Starting phenix.real_space_refine
on Wed Jul 23 10:12:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2025/7rtv_24690.cif"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
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      25      5.16       5
     C    1846      2.51       5
     N     460      2.21       5
     O     550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2881
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2803
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 7, 'TRANS': 358}
          Chain breaks: 1
    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: "C"
      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
  Time building chain proxies: 2.38, per 1000 atoms: 0.83
  Number of scatterers: 2881
  At special positions: 0
  Unit cell: (62.863, 52.669, 135.92, 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      25     16.00
     O     550      8.00
     N     460      7.00
     C    1846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 129 "
      " NAG C   1 " - " ASN A 352 "
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 348.0 milliseconds
  

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 0 sheets defined
      92.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 73
      removed outlier: 4.152A  pdb=" N   CYS A  73 " --> pdb=" O   CYS A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 161
    Processing helix  chain 'A' and resid 162 through 164
      No H-bonds generated for 'chain 'A' and resid 162 through 164'
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 191 through 236
    Processing helix  chain 'A' and resid 240 through 274
      removed outlier: 3.951A  pdb=" N   LEU A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   CYS A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   CYS A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
      removed outlier: 4.318A  pdb=" N   TYR A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 299
      removed outlier: 3.530A  pdb=" N   THR A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 333
      removed outlier: 3.507A  pdb=" N   LEU A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 366
      removed outlier: 3.618A  pdb=" N   GLU A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 366 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 409
      removed outlier: 4.054A  pdb=" N   ASP A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   GLU A 387 " --> pdb=" O   TYR A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 414

    280 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 903
        1.34 -     1.46: 530
        1.46 -     1.58: 1465
        1.58 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 2932
  Sorted by residual:
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.574 -0.055 2.00e-02 2.50e+03 7.58e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" O5  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.410  1.452 -0.042 2.00e-02 2.50e+03 4.32e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.09e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  ... (remaining 2927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 3857
        1.76 -     3.52: 101
        3.52 -     5.28: 16
        5.28 -     7.05: 10
        7.05 -     8.81: 5
  Bond angle restraints: 3989
  Sorted by residual:
  angle pdb=" C   GLN A 176 "
        pdb=" N   MET A 177 "
        pdb=" CA  MET A 177 "
      ideal   model   delta    sigma   weight residual
     121.58  113.37    8.21 1.95e+00 2.63e-01 1.77e+01
  angle pdb=" CA  MET A 177 "
        pdb=" CB  MET A 177 "
        pdb=" CG  MET A 177 "
      ideal   model   delta    sigma   weight residual
     114.10  120.21   -6.11 2.00e+00 2.50e-01 9.33e+00
  angle pdb=" CB  MET A 174 "
        pdb=" CG  MET A 174 "
        pdb=" SD  MET A 174 "
      ideal   model   delta    sigma   weight residual
     112.70  121.51   -8.81 3.00e+00 1.11e-01 8.62e+00
  angle pdb=" N   MET A 177 "
        pdb=" CA  MET A 177 "
        pdb=" CB  MET A 177 "
      ideal   model   delta    sigma   weight residual
     110.41  115.33   -4.92 1.68e+00 3.54e-01 8.59e+00
  angle pdb=" CA  GLN A 144 "
        pdb=" CB  GLN A 144 "
        pdb=" CG  GLN A 144 "
      ideal   model   delta    sigma   weight residual
     114.10  119.15   -5.05 2.00e+00 2.50e-01 6.37e+00
  ... (remaining 3984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.21: 1630
       24.21 -    48.42: 102
       48.42 -    72.63: 32
       72.63 -    96.84: 10
       96.84 -   121.05: 30
  Dihedral angle restraints: 1804
    sinusoidal: 746
      harmonic: 1058
  Sorted by residual:
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 382 "
           pdb=" CB  CYS A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.83  -79.83     1      1.00e+01 1.00e-02 7.90e+01
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.56  -39.56     1      1.00e+01 1.00e-02 2.20e+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  167.66  121.05     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 1801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 412
       0.054 -    0.107: 78
       0.107 -    0.161: 7
       0.161 -    0.214: 3
       0.214 -    0.268: 2
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  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   -2.54    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 499 not shown)

  Planarity restraints: 488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 410 "   -0.053 5.00e-02 4.00e+02   8.01e-02 1.03e+01
        pdb=" N   PRO A 411 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 411 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 411 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 381 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   ILE A 381 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE A 381 "    0.010 2.00e-02 2.50e+03
        pdb=" N   CYS A 382 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 382 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.11e+00
        pdb=" C   CYS A 382 "    0.025 2.00e-02 2.50e+03
        pdb=" O   CYS A 382 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   TYR A 383 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 485 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 387
        2.75 -     3.28: 3201
        3.28 -     3.82: 5090
        3.82 -     4.36: 5147
        4.36 -     4.90: 8800
  Nonbonded interactions: 22625
  Sorted by model distance:
  nonbonded pdb=" O   SER A 256 "
            pdb=" OG  SER A 396 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   GLY A 117 "
            pdb=" NE2 GLN A 120 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   SER A 183 "
            pdb=" OG  SER A 186 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   CYS A 300 "
            pdb=" NH2 ARG A 368 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" ND2 ASN A 115 "
            pdb=" OE2 GLU A 209 "
     model   vdw
     2.319 3.120
  ... (remaining 22620 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.120
  Find NCS groups from input model:        0.040
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
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   0.055   2940  Z= 0.182
  Angle     :  0.775   8.808   4011  Z= 0.353
  Chirality :  0.045   0.268    502
  Planarity :  0.005   0.080    486
  Dihedral  : 24.992 121.052   1118
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.95 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.44), residues: 362
  helix:  2.84 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.76 (1.14), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.022   0.002   PHE A 220 
 TYR   0.015   0.001   TYR A  66 
 ARG   0.003   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00600 (    2)
  link_NAG-ASN         : angle       2.99834 (    6)
  link_BETA1-4         : bond        0.00599 (    4)
  link_BETA1-4         : angle       1.29551 (   12)
  hydrogen bonds       : bond        0.07293 (  280)
  hydrogen bonds       : angle       4.57725 (  834)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       1.91192 (    4)
  covalent geometry    : bond        0.00369 ( 2932)
  covalent geometry    : angle       0.76286 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  127 ASN cc_start: 0.7972 (m110) cc_final: 0.7152 (m-40)
REVERT: A  132 PHE cc_start: 0.7293 (m-80) cc_final: 0.7026 (m-10)
REVERT: A  177 MET cc_start: 0.7020 (pmm) cc_final: 0.6597 (pmm)
REVERT: A  372 LYS cc_start: 0.8838 (tttp) cc_final: 0.8365 (tttm)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1310
  time to fit residues: 15.1073
Evaluate side-chains
  76 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0770
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 GLN
A 359 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.233262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.199976 restraints weight = 4578.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.206104 restraints weight = 2902.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.210287 restraints weight = 2046.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2940  Z= 0.139
  Angle     :  0.771   8.350   4011  Z= 0.349
  Chirality :  0.045   0.249    502
  Planarity :  0.004   0.048    486
  Dihedral  : 24.778 111.491    511
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.66 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.62 (0.43), residues: 362
  helix:  2.84 (0.27), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.81 (1.13), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.016   0.002   PHE A 395 
 TYR   0.020   0.001   TYR A 296 
 ARG   0.003   0.000   ARG A 236 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00718 (    2)
  link_NAG-ASN         : angle       3.58859 (    6)
  link_BETA1-4         : bond        0.00640 (    4)
  link_BETA1-4         : angle       2.85310 (   12)
  hydrogen bonds       : bond        0.03545 (  280)
  hydrogen bonds       : angle       4.11419 (  834)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       0.89576 (    4)
  covalent geometry    : bond        0.00281 ( 2932)
  covalent geometry    : angle       0.74355 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  127 ASN cc_start: 0.7643 (m110) cc_final: 0.6788 (m-40)
REVERT: A  150 LEU cc_start: 0.7939 (mt) cc_final: 0.7730 (mt)
REVERT: A  177 MET cc_start: 0.7168 (pmm) cc_final: 0.6560 (pmm)
REVERT: A  401 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 91
  average time/residue: 0.1198
  time to fit residues: 13.5236
Evaluate side-chains
  82 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.232750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.199053 restraints weight = 4492.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.204997 restraints weight = 2885.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.208922 restraints weight = 2066.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2940  Z= 0.140
  Angle     :  0.784   9.900   4011  Z= 0.347
  Chirality :  0.045   0.244    502
  Planarity :  0.004   0.036    486
  Dihedral  : 21.826 113.403    511
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.23 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.44 (0.43), residues: 362
  helix:  2.76 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.06 (1.09), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.019   0.002   PHE A 315 
 TYR   0.006   0.001   TYR A  66 
 ARG   0.003   0.001   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00704 (    2)
  link_NAG-ASN         : angle       3.78534 (    6)
  link_BETA1-4         : bond        0.00797 (    4)
  link_BETA1-4         : angle       2.80231 (   12)
  hydrogen bonds       : bond        0.03405 (  280)
  hydrogen bonds       : angle       4.07769 (  834)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.95002 (    4)
  covalent geometry    : bond        0.00285 ( 2932)
  covalent geometry    : angle       0.75610 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7892 (m110) cc_final: 0.7324 (m-40)
REVERT: A  132 PHE cc_start: 0.7285 (m-80) cc_final: 0.7073 (m-80)
REVERT: A  177 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6685 (pmm)
REVERT: A  392 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7728 (tt)
REVERT: A  401 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8410 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1289
  time to fit residues: 14.2944
Evaluate side-chains
  88 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0040
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.235224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.201977 restraints weight = 4450.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.207711 restraints weight = 2819.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.211754 restraints weight = 2012.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.4496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6425
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2940  Z= 0.132
  Angle     :  0.820  10.072   4011  Z= 0.354
  Chirality :  0.049   0.322    502
  Planarity :  0.004   0.029    486
  Dihedral  : 19.817 113.581    511
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.51 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.43), residues: 362
  helix:  2.78 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.97 (1.12), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 257 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.012   0.001   PHE A 395 
 TYR   0.005   0.001   TYR A  66 
 ARG   0.003   0.000   ARG A 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00804 (    2)
  link_NAG-ASN         : angle       3.99159 (    6)
  link_BETA1-4         : bond        0.00797 (    4)
  link_BETA1-4         : angle       2.86975 (   12)
  hydrogen bonds       : bond        0.03330 (  280)
  hydrogen bonds       : angle       4.05398 (  834)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.97091 (    4)
  covalent geometry    : bond        0.00268 ( 2932)
  covalent geometry    : angle       0.79101 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.7374 (t0) cc_final: 0.7166 (t0)
REVERT: A  127 ASN cc_start: 0.7588 (m110) cc_final: 0.7093 (m-40)
REVERT: A  143 THR cc_start: 0.8849 (p) cc_final: 0.8406 (t)
REVERT: A  177 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6718 (pmm)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1139
  time to fit residues: 13.9033
Evaluate side-chains
  96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  389 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    0.0060
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.232743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.198391 restraints weight = 4595.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.204427 restraints weight = 2909.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.208719 restraints weight = 2068.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2940  Z= 0.139
  Angle     :  0.843  10.509   4011  Z= 0.368
  Chirality :  0.048   0.268    502
  Planarity :  0.004   0.043    486
  Dihedral  : 18.036 112.999    511
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.08 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.44), residues: 362
  helix:  2.80 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.92 (1.15), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.012   0.001   PHE A 132 
 TYR   0.005   0.001   TYR A 280 
 ARG   0.013   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00874 (    2)
  link_NAG-ASN         : angle       4.27268 (    6)
  link_BETA1-4         : bond        0.00862 (    4)
  link_BETA1-4         : angle       2.94534 (   12)
  hydrogen bonds       : bond        0.03363 (  280)
  hydrogen bonds       : angle       4.01441 (  834)
  SS BOND              : bond        0.00031 (    2)
  SS BOND              : angle       0.98051 (    4)
  covalent geometry    : bond        0.00286 ( 2932)
  covalent geometry    : angle       0.81226 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7621 (m110) cc_final: 0.7109 (m-40)
REVERT: A  143 THR cc_start: 0.8883 (p) cc_final: 0.8439 (t)
REVERT: A  177 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6212 (pmm)
REVERT: A  236 ARG cc_start: 0.5551 (tpp80) cc_final: 0.5175 (tpp-160)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1312
  time to fit residues: 15.0747
Evaluate side-chains
  93 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  389 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.232656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.198528 restraints weight = 4608.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.204605 restraints weight = 2912.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.208854 restraints weight = 2058.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2940  Z= 0.144
  Angle     :  0.883  11.626   4011  Z= 0.380
  Chirality :  0.049   0.324    502
  Planarity :  0.004   0.058    486
  Dihedral  : 16.264 110.660    511
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.73 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.44), residues: 362
  helix:  2.77 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.89 (1.14), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.013   0.002   PHE A 308 
 TYR   0.009   0.001   TYR A  41 
 ARG   0.011   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00937 (    2)
  link_NAG-ASN         : angle       4.61569 (    6)
  link_BETA1-4         : bond        0.00900 (    4)
  link_BETA1-4         : angle       3.16241 (   12)
  hydrogen bonds       : bond        0.03328 (  280)
  hydrogen bonds       : angle       4.03109 (  834)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       1.13125 (    4)
  covalent geometry    : bond        0.00304 ( 2932)
  covalent geometry    : angle       0.84862 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7390 (m110) cc_final: 0.6620 (m-40)
REVERT: A  143 THR cc_start: 0.8874 (p) cc_final: 0.8446 (t)
REVERT: A  177 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6228 (pmm)
REVERT: A  192 ARG cc_start: 0.6558 (tmt-80) cc_final: 0.6341 (tmt-80)
REVERT: A  236 ARG cc_start: 0.5559 (tpp80) cc_final: 0.5188 (tpp-160)
  outliers start: 15
  outliers final: 13
  residues processed: 93
  average time/residue: 0.1321
  time to fit residues: 15.0595
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.231832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.198393 restraints weight = 4701.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.204665 restraints weight = 2941.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.208818 restraints weight = 2055.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2940  Z= 0.140
  Angle     :  0.891  12.851   4011  Z= 0.383
  Chirality :  0.045   0.296    502
  Planarity :  0.004   0.036    486
  Dihedral  : 15.000 107.757    511
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 22.40 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.44), residues: 362
  helix:  2.77 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.85 (1.14), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.012   0.002   PHE A 273 
 TYR   0.008   0.001   TYR A 280 
 ARG   0.007   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01013 (    2)
  link_NAG-ASN         : angle       4.92786 (    6)
  link_BETA1-4         : bond        0.00957 (    4)
  link_BETA1-4         : angle       3.41500 (   12)
  hydrogen bonds       : bond        0.03339 (  280)
  hydrogen bonds       : angle       4.10592 (  834)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       0.92358 (    4)
  covalent geometry    : bond        0.00293 ( 2932)
  covalent geometry    : angle       0.85148 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 THR cc_start: 0.8882 (p) cc_final: 0.8460 (t)
REVERT: A  177 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6228 (pmm)
REVERT: A  192 ARG cc_start: 0.6712 (tmt-80) cc_final: 0.6509 (tmt-80)
REVERT: A  196 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7564 (p)
REVERT: A  236 ARG cc_start: 0.5506 (tpp80) cc_final: 0.5136 (tpp-160)
REVERT: A  237 ARG cc_start: 0.5983 (tpt170) cc_final: 0.5587 (tpm170)
  outliers start: 16
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1147
  time to fit residues: 13.2467
Evaluate side-chains
  96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0170
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.234250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.200927 restraints weight = 4631.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.207111 restraints weight = 2918.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.211199 restraints weight = 2057.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.4497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2940  Z= 0.136
  Angle     :  0.917  13.276   4011  Z= 0.391
  Chirality :  0.047   0.333    502
  Planarity :  0.003   0.029    486
  Dihedral  : 14.149 104.899    511
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.32 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.50 (0.44), residues: 362
  helix:  2.77 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.82 (1.12), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.008   0.001   PHE A 395 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.005   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01069 (    2)
  link_NAG-ASN         : angle       5.05248 (    6)
  link_BETA1-4         : bond        0.00988 (    4)
  link_BETA1-4         : angle       3.62039 (   12)
  hydrogen bonds       : bond        0.03331 (  280)
  hydrogen bonds       : angle       4.08160 (  834)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       0.72285 (    4)
  covalent geometry    : bond        0.00274 ( 2932)
  covalent geometry    : angle       0.87625 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.7627 (t0) cc_final: 0.7393 (t0)
REVERT: A  127 ASN cc_start: 0.7582 (m-40) cc_final: 0.7066 (m-40)
REVERT: A  132 PHE cc_start: 0.7026 (m-80) cc_final: 0.6701 (m-80)
REVERT: A  143 THR cc_start: 0.8869 (p) cc_final: 0.8446 (t)
REVERT: A  177 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6162 (pmm)
REVERT: A  196 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7846 (p)
REVERT: A  236 ARG cc_start: 0.5445 (tpp80) cc_final: 0.5091 (tpp-160)
REVERT: A  237 ARG cc_start: 0.5871 (tpt170) cc_final: 0.5649 (tpm170)
  outliers start: 15
  outliers final: 11
  residues processed: 92
  average time/residue: 0.1313
  time to fit residues: 14.8513
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.233042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.199931 restraints weight = 4588.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.206214 restraints weight = 2895.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.210278 restraints weight = 2031.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2940  Z= 0.152
  Angle     :  0.934  12.813   4011  Z= 0.408
  Chirality :  0.047   0.302    502
  Planarity :  0.004   0.060    486
  Dihedral  : 13.069 100.518    511
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.00 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.36 (0.43), residues: 362
  helix:  2.67 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.78 (1.12), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.027   0.002   PHE A 220 
 TYR   0.013   0.001   TYR A 296 
 ARG   0.013   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01055 (    2)
  link_NAG-ASN         : angle       5.30714 (    6)
  link_BETA1-4         : bond        0.01108 (    4)
  link_BETA1-4         : angle       3.88239 (   12)
  hydrogen bonds       : bond        0.03483 (  280)
  hydrogen bonds       : angle       4.13241 (  834)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       1.15038 (    4)
  covalent geometry    : bond        0.00317 ( 2932)
  covalent geometry    : angle       0.88767 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  143 THR cc_start: 0.8884 (p) cc_final: 0.8465 (t)
REVERT: A  177 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6231 (pmm)
REVERT: A  236 ARG cc_start: 0.5553 (tpp80) cc_final: 0.5261 (tpp-160)
REVERT: A  237 ARG cc_start: 0.5877 (tpt170) cc_final: 0.5653 (tpm170)
  outliers start: 15
  outliers final: 14
  residues processed: 91
  average time/residue: 0.1221
  time to fit residues: 13.8878
Evaluate side-chains
  94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 18 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.233494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.201272 restraints weight = 4617.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.207496 restraints weight = 2906.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.211658 restraints weight = 2030.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2940  Z= 0.149
  Angle     :  0.956  12.859   4011  Z= 0.420
  Chirality :  0.049   0.299    502
  Planarity :  0.005   0.071    486
  Dihedral  : 12.339  96.385    511
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.97 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.43), residues: 362
  helix:  2.62 (0.27), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.64 (1.11), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.023   0.001   PHE A 220 
 TYR   0.013   0.001   TYR A 296 
 ARG   0.017   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01058 (    2)
  link_NAG-ASN         : angle       5.34398 (    6)
  link_BETA1-4         : bond        0.01131 (    4)
  link_BETA1-4         : angle       4.09071 (   12)
  hydrogen bonds       : bond        0.03553 (  280)
  hydrogen bonds       : angle       4.19452 (  834)
  SS BOND              : bond        0.00045 (    2)
  SS BOND              : angle       0.76487 (    4)
  covalent geometry    : bond        0.00303 ( 2932)
  covalent geometry    : angle       0.90862 ( 3989)

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

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

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  724 Ramachandran restraints generated.
    362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.7700 (t0) cc_final: 0.7477 (t0)
REVERT: A  132 PHE cc_start: 0.6964 (m-80) cc_final: 0.6699 (t80)
REVERT: A  143 THR cc_start: 0.8892 (p) cc_final: 0.8484 (t)
REVERT: A  177 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6117 (pmm)
REVERT: A  237 ARG cc_start: 0.5911 (tpt170) cc_final: 0.5604 (tpm170)
REVERT: A  366 ASP cc_start: 0.6492 (t70) cc_final: 0.6274 (m-30)
  outliers start: 15
  outliers final: 14
  residues processed: 92
  average time/residue: 0.1077
  time to fit residues: 12.3412
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0050
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.232711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.199342 restraints weight = 4510.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.206250 restraints weight = 2742.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.210619 restraints weight = 1863.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6380
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2940  Z= 0.151
  Angle     :  0.953  12.901   4011  Z= 0.418
  Chirality :  0.048   0.297    502
  Planarity :  0.005   0.077    486
  Dihedral  : 11.590  91.177    511
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 26.30 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.43), residues: 362
  helix:  2.54 (0.27), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.67 (1.11), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 191 
 HIS   0.004   0.001   HIS A 371 
 PHE   0.021   0.001   PHE A 220 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.016   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01026 (    2)
  link_NAG-ASN         : angle       5.48904 (    6)
  link_BETA1-4         : bond        0.01148 (    4)
  link_BETA1-4         : angle       4.24738 (   12)
  hydrogen bonds       : bond        0.03535 (  280)
  hydrogen bonds       : angle       4.24723 (  834)
  SS BOND              : bond        0.00034 (    2)
  SS BOND              : angle       0.84452 (    4)
  covalent geometry    : bond        0.00309 ( 2932)
  covalent geometry    : angle       0.90170 ( 3989)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1264.51 seconds
wall clock time: 22 minutes 38.48 seconds (1358.48 seconds total)