Starting phenix.real_space_refine
on Fri Oct 10 12:10:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p2z_17380/10_2025/8p2z_17380.map"
  }
  resolution = 3.5
  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=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     Cl      1      4.86       5
     C    3073      2.51       5
     N     712      2.21       5
     O     824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  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: 4641
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 199
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "C"
      Number of atoms: 4404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4404
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 20, 'TRANS': 552}
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 37
          Unusual residues: {'NAG': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.21, per 1000 atoms: 0.26
  Number of scatterers: 4641
  At special positions: 0
  Unit cell: (61.0785, 72.297, 103.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      31     16.00
     O     824      8.00
     N     712      7.00
     C    3073      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 701 " - " ASN C 131 "
      " NAG C 702 " - " ASN C 357 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 130.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 1 sheets defined
      82.9% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 740 through 768
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 24 through 29
      removed outlier: 3.569A  pdb=" N   VAL C  28 " --> pdb=" O   GLY C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 38
      removed outlier: 3.834A  pdb=" N   TYR C  33 " --> pdb=" O   TRP C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 54
      Proline residue:  C  46  - end of helix
      removed outlier: 3.666A  pdb=" N   VAL C  53 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 70
      removed outlier: 3.610A  pdb=" N   LEU C  58 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
      removed outlier: 4.030A  pdb=" N   SER C  81 " --> pdb=" O   TRP C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 84
      No H-bonds generated for 'chain 'C' and resid 82 through 84'
    Processing helix  chain 'C' and resid 85 through 115
      removed outlier: 3.645A  pdb=" N   VAL C  89 " --> pdb=" O   SER C  85 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL C  92 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER C  95 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ASN C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   VAL C 104 " --> pdb=" O   MET C 100 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ILE C 105 " --> pdb=" O   TYR C 101 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN C 106 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 142
    Processing helix  chain 'C' and resid 143 through 151
    Processing helix  chain 'C' and resid 167 through 188
      removed outlier: 3.536A  pdb=" N   GLY C 188 " --> pdb=" O   CYS C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 3.658A  pdb=" N   TYR C 197 " --> pdb=" O   GLY C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 215
    Processing helix  chain 'C' and resid 219 through 229
      removed outlier: 4.129A  pdb=" N   GLY C 223 " --> pdb=" O   GLY C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 253
      removed outlier: 3.758A  pdb=" N   TRP C 241 " --> pdb=" O   ASN C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 265
      removed outlier: 3.697A  pdb=" N   ALA C 261 " --> pdb=" O   GLY C 257 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR C 265 " --> pdb=" O   ALA C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 322
      removed outlier: 3.663A  pdb=" N   HIS C 275 " --> pdb=" O   ASN C 271 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE C 277 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR C 320 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 331
      No H-bonds generated for 'chain 'C' and resid 329 through 331'
    Processing helix  chain 'C' and resid 332 through 344
    Processing helix  chain 'C' and resid 344 through 352
      removed outlier: 3.813A  pdb=" N   TYR C 348 " --> pdb=" O   TYR C 344 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU C 350 " --> pdb=" O   SER C 346 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   MET C 351 " --> pdb=" O   LYS C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 367
    Processing helix  chain 'C' and resid 372 through 384
    Processing helix  chain 'C' and resid 387 through 421
      removed outlier: 3.570A  pdb=" N   TRP C 391 " --> pdb=" O   VAL C 387 " (cutoff:3.500A)
      Proline residue:  C 417  - end of helix
    Processing helix  chain 'C' and resid 421 through 426
    Processing helix  chain 'C' and resid 429 through 445
    Processing helix  chain 'C' and resid 446 through 450
      removed outlier: 3.842A  pdb=" N   MET C 450 " --> pdb=" O   VAL C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 464
      removed outlier: 3.795A  pdb=" N   TRP C 456 " --> pdb=" O   ALA C 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 467 through 482
    Processing helix  chain 'C' and resid 485 through 498
    Processing helix  chain 'C' and resid 502 through 511
    Processing helix  chain 'C' and resid 511 through 532
    Processing helix  chain 'C' and resid 552 through 582
      removed outlier: 3.640A  pdb=" N   LEU C 556 " --> pdb=" O   PRO C 552 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA C 557 " --> pdb=" O   ALA C 553 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL C 558 " --> pdb=" O   TYR C 554 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL C 563 " --> pdb=" O   ILE C 559 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   SER C 566 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE C 570 " --> pdb=" O   SER C 566 " (cutoff:3.500A)
      Proline residue:  C 571  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 535 through 540

    335 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.73

  Time building geometry restraints manager: 0.59 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 766
        2.76 -     3.29: 4580
        3.29 -     3.83: 8090
        3.83 -     4.36: 8712
        4.36 -     4.90: 15637
  Nonbonded interactions: 37785
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 298 "
            pdb=" O   LEU C 364 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" ND2 ASN C  27 "
            pdb=" OD1 ASN C 283 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   ASP C 540 "
            pdb=" N   GLY C 544 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OH  TYR C 204 "
            pdb=" OG1 THR C 286 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" ND2 ASN C  27 "
            pdb=" OG  SER C 287 "
     model   vdw
     2.271 3.120
  ... (remaining 37780 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.730
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   4768  Z= 0.174
  Angle     :  0.630   8.207   6521  Z= 0.354
  Chirality :  0.040   0.285    764
  Planarity :  0.006   0.138    794
  Dihedral  : 14.807  90.304   1623
  Min Nonbonded Distance : 2.219

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

Rama-Z 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:  1.32 (0.35), residues: 598
  helix:  1.64 (0.25), residues: 437
  sheet: -0.24 (1.30), residues: 14
  loop : -1.33 (0.48), residues: 147

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

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

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.142 
Fit side-chains
REVERT: C  100 MET cc_start: 0.8359 (mtp) cc_final: 0.8141 (ttp)
REVERT: C  271 ASN cc_start: 0.5772 (m-40) cc_final: 0.5401 (m-40)
REVERT: C  407 MET cc_start: 0.9006 (tpp) cc_final: 0.8390 (mmm)
REVERT: C  416 THR cc_start: 0.8660 (m) cc_final: 0.8332 (p)
REVERT: C  568 MET cc_start: 0.7106 (ttm) cc_final: 0.6615 (ttt)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0812
  time to fit residues: 7.5303
Evaluate side-chains
  63 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  447 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0370
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0070
   chunk 16 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.2974

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.162395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.136481 restraints weight = 5712.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.140252 restraints weight = 3293.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.142647 restraints weight = 2343.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.144326 restraints weight = 1884.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.145204 restraints weight = 1623.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4768  Z= 0.118
  Angle     :  0.518   6.853   6521  Z= 0.262
  Chirality :  0.040   0.278    764
  Planarity :  0.004   0.079    794
  Dihedral  :  6.015  79.565    691
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.13 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.09 (0.35), residues: 598
  helix:  2.16 (0.25), residues: 446
  sheet:  0.65 (1.34), residues: 12
  loop : -1.15 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 488 
 TYR   0.011   0.001   TYR C 463 
 PHE   0.011   0.001   PHE C 250 
 TRP   0.007   0.001   TRP C 178 
 HIS   0.002   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4764)
  covalent geometry    : angle       0.50788 ( 6511)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.53975 (    4)
  hydrogen bonds       : bond        0.04386 (  335)
  hydrogen bonds       : angle       4.23496 (  999)
  link_NAG-ASN         : bond        0.00464 (    2)
  link_NAG-ASN         : angle       3.34294 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.172 
Fit side-chains
REVERT: C   70 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7418 (mmm-85)
REVERT: C   71 GLN cc_start: 0.7564 (tt0) cc_final: 0.7360 (tt0)
REVERT: C   84 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (tt)
REVERT: C  271 ASN cc_start: 0.5694 (m-40) cc_final: 0.5365 (m-40)
REVERT: C  365 ASP cc_start: 0.8464 (m-30) cc_final: 0.8241 (m-30)
REVERT: C  387 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6697 (p)
REVERT: C  416 THR cc_start: 0.8477 (m) cc_final: 0.8141 (p)
REVERT: C  508 MET cc_start: 0.7188 (mmm) cc_final: 0.6651 (mmm)
REVERT: C  521 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7947 (m-10)
REVERT: C  568 MET cc_start: 0.7111 (ttm) cc_final: 0.6714 (ttt)
  outliers start: 12
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0695
  time to fit residues: 6.7034
Evaluate side-chains
  69 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0170
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.4818

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.161575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.135003 restraints weight = 5642.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.138827 restraints weight = 3255.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.141286 restraints weight = 2312.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.142712 restraints weight = 1864.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.143859 restraints weight = 1630.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4768  Z= 0.120
  Angle     :  0.489   6.233   6521  Z= 0.246
  Chirality :  0.039   0.270    764
  Planarity :  0.004   0.062    794
  Dihedral  :  5.833  77.085    690
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.55 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.25 (0.34), residues: 598
  helix:  2.24 (0.24), residues: 446
  sheet:  0.67 (1.28), residues: 12
  loop : -0.96 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 488 
 TYR   0.010   0.001   TYR C 101 
 PHE   0.013   0.001   PHE C 295 
 TRP   0.008   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4764)
  covalent geometry    : angle       0.48036 ( 6511)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.54431 (    4)
  hydrogen bonds       : bond        0.04158 (  335)
  hydrogen bonds       : angle       3.97321 (  999)
  link_NAG-ASN         : bond        0.00432 (    2)
  link_NAG-ASN         : angle       3.08331 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.169 
Fit side-chains
REVERT: C   70 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7339 (mtp180)
REVERT: C  365 ASP cc_start: 0.8426 (m-30) cc_final: 0.8148 (m-30)
REVERT: C  387 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7096 (p)
REVERT: C  508 MET cc_start: 0.7212 (mmm) cc_final: 0.6582 (mmm)
REVERT: C  521 PHE cc_start: 0.8199 (m-10) cc_final: 0.7949 (m-10)
REVERT: C  568 MET cc_start: 0.7214 (ttm) cc_final: 0.6835 (ttt)
  outliers start: 10
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0752
  time to fit residues: 6.9710
Evaluate side-chains
  66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    0.0000
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.158693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.132060 restraints weight = 5686.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.135833 restraints weight = 3322.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.138076 restraints weight = 2377.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.139736 restraints weight = 1937.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.140588 restraints weight = 1691.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.137
  Angle     :  0.506   5.947   6521  Z= 0.253
  Chirality :  0.040   0.267    764
  Planarity :  0.004   0.054    794
  Dihedral  :  5.840  77.047    690
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.55 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.22 (0.34), residues: 598
  helix:  2.20 (0.24), residues: 448
  sheet:  0.68 (1.27), residues: 12
  loop : -0.92 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  30 
 TYR   0.010   0.001   TYR C 101 
 PHE   0.015   0.001   PHE C 295 
 TRP   0.008   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4764)
  covalent geometry    : angle       0.49780 ( 6511)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.66622 (    4)
  hydrogen bonds       : bond        0.04208 (  335)
  hydrogen bonds       : angle       3.95976 (  999)
  link_NAG-ASN         : bond        0.00393 (    2)
  link_NAG-ASN         : angle       3.02278 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  750 MET cc_start: 0.7666 (tpp) cc_final: 0.7415 (tpp)
REVERT: C   70 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7397 (mtp180)
REVERT: C  183 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7593 (tp)
REVERT: C  365 ASP cc_start: 0.8375 (m-30) cc_final: 0.8033 (m-30)
REVERT: C  387 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7155 (p)
REVERT: C  508 MET cc_start: 0.7305 (mmm) cc_final: 0.6654 (mmm)
REVERT: C  521 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (m-10)
REVERT: C  568 MET cc_start: 0.7219 (ttm) cc_final: 0.6871 (ttt)
  outliers start: 15
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0725
  time to fit residues: 6.8332
Evaluate side-chains
  69 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.160795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.134042 restraints weight = 5705.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.137689 restraints weight = 3303.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.139979 restraints weight = 2379.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.141649 restraints weight = 1937.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.142525 restraints weight = 1688.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.141
  Angle     :  0.507   5.892   6521  Z= 0.255
  Chirality :  0.041   0.260    764
  Planarity :  0.003   0.050    794
  Dihedral  :  5.843  76.363    690
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.76 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.36 (0.34), residues: 598
  helix:  2.33 (0.23), residues: 439
  sheet:  0.80 (1.30), residues: 12
  loop : -0.79 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 488 
 TYR   0.013   0.001   TYR C  21 
 PHE   0.016   0.001   PHE C 295 
 TRP   0.009   0.001   TRP C 111 
 HIS   0.002   0.000   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4764)
  covalent geometry    : angle       0.49976 ( 6511)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       0.69039 (    4)
  hydrogen bonds       : bond        0.04278 (  335)
  hydrogen bonds       : angle       3.90943 (  999)
  link_NAG-ASN         : bond        0.00402 (    2)
  link_NAG-ASN         : angle       2.90959 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 MET cc_start: 0.7722 (tpp) cc_final: 0.7453 (tpp)
REVERT: C   70 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7323 (mtp180)
REVERT: C  271 ASN cc_start: 0.6212 (m-40) cc_final: 0.5975 (m-40)
REVERT: C  365 ASP cc_start: 0.8387 (m-30) cc_final: 0.8117 (m-30)
REVERT: C  387 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7292 (p)
REVERT: C  508 MET cc_start: 0.7039 (mmm) cc_final: 0.6523 (mmm)
REVERT: C  521 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7843 (m-10)
REVERT: C  568 MET cc_start: 0.7251 (ttm) cc_final: 0.6875 (ttt)
  outliers start: 17
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0791
  time to fit residues: 7.0296
Evaluate side-chains
  68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.9184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.158718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.131664 restraints weight = 5744.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.135408 restraints weight = 3338.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.137753 restraints weight = 2395.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.138817 restraints weight = 1949.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.140055 restraints weight = 1750.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4768  Z= 0.169
  Angle     :  0.536   6.073   6521  Z= 0.270
  Chirality :  0.042   0.263    764
  Planarity :  0.003   0.048    794
  Dihedral  :  5.945  76.904    690
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.55 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.23 (0.33), residues: 598
  helix:  2.26 (0.23), residues: 437
  sheet:  0.77 (1.33), residues: 12
  loop : -0.89 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  30 
 TYR   0.012   0.001   TYR C  21 
 PHE   0.017   0.001   PHE C 295 
 TRP   0.010   0.001   TRP C 111 
 HIS   0.002   0.001   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 4764)
  covalent geometry    : angle       0.52814 ( 6511)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.77911 (    4)
  hydrogen bonds       : bond        0.04592 (  335)
  hydrogen bonds       : angle       3.98116 (  999)
  link_NAG-ASN         : bond        0.00374 (    2)
  link_NAG-ASN         : angle       2.95607 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  750 MET cc_start: 0.7835 (tpp) cc_final: 0.7576 (tpp)
REVERT: C   70 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7415 (mtp180)
REVERT: C   84 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8171 (tt)
REVERT: C  183 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7513 (tp)
REVERT: C  271 ASN cc_start: 0.6291 (m-40) cc_final: 0.6074 (m-40)
REVERT: C  365 ASP cc_start: 0.8399 (m-30) cc_final: 0.8116 (m-30)
REVERT: C  508 MET cc_start: 0.7106 (mmm) cc_final: 0.6600 (mmm)
REVERT: C  521 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7874 (m-10)
REVERT: C  568 MET cc_start: 0.7333 (ttm) cc_final: 0.6993 (ttt)
  outliers start: 18
  outliers final: 12
  residues processed: 73
  average time/residue: 0.0749
  time to fit residues: 6.9992
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  336 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0060
   chunk 27 optimal weight:    0.1980
   chunk 55 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.162459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.135604 restraints weight = 5655.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.139444 restraints weight = 3200.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.141981 restraints weight = 2273.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.143318 restraints weight = 1828.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.144549 restraints weight = 1608.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4768  Z= 0.108
  Angle     :  0.478   5.678   6521  Z= 0.239
  Chirality :  0.039   0.241    764
  Planarity :  0.003   0.046    794
  Dihedral  :  5.728  76.568    690
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.39 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.59 (0.34), residues: 598
  helix:  2.53 (0.24), residues: 439
  sheet:  0.85 (1.36), residues: 12
  loop : -0.81 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 488 
 TYR   0.012   0.001   TYR C 101 
 PHE   0.012   0.001   PHE C 250 
 TRP   0.008   0.001   TRP C 111 
 HIS   0.000   0.000   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4764)
  covalent geometry    : angle       0.47110 ( 6511)
  SS BOND              : bond        0.00087 (    2)
  SS BOND              : angle       0.58200 (    4)
  hydrogen bonds       : bond        0.03925 (  335)
  hydrogen bonds       : angle       3.81554 (  999)
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       2.78701 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 MET cc_start: 0.7711 (tpp) cc_final: 0.7464 (tpp)
REVERT: C   70 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7325 (mtp180)
REVERT: C   84 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: C  365 ASP cc_start: 0.8384 (m-30) cc_final: 0.8077 (m-30)
REVERT: C  387 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7319 (p)
REVERT: C  508 MET cc_start: 0.7234 (mmm) cc_final: 0.6628 (mmm)
REVERT: C  521 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7801 (m-10)
REVERT: C  568 MET cc_start: 0.7142 (ttm) cc_final: 0.6823 (ttt)
  outliers start: 15
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0762
  time to fit residues: 6.8121
Evaluate side-chains
  69 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  447 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.161206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.134023 restraints weight = 5760.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.137882 restraints weight = 3261.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.140103 restraints weight = 2314.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.141838 restraints weight = 1888.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.142724 restraints weight = 1646.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.126
  Angle     :  0.495   5.834   6521  Z= 0.247
  Chirality :  0.040   0.242    764
  Planarity :  0.003   0.045    794
  Dihedral  :  5.748  76.464    690
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.39 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.56 (0.34), residues: 598
  helix:  2.50 (0.23), residues: 439
  sheet:  0.93 (1.36), residues: 12
  loop : -0.83 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.012   0.001   TYR C  21 
 PHE   0.013   0.001   PHE C 295 
 TRP   0.009   0.001   TRP C 111 
 HIS   0.001   0.000   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4764)
  covalent geometry    : angle       0.48875 ( 6511)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.61148 (    4)
  hydrogen bonds       : bond        0.04081 (  335)
  hydrogen bonds       : angle       3.82357 (  999)
  link_NAG-ASN         : bond        0.00372 (    2)
  link_NAG-ASN         : angle       2.68766 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 MET cc_start: 0.7757 (tpp) cc_final: 0.7507 (tpp)
REVERT: C   70 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7345 (mtp180)
REVERT: C   84 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7902 (tt)
REVERT: C  365 ASP cc_start: 0.8335 (m-30) cc_final: 0.7987 (m-30)
REVERT: C  387 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (p)
REVERT: C  508 MET cc_start: 0.7197 (mmm) cc_final: 0.6544 (mmm)
REVERT: C  515 LEU cc_start: 0.7705 (mm) cc_final: 0.7486 (mm)
REVERT: C  521 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7803 (m-10)
REVERT: C  540 ASP cc_start: 0.7102 (t0) cc_final: 0.6616 (t0)
REVERT: C  568 MET cc_start: 0.7207 (ttm) cc_final: 0.6891 (ttt)
  outliers start: 15
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0753
  time to fit residues: 6.7883
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  447 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.159842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.132816 restraints weight = 5629.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.136567 restraints weight = 3273.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.138700 restraints weight = 2350.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.140412 restraints weight = 1931.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.141336 restraints weight = 1687.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4768  Z= 0.146
  Angle     :  0.513   5.943   6521  Z= 0.257
  Chirality :  0.041   0.243    764
  Planarity :  0.003   0.044    794
  Dihedral  :  5.820  76.431    690
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.02 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.50 (0.33), residues: 598
  helix:  2.49 (0.23), residues: 433
  sheet:  0.92 (1.35), residues: 12
  loop : -0.82 (0.49), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 488 
 TYR   0.012   0.001   TYR C  21 
 PHE   0.014   0.001   PHE C 295 
 TRP   0.009   0.001   TRP C 111 
 HIS   0.002   0.001   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4764)
  covalent geometry    : angle       0.50702 ( 6511)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.67746 (    4)
  hydrogen bonds       : bond        0.04316 (  335)
  hydrogen bonds       : angle       3.89201 (  999)
  link_NAG-ASN         : bond        0.00360 (    2)
  link_NAG-ASN         : angle       2.69166 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  750 MET cc_start: 0.7802 (tpp) cc_final: 0.7546 (tpp)
REVERT: C   70 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7335 (mtp180)
REVERT: C   84 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: C  365 ASP cc_start: 0.8267 (m-30) cc_final: 0.7921 (m-30)
REVERT: C  387 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7262 (p)
REVERT: C  508 MET cc_start: 0.7039 (mmm) cc_final: 0.6572 (mmm)
REVERT: C  521 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7822 (m-10)
REVERT: C  540 ASP cc_start: 0.7151 (t0) cc_final: 0.6661 (t0)
REVERT: C  568 MET cc_start: 0.7217 (ttm) cc_final: 0.6910 (ttt)
  outliers start: 15
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0788
  time to fit residues: 7.2067
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  447 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.159277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.132243 restraints weight = 5653.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.135990 restraints weight = 3254.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.138168 restraints weight = 2330.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.139549 restraints weight = 1911.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.140720 restraints weight = 1691.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4768  Z= 0.127
  Angle     :  0.500   5.855   6521  Z= 0.249
  Chirality :  0.040   0.235    764
  Planarity :  0.003   0.044    794
  Dihedral  :  5.762  76.487    690
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.02 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.53 (0.34), residues: 598
  helix:  2.48 (0.23), residues: 439
  sheet:  0.98 (1.37), residues: 12
  loop : -0.83 (0.50), residues: 147

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4764)
  covalent geometry    : angle       0.49345 ( 6511)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       0.60000 (    4)
  hydrogen bonds       : bond        0.04115 (  335)
  hydrogen bonds       : angle       3.84164 (  999)
  link_NAG-ASN         : bond        0.00358 (    2)
  link_NAG-ASN         : angle       2.66719 (    6)

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

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

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

  1196 Ramachandran restraints generated.
    598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 MET cc_start: 0.7758 (tpp) cc_final: 0.7493 (tpp)
REVERT: C   70 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7377 (mtp180)
REVERT: C  365 ASP cc_start: 0.8260 (m-30) cc_final: 0.7906 (m-30)
REVERT: C  387 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7276 (p)
REVERT: C  508 MET cc_start: 0.7195 (mmm) cc_final: 0.6572 (mmm)
REVERT: C  521 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7837 (m-10)
REVERT: C  540 ASP cc_start: 0.7132 (t0) cc_final: 0.6652 (t0)
REVERT: C  568 MET cc_start: 0.7215 (ttm) cc_final: 0.6921 (ttt)
  outliers start: 15
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0741
  time to fit residues: 6.6818
Evaluate side-chains
  70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  742 TRP
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain C residue   33 TYR
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  447 VAL
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  521 PHE
Chi-restraints excluded: chain C residue  569 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.160071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.132848 restraints weight = 5749.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.136662 restraints weight = 3321.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.138995 restraints weight = 2370.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.140469 restraints weight = 1937.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.141409 restraints weight = 1699.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4768  Z= 0.145
  Angle     :  0.539  10.700   6521  Z= 0.263
  Chirality :  0.041   0.236    764
  Planarity :  0.003   0.043    794
  Dihedral  :  5.813  76.566    690
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.02 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.46 (0.33), residues: 598
  helix:  2.42 (0.23), residues: 439
  sheet:  1.03 (1.37), residues: 12
  loop : -0.83 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 488 
 TYR   0.012   0.001   TYR C  21 
 PHE   0.014   0.001   PHE C 295 
 TRP   0.009   0.001   TRP C 111 
 HIS   0.002   0.001   HIS C 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4764)
  covalent geometry    : angle       0.53275 ( 6511)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.66914 (    4)
  hydrogen bonds       : bond        0.04287 (  335)
  hydrogen bonds       : angle       3.88245 (  999)
  link_NAG-ASN         : bond        0.00343 (    2)
  link_NAG-ASN         : angle       2.63340 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 877.74 seconds
wall clock time: 15 minutes 48.97 seconds (948.97 seconds total)