: 38.1157
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  : 0.310 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3738 r_free = 0.3738 target = 0.085067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.071437 restraints weight = 33146.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.073596 restraints weight = 19777.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.075126 restraints weight = 13866.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.076181 restraints weight = 10705.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.077009 restraints weight = 8809.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8148  Z= 0.163
  Angle     :  0.667   8.274  11023  Z= 0.347
  Chirality :  0.047   0.257   1254
  Planarity :  0.004   0.043   1361
  Dihedral  :  8.355  78.850   1152
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 19.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.51 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.26), residues: 967
  helix:  2.11 (0.20), residues: 610
  sheet: -1.62 (0.79), residues: 42
  loop : -0.11 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 335 
 TYR   0.019   0.002   TYR A 442 
 PHE   0.023   0.002   PHE A1454 
 TRP   0.008   0.001   TRP A1237 
 HIS   0.019   0.002   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8147)
  covalent geometry    : angle       0.66610 (11020)
  hydrogen bonds       : bond        0.05002 (  513)
  hydrogen bonds       : angle       4.98847 ( 1488)
  link_NAG-ASN         : bond        0.00722 (    1)
  link_NAG-ASN         : angle       2.54449 (    3)

*********************** 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
  261 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.9293 (mmmt) cc_final: 0.9036 (mmmt)
REVERT: A  169 PHE cc_start: 0.8152 (m-10) cc_final: 0.6888 (m-80)
REVERT: A  334 LEU cc_start: 0.8793 (mm) cc_final: 0.8561 (mm)
REVERT: A  352 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8898 (pp)
REVERT: A  424 MET cc_start: 0.8385 (tpp) cc_final: 0.8118 (tpp)
REVERT: A  452 PHE cc_start: 0.9435 (m-10) cc_final: 0.9102 (m-80)
REVERT: A  573 PHE cc_start: 0.8816 (m-80) cc_final: 0.8317 (m-80)
REVERT: A  611 ILE cc_start: 0.9387 (mt) cc_final: 0.9182 (mm)
REVERT: A  724 TYR cc_start: 0.8800 (m-80) cc_final: 0.8594 (m-80)
REVERT: A  726 TRP cc_start: 0.8767 (t60) cc_final: 0.8439 (t60)
REVERT: A  728 HIS cc_start: 0.8532 (t70) cc_final: 0.8155 (t70)
REVERT: A 1099 MET cc_start: 0.5412 (ptp) cc_final: 0.5097 (tpp)
REVERT: A 1232 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8817 (mm-30)
REVERT: A 1296 MET cc_start: 0.8856 (mmm) cc_final: 0.7531 (mmm)
REVERT: A 1356 PHE cc_start: 0.8470 (t80) cc_final: 0.8066 (t80)
REVERT: A 1384 HIS cc_start: 0.9118 (m90) cc_final: 0.8628 (m90)
REVERT: A 1396 MET cc_start: 0.7159 (tpt) cc_final: 0.6763 (mmm)
REVERT: A 1420 LEU cc_start: 0.9290 (mt) cc_final: 0.8951 (mt)
  outliers start: 36
  outliers final: 12
  residues processed: 246
  average time/residue: 0.0773
  time to fit residues: 27.1359
Evaluate side-chains
  201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  635 SER
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1425 VAL
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 10 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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**
** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.082914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.069277 restraints weight = 34002.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.071356 restraints weight = 20504.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.072849 restraints weight = 14487.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.073851 restraints weight = 11240.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.074655 restraints weight = 9339.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8148  Z= 0.205
  Angle     :  0.707  13.452  11023  Z= 0.366
  Chirality :  0.047   0.258   1254
  Planarity :  0.004   0.049   1361
  Dihedral  :  7.095  74.172   1144
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.37 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.26), residues: 967
  helix:  1.86 (0.20), residues: 613
  sheet: -1.23 (0.91), residues: 36
  loop : -0.22 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 335 
 TYR   0.020   0.002   TYR A  75 
 PHE   0.037   0.002   PHE A1424 
 TRP   0.006   0.001   TRP A1423 
 HIS   0.005   0.001   HIS A1417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 8147)
  covalent geometry    : angle       0.70539 (11020)
  hydrogen bonds       : bond        0.04968 (  513)
  hydrogen bonds       : angle       5.00662 ( 1488)
  link_NAG-ASN         : bond        0.00673 (    1)
  link_NAG-ASN         : angle       2.62408 (    3)

*********************** 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
  227 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 0.324 
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  169 PHE cc_start: 0.8094 (m-10) cc_final: 0.6903 (m-80)
REVERT: A  334 LEU cc_start: 0.8750 (mm) cc_final: 0.8519 (mm)
REVERT: A  352 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8990 (pp)
REVERT: A  424 MET cc_start: 0.8475 (tpp) cc_final: 0.8191 (tpp)
REVERT: A  573 PHE cc_start: 0.8976 (m-80) cc_final: 0.8525 (m-80)
REVERT: A  594 MET cc_start: 0.8741 (mmt) cc_final: 0.8423 (mmm)
REVERT: A  596 LEU cc_start: 0.9184 (tp) cc_final: 0.8888 (tp)
REVERT: A  642 MET cc_start: 0.8477 (mtp) cc_final: 0.8088 (ttm)
REVERT: A  724 TYR cc_start: 0.8995 (m-80) cc_final: 0.8778 (m-80)
REVERT: A  728 HIS cc_start: 0.8620 (t70) cc_final: 0.8318 (t70)
REVERT: A 1088 ILE cc_start: 0.9594 (mm) cc_final: 0.9374 (mm)
REVERT: A 1099 MET cc_start: 0.5542 (ptp) cc_final: 0.5098 (tpt)
REVERT: A 1131 ASP cc_start: 0.7832 (m-30) cc_final: 0.7567 (m-30)
REVERT: A 1232 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8804 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8502 (t80)
REVERT: A 1296 MET cc_start: 0.8815 (mmm) cc_final: 0.7623 (mmm)
REVERT: A 1317 LEU cc_start: 0.9053 (tt) cc_final: 0.8800 (pp)
REVERT: A 1319 ASN cc_start: 0.9063 (m-40) cc_final: 0.8758 (m110)
REVERT: A 1328 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8833 (mm)
REVERT: A 1384 HIS cc_start: 0.9075 (m90) cc_final: 0.8620 (m90)
REVERT: A 1396 MET cc_start: 0.7351 (tpt) cc_final: 0.6987 (mmm)
REVERT: A 1420 LEU cc_start: 0.9273 (mt) cc_final: 0.9008 (mt)
  outliers start: 37
  outliers final: 24
  residues processed: 214
  average time/residue: 0.0719
  time to fit residues: 22.3515
Evaluate side-chains
  195 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   38 THR
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  341 LEU
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  368 TYR
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 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 1425 VAL
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 26 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0770
   chunk 72 optimal weight:    0.2980
   chunk 56 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.085223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.071349 restraints weight = 34050.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.073489 restraints weight = 20570.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.075015 restraints weight = 14486.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.076117 restraints weight = 11228.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.076904 restraints weight = 9235.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8148  Z= 0.143
  Angle     :  0.675  15.512  11023  Z= 0.340
  Chirality :  0.046   0.327   1254
  Planarity :  0.004   0.049   1361
  Dihedral  :  6.306  74.108   1144
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 17.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.27), residues: 967
  helix:  1.88 (0.20), residues: 613
  sheet: -1.40 (0.84), residues: 42
  loop : -0.16 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 108 
 TYR   0.014   0.002   TYR A 442 
 PHE   0.043   0.002   PHE A1424 
 TRP   0.008   0.002   TRP A1279 
 HIS   0.007   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8147)
  covalent geometry    : angle       0.67368 (11020)
  hydrogen bonds       : bond        0.04563 (  513)
  hydrogen bonds       : angle       4.83381 ( 1488)
  link_NAG-ASN         : bond        0.00764 (    1)
  link_NAG-ASN         : angle       2.77211 (    3)

*********************** 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
  242 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 197
  time to evaluate  : 0.334 
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   94 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8799 (tt)
REVERT: A  169 PHE cc_start: 0.8074 (m-10) cc_final: 0.6896 (m-80)
REVERT: A  334 LEU cc_start: 0.8749 (mm) cc_final: 0.8495 (mm)
REVERT: A  352 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8918 (pp)
REVERT: A  416 ILE cc_start: 0.8013 (mt) cc_final: 0.7660 (mm)
REVERT: A  424 MET cc_start: 0.8567 (tpp) cc_final: 0.8272 (tpp)
REVERT: A  458 ILE cc_start: 0.8424 (tp) cc_final: 0.7912 (tp)
REVERT: A  594 MET cc_start: 0.8738 (mmt) cc_final: 0.8380 (mmm)
REVERT: A  724 TYR cc_start: 0.8824 (m-80) cc_final: 0.8463 (m-80)
REVERT: A  728 HIS cc_start: 0.8691 (t70) cc_final: 0.8313 (t-170)
REVERT: A 1084 MET cc_start: 0.8979 (ptp) cc_final: 0.8715 (ptp)
REVERT: A 1088 ILE cc_start: 0.9611 (mm) cc_final: 0.9371 (mm)
REVERT: A 1099 MET cc_start: 0.5380 (ptp) cc_final: 0.4970 (tpt)
REVERT: A 1131 ASP cc_start: 0.7846 (m-30) cc_final: 0.7571 (m-30)
REVERT: A 1188 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9116 (mp10)
REVERT: A 1232 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8829 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8560 (t80)
REVERT: A 1296 MET cc_start: 0.8750 (mmm) cc_final: 0.7542 (mmm)
REVERT: A 1317 LEU cc_start: 0.9017 (tt) cc_final: 0.8771 (pp)
REVERT: A 1319 ASN cc_start: 0.9041 (m-40) cc_final: 0.8786 (m110)
REVERT: A 1328 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8806 (mm)
REVERT: A 1356 PHE cc_start: 0.8233 (t80) cc_final: 0.7944 (t80)
REVERT: A 1384 HIS cc_start: 0.9092 (m90) cc_final: 0.8518 (m90)
REVERT: A 1396 MET cc_start: 0.7282 (tpt) cc_final: 0.6796 (mmm)
REVERT: A 1420 LEU cc_start: 0.9271 (mt) cc_final: 0.9062 (mt)
REVERT: A 1458 PHE cc_start: 0.8903 (t80) cc_final: 0.8689 (t80)
  outliers start: 45
  outliers final: 23
  residues processed: 221
  average time/residue: 0.0751
  time to fit residues: 24.0583
Evaluate side-chains
  206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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  363 SER
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  368 TYR
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  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 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 1 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 45 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 20 optimal weight:    0.1980
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.085640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.071750 restraints weight = 33878.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.073900 restraints weight = 20302.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.075441 restraints weight = 14292.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.076510 restraints weight = 11090.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.077254 restraints weight = 9144.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8148  Z= 0.142
  Angle     :  0.717  16.671  11023  Z= 0.351
  Chirality :  0.046   0.280   1254
  Planarity :  0.004   0.050   1361
  Dihedral  :  5.899  74.221   1144
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 19.39 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.27), residues: 967
  helix:  1.80 (0.20), residues: 614
  sheet: -1.30 (0.83), residues: 42
  loop : -0.12 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.026   0.002   TYR A 408 
 PHE   0.044   0.002   PHE A1424 
 TRP   0.011   0.002   TRP A 726 
 HIS   0.006   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8147)
  covalent geometry    : angle       0.71598 (11020)
  hydrogen bonds       : bond        0.04422 (  513)
  hydrogen bonds       : angle       4.84484 ( 1488)
  link_NAG-ASN         : bond        0.00731 (    1)
  link_NAG-ASN         : angle       2.90424 (    3)

*********************** 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
  233 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 192
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9162 (mm) cc_final: 0.8802 (tp)
REVERT: A   79 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7944 (mm-30)
REVERT: A   82 ASN cc_start: 0.9196 (m-40) cc_final: 0.8877 (m-40)
REVERT: A   94 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8845 (tt)
REVERT: A   96 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8045 (tm-30)
REVERT: A  169 PHE cc_start: 0.8128 (m-10) cc_final: 0.7023 (m-80)
REVERT: A  352 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8866 (pp)
REVERT: A  424 MET cc_start: 0.8635 (tpp) cc_final: 0.8351 (tpp)
REVERT: A  458 ILE cc_start: 0.8399 (tp) cc_final: 0.8172 (tp)
REVERT: A  594 MET cc_start: 0.8723 (mmt) cc_final: 0.8354 (mmm)
REVERT: A  724 TYR cc_start: 0.8839 (m-80) cc_final: 0.8395 (m-80)
REVERT: A  728 HIS cc_start: 0.8686 (t70) cc_final: 0.8305 (t-170)
REVERT: A 1088 ILE cc_start: 0.9601 (mm) cc_final: 0.9279 (mm)
REVERT: A 1099 MET cc_start: 0.5634 (ptp) cc_final: 0.5159 (tpt)
REVERT: A 1232 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8808 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8563 (t80)
REVERT: A 1317 LEU cc_start: 0.9008 (tt) cc_final: 0.8787 (pp)
REVERT: A 1319 ASN cc_start: 0.9026 (m-40) cc_final: 0.8758 (m110)
REVERT: A 1328 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8811 (mm)
REVERT: A 1384 HIS cc_start: 0.9119 (m90) cc_final: 0.8385 (m90)
REVERT: A 1396 MET cc_start: 0.7232 (tpt) cc_final: 0.6738 (mmm)
REVERT: A 1458 PHE cc_start: 0.9002 (t80) cc_final: 0.8688 (t80)
  outliers start: 41
  outliers final: 23
  residues processed: 221
  average time/residue: 0.0666
  time to fit residues: 21.4387
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  : 0.320 
-------------------------------------------------------------------------------
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  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  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 1149 LEU
Chi-restraints excluded: chain A residue 1266 PHE
Chi-restraints excluded: chain A residue 1276 SER
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 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 69 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0010
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.3590

-------------------------------------------------------------------------------
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
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 GLN
** 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 = 0.3723 r_free = 0.3723 target = 0.084635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.070993 restraints weight = 33681.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.073089 restraints weight = 20204.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.074552 restraints weight = 14249.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.075579 restraints weight = 11091.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.076400 restraints weight = 9205.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.4727

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= 0.160
  Angle     :  0.709  17.143  11023  Z= 0.353
  Chirality :  0.046   0.259   1254
  Planarity :  0.004   0.050   1361
  Dihedral  :  5.711  73.997   1144
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.52 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.27), residues: 967
  helix:  1.83 (0.21), residues: 615
  sheet: -1.33 (1.35), residues: 21
  loop : -0.18 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.019   0.002   TYR A 408 
 PHE   0.044   0.002   PHE A1380 
 TRP   0.009   0.002   TRP A 726 
 HIS   0.005   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8147)
  covalent geometry    : angle       0.70661 (11020)
  hydrogen bonds       : bond        0.04442 (  513)
  hydrogen bonds       : angle       4.88529 ( 1488)
  link_NAG-ASN         : bond        0.00669 (    1)
  link_NAG-ASN         : angle       3.50684 (    3)

*********************** 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
  223 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 184
  time to evaluate  : 0.338 
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   60 GLU cc_start: 0.6966 (tp30) cc_final: 0.6551 (tp30)
REVERT: A   94 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8810 (tt)
REVERT: A  169 PHE cc_start: 0.8145 (m-10) cc_final: 0.6985 (m-80)
REVERT: A  352 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8914 (pp)
REVERT: A  424 MET cc_start: 0.8687 (tpp) cc_final: 0.8397 (tpp)
REVERT: A  594 MET cc_start: 0.8673 (mmt) cc_final: 0.8272 (mmm)
REVERT: A  596 LEU cc_start: 0.9186 (tp) cc_final: 0.8874 (tp)
REVERT: A  724 TYR cc_start: 0.8940 (m-80) cc_final: 0.8476 (m-80)
REVERT: A  728 HIS cc_start: 0.8710 (t70) cc_final: 0.8347 (t-170)
REVERT: A 1088 ILE cc_start: 0.9564 (mm) cc_final: 0.9279 (mm)
REVERT: A 1099 MET cc_start: 0.5663 (ptp) cc_final: 0.5113 (tpt)
REVERT: A 1232 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8814 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8583 (t80)
REVERT: A 1317 LEU cc_start: 0.9020 (tt) cc_final: 0.8785 (pp)
REVERT: A 1319 ASN cc_start: 0.9033 (m-40) cc_final: 0.8767 (m110)
REVERT: A 1349 PHE cc_start: 0.8470 (t80) cc_final: 0.8200 (t80)
REVERT: A 1384 HIS cc_start: 0.9119 (m90) cc_final: 0.8759 (m90)
REVERT: A 1396 MET cc_start: 0.7269 (tpt) cc_final: 0.6777 (mmm)
REVERT: A 1458 PHE cc_start: 0.8984 (t80) cc_final: 0.8581 (t80)
  outliers start: 39
  outliers final: 23
  residues processed: 205
  average time/residue: 0.0720
  time to fit residues: 21.2911
Evaluate side-chains
  196 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  367 LEU
Chi-restraints excluded: chain A residue  368 TYR
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  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 1149 LEU
Chi-restraints excluded: chain A residue 1188 GLN
Chi-restraints excluded: chain A residue 1266 PHE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0040
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.086247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.072289 restraints weight = 33262.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.074420 restraints weight = 20057.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.075917 restraints weight = 14209.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.077008 restraints weight = 11062.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.077782 restraints weight = 9145.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8148  Z= 0.136
  Angle     :  0.726  17.259  11023  Z= 0.356
  Chirality :  0.047   0.307   1254
  Planarity :  0.004   0.050   1361
  Dihedral  :  5.509  74.185   1144
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.98 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.27), residues: 967
  helix:  1.71 (0.20), residues: 618
  sheet: -1.54 (1.10), residues: 27
  loop : -0.14 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1061 
 TYR   0.036   0.002   TYR A 304 
 PHE   0.046   0.002   PHE A1424 
 TRP   0.013   0.002   TRP A 726 
 HIS   0.005   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8147)
  covalent geometry    : angle       0.72453 (11020)
  hydrogen bonds       : bond        0.04304 (  513)
  hydrogen bonds       : angle       4.82073 ( 1488)
  link_NAG-ASN         : bond        0.00696 (    1)
  link_NAG-ASN         : angle       3.30496 (    3)

*********************** 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
  226 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 184
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9151 (mm) cc_final: 0.8845 (tp)
REVERT: A   60 GLU cc_start: 0.6965 (tp30) cc_final: 0.6518 (tp30)
REVERT: A   94 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8852 (tt)
REVERT: A  169 PHE cc_start: 0.8171 (m-10) cc_final: 0.7013 (m-80)
REVERT: A  352 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8912 (pp)
REVERT: A  424 MET cc_start: 0.8728 (tpp) cc_final: 0.8417 (tpp)
REVERT: A  594 MET cc_start: 0.8663 (mmt) cc_final: 0.8257 (mmm)
REVERT: A  596 LEU cc_start: 0.9111 (tp) cc_final: 0.8800 (tp)
REVERT: A  623 TYR cc_start: 0.7960 (t80) cc_final: 0.7530 (t80)
REVERT: A  724 TYR cc_start: 0.8891 (m-80) cc_final: 0.8400 (m-80)
REVERT: A  728 HIS cc_start: 0.8713 (t70) cc_final: 0.8325 (t-170)
REVERT: A 1088 ILE cc_start: 0.9551 (mm) cc_final: 0.9250 (mm)
REVERT: A 1099 MET cc_start: 0.5583 (ptp) cc_final: 0.5130 (tpt)
REVERT: A 1232 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8847 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8528 (t80)
REVERT: A 1319 ASN cc_start: 0.8975 (m-40) cc_final: 0.8718 (m110)
REVERT: A 1349 PHE cc_start: 0.8449 (t80) cc_final: 0.8183 (t80)
REVERT: A 1384 HIS cc_start: 0.9139 (m90) cc_final: 0.8781 (m90)
REVERT: A 1396 MET cc_start: 0.7277 (tpt) cc_final: 0.6725 (mmm)
REVERT: A 1458 PHE cc_start: 0.8963 (t80) cc_final: 0.8514 (t80)
  outliers start: 42
  outliers final: 28
  residues processed: 205
  average time/residue: 0.0667
  time to fit residues: 20.1633
Evaluate side-chains
  202 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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  341 LEU
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  368 TYR
Chi-restraints excluded: chain A residue  406 MET
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  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 1327 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 1415 VAL
Chi-restraints excluded: chain A residue 1441 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    0.3980
   chunk 6 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 92 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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**
** 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 = 0.3758 r_free = 0.3758 target = 0.086461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.072321 restraints weight = 33548.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.074444 restraints weight = 20390.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.075956 restraints weight = 14470.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.077032 restraints weight = 11277.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.077685 restraints weight = 9373.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8148  Z= 0.140
  Angle     :  0.751  17.473  11023  Z= 0.366
  Chirality :  0.047   0.329   1254
  Planarity :  0.004   0.051   1361
  Dihedral  :  5.402  74.453   1144
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 22.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.27), residues: 967
  helix:  1.68 (0.20), residues: 618
  sheet: -1.45 (1.10), residues: 27
  loop : -0.09 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1061 
 TYR   0.030   0.002   TYR A 304 
 PHE   0.050   0.002   PHE A1424 
 TRP   0.010   0.001   TRP A 726 
 HIS   0.004   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8147)
  covalent geometry    : angle       0.74965 (11020)
  hydrogen bonds       : bond        0.04339 (  513)
  hydrogen bonds       : angle       4.77227 ( 1488)
  link_NAG-ASN         : bond        0.00631 (    1)
  link_NAG-ASN         : angle       3.21752 (    3)

*********************** 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
  221 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 181
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9151 (mm) cc_final: 0.8829 (tp)
REVERT: A   60 GLU cc_start: 0.6971 (tp30) cc_final: 0.6530 (tp30)
REVERT: A  169 PHE cc_start: 0.8218 (m-10) cc_final: 0.7009 (m-80)
REVERT: A  352 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8952 (pp)
REVERT: A  424 MET cc_start: 0.8759 (tpp) cc_final: 0.8433 (tpp)
REVERT: A  482 LEU cc_start: 0.9436 (pp) cc_final: 0.9186 (tp)
REVERT: A  594 MET cc_start: 0.8667 (mmt) cc_final: 0.8264 (mmm)
REVERT: A  596 LEU cc_start: 0.9065 (tp) cc_final: 0.8751 (tp)
REVERT: A  623 TYR cc_start: 0.7913 (t80) cc_final: 0.7657 (t80)
REVERT: A  636 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (mm)
REVERT: A  724 TYR cc_start: 0.8922 (m-80) cc_final: 0.8446 (m-80)
REVERT: A  728 HIS cc_start: 0.8721 (t70) cc_final: 0.8356 (t-170)
REVERT: A 1088 ILE cc_start: 0.9555 (mm) cc_final: 0.9251 (mm)
REVERT: A 1099 MET cc_start: 0.5474 (ptp) cc_final: 0.5041 (tpt)
REVERT: A 1116 ARG cc_start: 0.8759 (tpt170) cc_final: 0.8514 (tpt170)
REVERT: A 1190 GLU cc_start: 0.9138 (tp30) cc_final: 0.8930 (tp30)
REVERT: A 1232 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8812 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8540 (t80)
REVERT: A 1281 LYS cc_start: 0.9532 (pttm) cc_final: 0.9240 (mtmm)
REVERT: A 1349 PHE cc_start: 0.8447 (t80) cc_final: 0.8193 (t80)
REVERT: A 1356 PHE cc_start: 0.7937 (t80) cc_final: 0.7727 (t80)
REVERT: A 1384 HIS cc_start: 0.9138 (m90) cc_final: 0.8796 (m90)
REVERT: A 1396 MET cc_start: 0.7258 (tpt) cc_final: 0.6698 (mmm)
REVERT: A 1458 PHE cc_start: 0.8970 (t80) cc_final: 0.8510 (t80)
  outliers start: 40
  outliers final: 31
  residues processed: 202
  average time/residue: 0.0721
  time to fit residues: 21.6414
Evaluate side-chains
  204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  321 LEU
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 LEU
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  368 TYR
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain A residue  507 ILE
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  629 SER
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain A residue  643 VAL
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 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 1415 VAL
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 90 optimal weight:    9.9990
   chunk 52 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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**
** 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 = 0.3769 r_free = 0.3769 target = 0.086862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.072725 restraints weight = 33280.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.074870 restraints weight = 20224.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.076367 restraints weight = 14331.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.077456 restraints weight = 11181.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.078221 restraints weight = 9264.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.5387

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= 0.134
  Angle     :  0.752  17.298  11023  Z= 0.363
  Chirality :  0.047   0.340   1254
  Planarity :  0.004   0.049   1361
  Dihedral  :  5.213  74.903   1144
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 22.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.27), residues: 967
  helix:  1.66 (0.20), residues: 617
  sheet: -0.72 (0.91), residues: 37
  loop : -0.08 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1061 
 TYR   0.025   0.002   TYR A 304 
 PHE   0.050   0.002   PHE A1424 
 TRP   0.013   0.002   TRP A 726 
 HIS   0.004   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8147)
  covalent geometry    : angle       0.75083 (11020)
  hydrogen bonds       : bond        0.04241 (  513)
  hydrogen bonds       : angle       4.73422 ( 1488)
  link_NAG-ASN         : bond        0.00613 (    1)
  link_NAG-ASN         : angle       2.90898 (    3)

*********************** 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
  219 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 180
  time to evaluate  : 0.321 
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: 0.9134 (mm) cc_final: 0.8808 (tp)
REVERT: A   60 GLU cc_start: 0.6769 (tp30) cc_final: 0.6363 (tp30)
REVERT: A   94 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8920 (tt)
REVERT: A  108 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8555 (mtt-85)
REVERT: A  169 PHE cc_start: 0.8208 (m-10) cc_final: 0.6976 (m-80)
REVERT: A  352 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8936 (pp)
REVERT: A  482 LEU cc_start: 0.9446 (pp) cc_final: 0.9206 (tp)
REVERT: A  594 MET cc_start: 0.8650 (mmt) cc_final: 0.8244 (mmm)
REVERT: A  596 LEU cc_start: 0.9075 (tp) cc_final: 0.8777 (tp)
REVERT: A  623 TYR cc_start: 0.7952 (t80) cc_final: 0.7672 (t80)
REVERT: A  636 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9118 (mm)
REVERT: A  642 MET cc_start: 0.8629 (ptm) cc_final: 0.8289 (tmm)
REVERT: A  724 TYR cc_start: 0.8827 (m-80) cc_final: 0.8296 (m-80)
REVERT: A  728 HIS cc_start: 0.8778 (t70) cc_final: 0.8407 (t-170)
REVERT: A 1088 ILE cc_start: 0.9569 (mm) cc_final: 0.9268 (mm)
REVERT: A 1099 MET cc_start: 0.5526 (ptp) cc_final: 0.5109 (tpt)
REVERT: A 1232 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8814 (mm-30)
REVERT: A 1266 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8578 (t80)
REVERT: A 1288 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8290 (mmmm)
REVERT: A 1296 MET cc_start: 0.8697 (mmt) cc_final: 0.8108 (mmt)
REVERT: A 1319 ASN cc_start: 0.8958 (m-40) cc_final: 0.8705 (m110)
REVERT: A 1349 PHE cc_start: 0.8384 (t80) cc_final: 0.8152 (t80)
REVERT: A 1356 PHE cc_start: 0.7838 (t80) cc_final: 0.7601 (t80)
REVERT: A 1384 HIS cc_start: 0.9168 (m90) cc_final: 0.8832 (m90)
REVERT: A 1396 MET cc_start: 0.7278 (tpt) cc_final: 0.6695 (mmm)
REVERT: A 1423 TRP cc_start: 0.7468 (t60) cc_final: 0.7236 (t60)
REVERT: A 1458 PHE cc_start: 0.8957 (t80) cc_final: 0.8461 (t80)
  outliers start: 39
  outliers final: 30
  residues processed: 202
  average time/residue: 0.0742
  time to fit residues: 22.0073
Evaluate side-chains
  206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  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  341 LEU
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  368 TYR
Chi-restraints excluded: chain A residue  406 MET
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  569 VAL
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  643 VAL
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 1415 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 88 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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**
** 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 = 0.3724 r_free = 0.3724 target = 0.084456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.070578 restraints weight = 33761.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.072635 restraints weight = 20701.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.074060 restraints weight = 14740.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.075112 restraints weight = 11547.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.075837 restraints weight = 9591.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.5459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8148  Z= 0.198
  Angle     :  0.786  17.905  11023  Z= 0.388
  Chirality :  0.048   0.359   1254
  Planarity :  0.004   0.052   1361
  Dihedral  :  5.264  74.535   1144
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 23.13 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.27), residues: 967
  helix:  1.79 (0.21), residues: 609
  sheet: -0.76 (0.93), residues: 37
  loop : -0.24 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1061 
 TYR   0.027   0.002   TYR A 304 
 PHE   0.053   0.002   PHE A1424 
 TRP   0.008   0.002   TRP A 726 
 HIS   0.004   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 8147)
  covalent geometry    : angle       0.78436 (11020)
  hydrogen bonds       : bond        0.04550 (  513)
  hydrogen bonds       : angle       4.80909 ( 1488)
  link_NAG-ASN         : bond        0.00501 (    1)
  link_NAG-ASN         : angle       3.06399 (    3)

********************** 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
  204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.6926 (tp30) cc_final: 0.6481 (tp30)
REVERT: A   94 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8838 (tt)
REVERT: A  112 LYS cc_start: 0.9101 (mttm) cc_final: 0.8898 (mttm)
REVERT: A  169 PHE cc_start: 0.8311 (m-10) cc_final: 0.6984 (m-80)
REVERT: A  352 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9032 (pp)
REVERT: A  424 MET cc_start: 0.8804 (tpp) cc_final: 0.8554 (tpp)
REVERT: A  482 LEU cc_start: 0.9437 (pp) cc_final: 0.9198 (tp)
REVERT: A  594 MET cc_start: 0.8623 (mmt) cc_final: 0.8221 (mmm)
REVERT: A  596 LEU cc_start: 0.9158 (tp) cc_final: 0.8858 (tp)
REVERT: A  636 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9132 (mm)
REVERT: A  724 TYR cc_start: 0.9149 (m-80) cc_final: 0.8791 (m-80)
REVERT: A  728 HIS cc_start: 0.8808 (t70) cc_final: 0.8595 (t70)
REVERT: A 1088 ILE cc_start: 0.9592 (mm) cc_final: 0.9309 (mm)
REVERT: A 1099 MET cc_start: 0.5755 (ptp) cc_final: 0.5323 (tpt)
REVERT: A 1266 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8471 (t80)
REVERT: A 1296 MET cc_start: 0.8772 (mmt) cc_final: 0.8145 (mmt)
REVERT: A 1319 ASN cc_start: 0.8990 (m-40) cc_final: 0.8736 (m110)
REVERT: A 1349 PHE cc_start: 0.8413 (t80) cc_final: 0.8173 (t80)
REVERT: A 1356 PHE cc_start: 0.7849 (t80) cc_final: 0.7603 (t80)
REVERT: A 1384 HIS cc_start: 0.9106 (m90) cc_final: 0.8739 (m90)
REVERT: A 1396 MET cc_start: 0.7291 (tpt) cc_final: 0.6824 (mmm)
REVERT: A 1423 TRP cc_start: 0.7773 (t60) cc_final: 0.7460 (t60)
REVERT: A 1458 PHE cc_start: 0.9003 (t80) cc_final: 0.8479 (t80)
  outliers start: 38
  outliers final: 27
  residues processed: 186
  average time/residue: 0.0688
  time to fit residues: 19.1880
Evaluate side-chains
  193 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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  368 TYR
Chi-restraints excluded: chain A residue  406 MET
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  569 VAL
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  643 VAL
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 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 1415 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 62 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0270
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7240

-------------------------------------------------------------------------------
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**
** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1300 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.086217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.072160 restraints weight = 33225.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.074240 restraints weight = 20332.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.075713 restraints weight = 14532.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.076804 restraints weight = 11347.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.077543 restraints weight = 9425.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8148  Z= 0.141
  Angle     :  0.778  18.082  11023  Z= 0.375
  Chirality :  0.047   0.374   1254
  Planarity :  0.004   0.053   1361
  Dihedral  :  5.180  74.781   1144
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.38 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.27), residues: 967
  helix:  1.74 (0.20), residues: 610
  sheet: -0.52 (0.96), residues: 37
  loop : -0.13 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1061 
 TYR   0.021   0.002   TYR A 623 
 PHE   0.055   0.002   PHE A1424 
 TRP   0.013   0.001   TRP A 726 
 HIS   0.005   0.001   HIS A1300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8147)
  covalent geometry    : angle       0.77732 (11020)
  hydrogen bonds       : bond        0.04350 (  513)
  hydrogen bonds       : angle       4.76760 ( 1488)
  link_NAG-ASN         : bond        0.00576 (    1)
  link_NAG-ASN         : angle       2.68336 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1516.71 seconds
wall clock time: 27 minutes 12.00 seconds (1632.00 seconds total)