Starting phenix.real_space_refine
on Fri Aug 22 14:12:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j75_36027/08_2025/8j75_36027.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.074
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2625      2.51       5
     N     605      2.21       5
     O     707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3956
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 3887
          Classifications: {'peptide': 515}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 22, 'TRANS': 492}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'HC6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.18, per 1000 atoms: 0.30
  Number of scatterers: 3956
  At special positions: 0
  Unit cell: (87.74, 73.8, 86.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     707      8.00
     N     605      7.00
     C    2625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 301 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 168.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  936

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 1 sheets defined
      76.7% alpha, 0.8% 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 4 through 30
      removed outlier: 3.934A  pdb=" N   LEU A   8 " --> pdb=" O   HIS A   4 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG A  28 " --> pdb=" O   TRP A  24 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 50 through 63
      removed outlier: 3.559A  pdb=" N   GLY A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 77
    Processing helix  chain 'A' and resid 81 through 84
    Processing helix  chain 'A' and resid 85 through 102
      removed outlier: 4.702A  pdb=" N   ILE A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 110
      removed outlier: 3.712A  pdb=" N   LYS A 109 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   GLY A 110 " --> pdb=" O   MET A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 123 through 157
      removed outlier: 3.555A  pdb=" N   LEU A 129 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ILE A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      Proline residue:  A 133  - end of helix
    Processing helix  chain 'A' and resid 160 through 179
      removed outlier: 4.023A  pdb=" N   SER A 164 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 208
      removed outlier: 3.675A  pdb=" N   VAL A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 237 through 250
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 266 through 297
      removed outlier: 4.023A  pdb=" N   ILE A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 299 through 303
    Processing helix  chain 'A' and resid 309 through 313
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 318 through 327
      removed outlier: 3.620A  pdb=" N   ILE A 322 " --> pdb=" O   MET A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 368
      removed outlier: 3.973A  pdb=" N   PHE A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 366 " --> pdb=" O   ASN A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 398
      removed outlier: 3.538A  pdb=" N   VAL A 378 " --> pdb=" O   ASP A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 427
      removed outlier: 4.641A  pdb=" N   PHE A 418 " --> pdb=" O   TYR A 414 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 450
      removed outlier: 3.596A  pdb=" N   ALA A 435 " --> pdb=" O   ASN A 431 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 502
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 467

    273 hydrogen bonds defined for protein.
    804 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: 0.57

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1132
        1.34 -     1.46: 833
        1.46 -     1.58: 2066
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 4065
  Sorted by residual:
  bond pdb=" C   TYR A 462 "
       pdb=" N   PRO A 463 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.035 1.30e-02 5.92e+03 7.06e+00
  bond pdb=" N   VAL A 237 "
       pdb=" CA  VAL A 237 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.12e+00
  bond pdb=" CA  TYR A 462 "
       pdb=" CB  TYR A 462 "
    ideal  model  delta    sigma   weight residual
    1.528  1.489  0.039 1.57e-02 4.06e+03 6.11e+00
  bond pdb=" N   TYR A  67 "
       pdb=" CA  TYR A  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.31e+00
  bond pdb=" N   GLU A 236 "
       pdb=" CA  GLU A 236 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.024 1.20e-02 6.94e+03 4.13e+00
  ... (remaining 4060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 5368
        1.70 -     3.40: 147
        3.40 -     5.10: 32
        5.10 -     6.81: 11
        6.81 -     8.51: 4
  Bond angle restraints: 5562
  Sorted by residual:
  angle pdb=" N   PRO A 508 "
        pdb=" CA  PRO A 508 "
        pdb=" C   PRO A 508 "
      ideal   model   delta    sigma   weight residual
     110.70  114.66   -3.96 1.22e+00 6.72e-01 1.05e+01
  angle pdb=" CB  MET A 139 "
        pdb=" CG  MET A 139 "
        pdb=" SD  MET A 139 "
      ideal   model   delta    sigma   weight residual
     112.70  121.21   -8.51 3.00e+00 1.11e-01 8.04e+00
  angle pdb=" N   GLY A  79 "
        pdb=" CA  GLY A  79 "
        pdb=" C   GLY A  79 "
      ideal   model   delta    sigma   weight residual
     114.67  110.71    3.96 1.41e+00 5.03e-01 7.90e+00
  angle pdb=" N   TYR A 462 "
        pdb=" CA  TYR A 462 "
        pdb=" C   TYR A 462 "
      ideal   model   delta    sigma   weight residual
     109.48  113.24   -3.76 1.44e+00 4.82e-01 6.81e+00
  angle pdb=" N   VAL A 220 "
        pdb=" CA  VAL A 220 "
        pdb=" C   VAL A 220 "
      ideal   model   delta    sigma   weight residual
     109.34  114.63   -5.29 2.08e+00 2.31e-01 6.48e+00
  ... (remaining 5557 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.99: 2188
       25.99 -    51.98: 136
       51.98 -    77.97: 17
       77.97 -   103.96: 21
      103.96 -   129.95: 4
  Dihedral angle restraints: 2366
    sinusoidal: 887
      harmonic: 1479
  Sorted by residual:
  dihedral pdb=" CAS HC6 A 601 "
           pdb=" CAU HC6 A 601 "
           pdb=" OAT HC6 A 601 "
           pdb=" CAV HC6 A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.78   70.17 -129.95     1      3.00e+01 1.11e-03 1.75e+01
  dihedral pdb=" CAB HC6 A 601 "
           pdb=" CAF HC6 A 601 "
           pdb=" OAE HC6 A 601 "
           pdb=" CAD HC6 A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.04  -70.03  129.07     1      3.00e+01 1.11e-03 1.74e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  179.99  108.72     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 2363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 523
       0.055 -    0.109: 119
       0.109 -    0.164: 7
       0.164 -    0.219: 1
       0.219 -    0.274: 2
  Chirality restraints: 652
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  VAL A 237 "
            pdb=" N   VAL A 237 "
            pdb=" C   VAL A 237 "
            pdb=" CB  VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  TYR A 238 "
            pdb=" N   TYR A 238 "
            pdb=" C   TYR A 238 "
            pdb=" CB  TYR A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.60e-01
  ... (remaining 649 not shown)

  Planarity restraints: 675
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAD HC6 A 601 "   -0.030 2.00e-02 2.50e+03   1.76e-02 6.18e+00
        pdb=" CAG HC6 A 601 "    0.009 2.00e-02 2.50e+03
        pdb=" CAH HC6 A 601 "    0.010 2.00e-02 2.50e+03
        pdb=" CAI HC6 A 601 "    0.010 2.00e-02 2.50e+03
        pdb=" CAJ HC6 A 601 "    0.009 2.00e-02 2.50e+03
        pdb=" CAK HC6 A 601 "    0.010 2.00e-02 2.50e+03
        pdb=" CAL HC6 A 601 "    0.011 2.00e-02 2.50e+03
        pdb=" CAM HC6 A 601 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 451 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 452 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 452 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 452 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 461 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   PHE A 461 "    0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 461 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A 462 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 672 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1037
        2.79 -     3.32: 3999
        3.32 -     3.84: 6572
        3.84 -     4.37: 7148
        4.37 -     4.90: 12449
  Nonbonded interactions: 31205
  Sorted by model distance:
  nonbonded pdb=" O3  NAG B   2 "
            pdb=" O2  BMA B   3 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ALA A 390 "
            pdb=" OG1 THR A 393 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ALA A 213 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" NH2 ARG A  47 "
            pdb=" O   TYR A 111 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" N   SER A  34 "
            pdb=" OE1 GLU A  37 "
     model   vdw
     2.354 3.120
  ... (remaining 31200 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:             1.200
  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:                    0.010
  Process input model:                     5.980
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
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   0.039   4068  Z= 0.201
  Angle     :  0.726   8.507   5571  Z= 0.372
  Chirality :  0.045   0.274    652
  Planarity :  0.005   0.046    674
  Dihedral  : 20.252 129.948   1430
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.99 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.97 %
    Favored  : 73.03 %
  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:  0.40 (0.40), residues: 513
  helix:  1.45 (0.29), residues: 352
  sheet:  None (None), residues: 0
  loop : -2.53 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  28 
 TYR   0.017   0.001   TYR A 175 
 PHE   0.014   0.001   PHE A 244 
 TRP   0.019   0.002   TRP A 228 
 HIS   0.001   0.000   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4065)
  covalent geometry    : angle       0.72112 ( 5562)
  hydrogen bonds       : bond        0.08040 (  273)
  hydrogen bonds       : angle       5.08490 (  804)
  link_BETA1-4         : bond        0.00701 (    2)
  link_BETA1-4         : angle       1.30665 (    6)
  link_NAG-ASN         : bond        0.00328 (    1)
  link_NAG-ASN         : angle       3.45797 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.117 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0552
  time to fit residues: 6.1306
Evaluate side-chains
  84 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.198202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.184134 restraints weight = 6376.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.187456 restraints weight = 3616.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.189723 restraints weight = 2343.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.191249 restraints weight = 1645.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.192176 restraints weight = 1245.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4068  Z= 0.141
  Angle     :  0.677   7.449   5571  Z= 0.329
  Chirality :  0.044   0.293    652
  Planarity :  0.004   0.032    674
  Dihedral  : 14.568  89.957    650
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.19 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 24.43 %
    Favored  : 69.97 %
  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:  0.70 (0.40), residues: 513
  helix:  1.65 (0.29), residues: 354
  sheet:  None (None), residues: 0
  loop : -2.42 (0.51), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 260 
 TYR   0.015   0.001   TYR A 175 
 PHE   0.013   0.001   PHE A 368 
 TRP   0.011   0.001   TRP A  24 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4065)
  covalent geometry    : angle       0.67070 ( 5562)
  hydrogen bonds       : bond        0.04347 (  273)
  hydrogen bonds       : angle       4.65791 (  804)
  link_BETA1-4         : bond        0.00968 (    2)
  link_BETA1-4         : angle       1.84725 (    6)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       3.16004 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.145 
Fit side-chains
  outliers start: 22
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0645
  time to fit residues: 8.1698
Evaluate side-chains
  97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.197511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.183503 restraints weight = 6240.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.186840 restraints weight = 3543.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.189121 restraints weight = 2276.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.190590 restraints weight = 1603.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.191667 restraints weight = 1222.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4068  Z= 0.137
  Angle     :  0.619   7.664   5571  Z= 0.310
  Chirality :  0.042   0.160    652
  Planarity :  0.004   0.035    674
  Dihedral  : 11.467  72.607    650
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.21 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 26.46 %
    Favored  : 67.43 %
  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:  0.77 (0.40), residues: 513
  helix:  1.68 (0.29), residues: 354
  sheet:  None (None), residues: 0
  loop : -2.31 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  28 
 TYR   0.012   0.001   TYR A 111 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.010   0.001   TRP A  24 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4065)
  covalent geometry    : angle       0.61151 ( 5562)
  hydrogen bonds       : bond        0.04301 (  273)
  hydrogen bonds       : angle       4.65667 (  804)
  link_BETA1-4         : bond        0.00908 (    2)
  link_BETA1-4         : angle       1.94763 (    6)
  link_NAG-ASN         : bond        0.00073 (    1)
  link_NAG-ASN         : angle       3.22547 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.139 
Fit side-chains
  outliers start: 24
  outliers final: 20
  residues processed: 98
  average time/residue: 0.0587
  time to fit residues: 7.3784
Evaluate side-chains
  97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  428 LYS
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 50 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.197985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.184110 restraints weight = 6221.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.187461 restraints weight = 3533.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.189764 restraints weight = 2270.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.191290 restraints weight = 1592.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.192333 restraints weight = 1187.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4068  Z= 0.131
  Angle     :  0.609   7.636   5571  Z= 0.306
  Chirality :  0.041   0.156    652
  Planarity :  0.004   0.034    674
  Dihedral  :  9.405  58.310    650
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.41 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 27.23 %
    Favored  : 65.90 %
  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:  0.82 (0.40), residues: 513
  helix:  1.70 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.27 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  28 
 TYR   0.009   0.001   TYR A 111 
 PHE   0.009   0.001   PHE A 140 
 TRP   0.011   0.001   TRP A  24 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4065)
  covalent geometry    : angle       0.60254 ( 5562)
  hydrogen bonds       : bond        0.04161 (  273)
  hydrogen bonds       : angle       4.62115 (  804)
  link_BETA1-4         : bond        0.00910 (    2)
  link_BETA1-4         : angle       1.91687 (    6)
  link_NAG-ASN         : bond        0.00000 (    1)
  link_NAG-ASN         : angle       2.99612 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.4126 (m-70)
  outliers start: 27
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0556
  time to fit residues: 6.9698
Evaluate side-chains
  100 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.200295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.185895 restraints weight = 6263.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.189447 restraints weight = 3547.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.191708 restraints weight = 2273.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.193285 restraints weight = 1601.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.194452 restraints weight = 1205.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4068  Z= 0.133
  Angle     :  0.609   7.735   5571  Z= 0.302
  Chirality :  0.040   0.160    652
  Planarity :  0.004   0.035    674
  Dihedral  :  7.822  42.336    650
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.41 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 27.74 %
    Favored  : 65.65 %
  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:  0.87 (0.40), residues: 513
  helix:  1.73 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.23 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  28 
 TYR   0.013   0.001   TYR A 111 
 PHE   0.009   0.001   PHE A 140 
 TRP   0.010   0.001   TRP A  24 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4065)
  covalent geometry    : angle       0.60256 ( 5562)
  hydrogen bonds       : bond        0.04042 (  273)
  hydrogen bonds       : angle       4.60917 (  804)
  link_BETA1-4         : bond        0.00850 (    2)
  link_BETA1-4         : angle       1.83882 (    6)
  link_NAG-ASN         : bond        0.00025 (    1)
  link_NAG-ASN         : angle       2.97977 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5460 (OUTLIER) cc_final: 0.4180 (m-70)
  outliers start: 26
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0665
  time to fit residues: 8.5819
Evaluate side-chains
  103 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  428 LYS
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.198089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.183552 restraints weight = 6358.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.187083 restraints weight = 3612.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.189483 restraints weight = 2308.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.191041 restraints weight = 1605.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.192134 restraints weight = 1212.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4068  Z= 0.153
  Angle     :  0.647   8.261   5571  Z= 0.321
  Chirality :  0.041   0.137    652
  Planarity :  0.004   0.039    674
  Dihedral  :  6.876  39.732    650
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.38 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 29.01 %
    Favored  : 64.12 %
  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:  0.80 (0.40), residues: 513
  helix:  1.68 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.26 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  28 
 TYR   0.013   0.001   TYR A 175 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.011   0.001   TRP A  24 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4065)
  covalent geometry    : angle       0.64057 ( 5562)
  hydrogen bonds       : bond        0.04307 (  273)
  hydrogen bonds       : angle       4.67226 (  804)
  link_BETA1-4         : bond        0.00925 (    2)
  link_BETA1-4         : angle       1.88193 (    6)
  link_NAG-ASN         : bond        0.00150 (    1)
  link_NAG-ASN         : angle       3.21077 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5478 (OUTLIER) cc_final: 0.4188 (m-70)
REVERT: A  242 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7393 (t0)
  outliers start: 27
  outliers final: 23
  residues processed: 101
  average time/residue: 0.0681
  time to fit residues: 8.7173
Evaluate side-chains
  105 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  428 LYS
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.200510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.186120 restraints weight = 6406.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.189603 restraints weight = 3604.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.192025 restraints weight = 2313.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.193571 restraints weight = 1609.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.194735 restraints weight = 1210.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4068  Z= 0.133
  Angle     :  0.629   7.778   5571  Z= 0.309
  Chirality :  0.040   0.160    652
  Planarity :  0.004   0.035    674
  Dihedral  :  6.258  38.350    650
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.02 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 30.03 %
    Favored  : 63.36 %
  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:  0.86 (0.40), residues: 513
  helix:  1.71 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.21 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  28 
 TYR   0.015   0.001   TYR A 111 
 PHE   0.007   0.001   PHE A 244 
 TRP   0.015   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4065)
  covalent geometry    : angle       0.62282 ( 5562)
  hydrogen bonds       : bond        0.04062 (  273)
  hydrogen bonds       : angle       4.63302 (  804)
  link_BETA1-4         : bond        0.00861 (    2)
  link_BETA1-4         : angle       1.74568 (    6)
  link_NAG-ASN         : bond        0.00049 (    1)
  link_NAG-ASN         : angle       3.11824 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5481 (OUTLIER) cc_final: 0.4198 (m-70)
  outliers start: 26
  outliers final: 22
  residues processed: 99
  average time/residue: 0.0655
  time to fit residues: 8.2812
Evaluate side-chains
  103 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  428 LYS
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.199818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.185621 restraints weight = 6332.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.189087 restraints weight = 3632.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.191301 restraints weight = 2341.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.192886 restraints weight = 1657.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.193912 restraints weight = 1248.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4068  Z= 0.140
  Angle     :  0.658   9.561   5571  Z= 0.323
  Chirality :  0.041   0.183    652
  Planarity :  0.004   0.041    674
  Dihedral  :  5.987  38.566    650
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.80 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 30.28 %
    Favored  : 63.61 %
  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:  0.85 (0.40), residues: 513
  helix:  1.71 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.23 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  28 
 TYR   0.011   0.001   TYR A 175 
 PHE   0.008   0.001   PHE A 140 
 TRP   0.011   0.001   TRP A 240 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4065)
  covalent geometry    : angle       0.65183 ( 5562)
  hydrogen bonds       : bond        0.04121 (  273)
  hydrogen bonds       : angle       4.62035 (  804)
  link_BETA1-4         : bond        0.00886 (    2)
  link_BETA1-4         : angle       1.77510 (    6)
  link_NAG-ASN         : bond        0.00085 (    1)
  link_NAG-ASN         : angle       3.16180 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5473 (OUTLIER) cc_final: 0.4249 (m-70)
  outliers start: 24
  outliers final: 21
  residues processed: 95
  average time/residue: 0.0706
  time to fit residues: 8.5216
Evaluate side-chains
  102 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.200554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.185826 restraints weight = 6454.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.189419 restraints weight = 3660.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.191703 restraints weight = 2343.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.193343 restraints weight = 1653.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.194439 restraints weight = 1237.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4068  Z= 0.137
  Angle     :  0.663   9.258   5571  Z= 0.325
  Chirality :  0.041   0.166    652
  Planarity :  0.004   0.041    674
  Dihedral  :  5.769  38.412    650
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.82 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 30.79 %
    Favored  : 62.85 %
  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:  0.82 (0.41), residues: 513
  helix:  1.62 (0.29), residues: 361
  sheet:  None (None), residues: 0
  loop : -2.20 (0.55), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  28 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.011   0.001   PHE A 140 
 TRP   0.013   0.001   TRP A 240 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4065)
  covalent geometry    : angle       0.65717 ( 5562)
  hydrogen bonds       : bond        0.04118 (  273)
  hydrogen bonds       : angle       4.61610 (  804)
  link_BETA1-4         : bond        0.00872 (    2)
  link_BETA1-4         : angle       1.75054 (    6)
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       3.15474 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.4302 (m-70)
REVERT: A  320 LEU cc_start: 0.8856 (tp) cc_final: 0.8641 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 97
  average time/residue: 0.0632
  time to fit residues: 7.8261
Evaluate side-chains
  102 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  428 LYS
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0010
   chunk 44 optimal weight:    0.0010
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.201054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.187059 restraints weight = 6214.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.190404 restraints weight = 3564.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.192621 restraints weight = 2304.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.194268 restraints weight = 1635.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.195335 restraints weight = 1222.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4068  Z= 0.132
  Angle     :  0.658   8.230   5571  Z= 0.322
  Chirality :  0.040   0.134    652
  Planarity :  0.004   0.039    674
  Dihedral  :  5.608  37.428    650
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.41 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 31.30 %
    Favored  : 63.61 %
  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:  0.90 (0.40), residues: 513
  helix:  1.75 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.23 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  28 
 TYR   0.012   0.001   TYR A 175 
 PHE   0.010   0.001   PHE A 140 
 TRP   0.012   0.001   TRP A 240 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4065)
  covalent geometry    : angle       0.65216 ( 5562)
  hydrogen bonds       : bond        0.03920 (  273)
  hydrogen bonds       : angle       4.56730 (  804)
  link_BETA1-4         : bond        0.00890 (    2)
  link_BETA1-4         : angle       1.71814 (    6)
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       3.06924 (    3)

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

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

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1026 Ramachandran restraints generated.
    513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A    4 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.4259 (m-70)
REVERT: A  139 MET cc_start: 0.7155 (mmm) cc_final: 0.6837 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 91
  average time/residue: 0.0692
  time to fit residues: 7.9654
Evaluate side-chains
  98 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   24 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  490 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.8140

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.198642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.184492 restraints weight = 6227.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.187829 restraints weight = 3559.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.190124 restraints weight = 2305.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.191744 restraints weight = 1629.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.192805 restraints weight = 1222.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4068  Z= 0.149
  Angle     :  0.667   7.856   5571  Z= 0.329
  Chirality :  0.041   0.146    652
  Planarity :  0.004   0.048    674
  Dihedral  :  5.675  39.247    650
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.41 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 31.30 %
    Favored  : 64.12 %
  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:  0.76 (0.40), residues: 513
  helix:  1.66 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.31 (0.54), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  28 
 TYR   0.017   0.001   TYR A 175 
 PHE   0.009   0.001   PHE A 244 
 TRP   0.012   0.001   TRP A 240 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4065)
  covalent geometry    : angle       0.66110 ( 5562)
  hydrogen bonds       : bond        0.04241 (  273)
  hydrogen bonds       : angle       4.62926 (  804)
  link_BETA1-4         : bond        0.00889 (    2)
  link_BETA1-4         : angle       1.78338 (    6)
  link_NAG-ASN         : bond        0.00129 (    1)
  link_NAG-ASN         : angle       3.20853 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 903.19 seconds
wall clock time: 16 minutes 19.63 seconds (979.63 seconds total)