Starting phenix.real_space_refine
on Tue Mar  3 11:14:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_24690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_24690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_24690.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_24690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtv_24690/03_2026/7rtv_24690.map"
  }
  resolution = 3.96
  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=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.82, per 1000 atoms: 0.28
  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: 0.33
  Conformation dependent library (CDL) restraints added in 116.7 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: 0.04
  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: 0.41

  Time building geometry restraints manager: 0.42 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:             0.430
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     5.100
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.001   ARG A 192 
 TYR   0.015   0.001   TYR A  66 
 PHE   0.022   0.002   PHE A 220 
 TRP   0.005   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 359 

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

*********************** 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  : 0.102 
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: 0.6598 (pmm)
REVERT: A  372 LYS cc_start: 0.8838 (tttp) cc_final: 0.8378 (tttm)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0520
  time to fit residues: 6.0836
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  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0270
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
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 = 0.4695 r_free = 0.4695 target = 0.232188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.198653 restraints weight = 4524.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.204737 restraints weight = 2886.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.208834 restraints weight = 2049.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.211251 restraints weight = 1570.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.213323 restraints weight = 1298.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6384
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2940  Z= 0.144
  Angle     :  0.773   8.688   4011  Z= 0.352
  Chirality :  0.046   0.263    502
  Planarity :  0.004   0.048    486
  Dihedral  : 24.727 111.401    511
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.66 %
    Favored  : 84.42 %
  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 are not related in a simple way.
  whole:  3.55 (0.43), residues: 362
  helix:  2.80 (0.27), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.82 (1.13), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 236 
 TYR   0.020   0.001   TYR A 296 
 PHE   0.018   0.002   PHE A 395 
 TRP   0.005   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2932)
  covalent geometry    : angle       0.74567 ( 3989)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       1.03091 (    4)
  hydrogen bonds       : bond        0.03557 (  280)
  hydrogen bonds       : angle       4.13203 (  834)
  link_BETA1-4         : bond        0.00536 (    4)
  link_BETA1-4         : angle       2.81472 (   12)
  link_NAG-ASN         : bond        0.00684 (    2)
  link_NAG-ASN         : angle       3.64530 (    6)

*********************** 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
  100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  127 ASN cc_start: 0.7609 (m110) cc_final: 0.7053 (m-40)
REVERT: A  177 MET cc_start: 0.7173 (pmm) cc_final: 0.6578 (pmm)
REVERT: A  401 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8469 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 92
  average time/residue: 0.0456
  time to fit residues: 5.3310
Evaluate side-chains
  84 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
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  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 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0470
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.6278

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.234230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.200204 restraints weight = 4453.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.206285 restraints weight = 2818.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.210378 restraints weight = 1980.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.213154 restraints weight = 1518.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.214491 restraints weight = 1242.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
moved from start:          0.1739

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= 0.135
  Angle     :  0.795  10.165   4011  Z= 0.349
  Chirality :  0.045   0.242    502
  Planarity :  0.004   0.028    486
  Dihedral  : 22.018 113.542    511
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.23 %
    Favored  : 80.52 %
  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 are not related in a simple way.
  whole:  3.46 (0.43), residues: 362
  helix:  2.76 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.98 (1.10), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 368 
 TYR   0.013   0.001   TYR A 296 
 PHE   0.019   0.002   PHE A 315 
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 2932)
  covalent geometry    : angle       0.76782 ( 3989)
  SS BOND              : bond        0.00027 (    2)
  SS BOND              : angle       0.87804 (    4)
  hydrogen bonds       : bond        0.03389 (  280)
  hydrogen bonds       : angle       4.06496 (  834)
  link_BETA1-4         : bond        0.00748 (    4)
  link_BETA1-4         : angle       2.80541 (   12)
  link_NAG-ASN         : bond        0.00730 (    2)
  link_NAG-ASN         : angle       3.73690 (    6)

*********************** 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
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7597 (m110) cc_final: 0.7068 (m-40)
REVERT: A  177 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6659 (pmm)
REVERT: A  401 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8424 (mp)
  outliers start: 10
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0479
  time to fit residues: 5.4224
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  : 0.078 
-------------------------------------------------------------------------------
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  177 MET
Chi-restraints excluded: chain A residue  253 LEU
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 33 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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**
A 152 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.232214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.197364 restraints weight = 4586.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.203711 restraints weight = 2915.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.207785 restraints weight = 2057.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.210472 restraints weight = 1586.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.212277 restraints weight = 1309.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.2013

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     :  0.830  10.260   4011  Z= 0.361
  Chirality :  0.049   0.330    502
  Planarity :  0.004   0.028    486
  Dihedral  : 19.866 113.265    511
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.18 %
    Favored  : 77.60 %
  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 are not related in a simple way.
  whole:  3.43 (0.43), residues: 362
  helix:  2.74 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.94 (1.13), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 368 
 TYR   0.011   0.001   TYR A 296 
 PHE   0.013   0.002   PHE A 395 
 TRP   0.007   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2932)
  covalent geometry    : angle       0.80092 ( 3989)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       1.06003 (    4)
  hydrogen bonds       : bond        0.03382 (  280)
  hydrogen bonds       : angle       4.08671 (  834)
  link_BETA1-4         : bond        0.00797 (    4)
  link_BETA1-4         : angle       2.86856 (   12)
  link_NAG-ASN         : bond        0.00759 (    2)
  link_NAG-ASN         : angle       4.04141 (    6)

*********************** 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
  109 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7593 (m110) cc_final: 0.7077 (m-40)
REVERT: A  143 THR cc_start: 0.8872 (p) cc_final: 0.8446 (t)
REVERT: A  177 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6717 (pmm)
REVERT: A  370 LEU cc_start: 0.7033 (tp) cc_final: 0.6759 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0473
  time to fit residues: 5.8420
Evaluate side-chains
  89 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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  389 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.232739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.198754 restraints weight = 4529.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.204939 restraints weight = 2909.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.208980 restraints weight = 2061.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.210942 restraints weight = 1590.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.213087 restraints weight = 1345.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
moved from start:          0.2278

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= 0.146
  Angle     :  0.841  10.457   4011  Z= 0.370
  Chirality :  0.048   0.269    502
  Planarity :  0.004   0.040    486
  Dihedral  : 17.932 112.410    511
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 21.75 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.50 (0.44), residues: 362
  helix:  2.77 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.79 (1.18), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 192 
 TYR   0.010   0.001   TYR A 296 
 PHE   0.013   0.002   PHE A 308 
 TRP   0.008   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2932)
  covalent geometry    : angle       0.80896 ( 3989)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       1.11313 (    4)
  hydrogen bonds       : bond        0.03377 (  280)
  hydrogen bonds       : angle       4.03646 (  834)
  link_BETA1-4         : bond        0.00907 (    4)
  link_BETA1-4         : angle       2.98741 (   12)
  link_NAG-ASN         : bond        0.00808 (    2)
  link_NAG-ASN         : angle       4.32505 (    6)

*********************** 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
  100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  127 ASN cc_start: 0.7388 (m110) cc_final: 0.6587 (m-40)
REVERT: A  177 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6716 (pmm)
REVERT: A  236 ARG cc_start: 0.5480 (tpp80) cc_final: 0.5184 (tpp-160)
  outliers start: 12
  outliers final: 8
  residues processed: 92
  average time/residue: 0.0586
  time to fit residues: 6.5470
Evaluate side-chains
  92 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0040
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.4710 r_free = 0.4710 target = 0.234738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.200703 restraints weight = 4459.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.206922 restraints weight = 2801.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.211067 restraints weight = 1954.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.213451 restraints weight = 1487.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.215499 restraints weight = 1231.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.2473

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= 0.135
  Angle     :  0.871  11.427   4011  Z= 0.374
  Chirality :  0.049   0.362    502
  Planarity :  0.005   0.066    486
  Dihedral  : 16.284 110.810    511
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 23.05 %
    Favored  : 71.75 %
  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 are not related in a simple way.
  whole:  3.60 (0.44), residues: 362
  helix:  2.83 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.75 (1.17), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 192 
 TYR   0.011   0.001   TYR A 296 
 PHE   0.010   0.001   PHE A 395 
 TRP   0.004   0.001   TRP A 191 
 HIS   0.002   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2932)
  covalent geometry    : angle       0.83604 ( 3989)
  SS BOND              : bond        0.00025 (    2)
  SS BOND              : angle       1.03652 (    4)
  hydrogen bonds       : bond        0.03322 (  280)
  hydrogen bonds       : angle       4.02053 (  834)
  link_BETA1-4         : bond        0.00959 (    4)
  link_BETA1-4         : angle       3.19482 (   12)
  link_NAG-ASN         : bond        0.00899 (    2)
  link_NAG-ASN         : angle       4.56104 (    6)

*********************** 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: 16
    poor density    : 87
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.7794 (t0) cc_final: 0.7566 (t0)
REVERT: A  177 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6199 (pmm)
REVERT: A  236 ARG cc_start: 0.5471 (tpp80) cc_final: 0.5122 (tpp-160)
  outliers start: 16
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0467
  time to fit residues: 5.4685
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  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   59 ASN
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  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  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
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 7 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4709 r_free = 0.4709 target = 0.233947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.200890 restraints weight = 4392.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.206873 restraints weight = 2793.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.210963 restraints weight = 1965.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.213603 restraints weight = 1500.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.215382 restraints weight = 1226.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.2565

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= 0.141
  Angle     :  0.886  12.025   4011  Z= 0.381
  Chirality :  0.047   0.299    502
  Planarity :  0.005   0.073    486
  Dihedral  : 15.378 108.673    511
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.70 %
    Favored  : 71.75 %
  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 are not related in a simple way.
  whole:  3.61 (0.44), residues: 362
  helix:  2.85 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.80 (1.16), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 192 
 TYR   0.008   0.001   TYR A 296 
 PHE   0.012   0.001   PHE A 308 
 TRP   0.006   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2932)
  covalent geometry    : angle       0.84790 ( 3989)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.99950 (    4)
  hydrogen bonds       : bond        0.03360 (  280)
  hydrogen bonds       : angle       4.04464 (  834)
  link_BETA1-4         : bond        0.01018 (    4)
  link_BETA1-4         : angle       3.39507 (   12)
  link_NAG-ASN         : bond        0.00950 (    2)
  link_NAG-ASN         : angle       4.79092 (    6)

*********************** 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
  103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6212 (pmm)
REVERT: A  236 ARG cc_start: 0.5447 (tpp80) cc_final: 0.5124 (tpp-160)
  outliers start: 14
  outliers final: 11
  residues processed: 95
  average time/residue: 0.0516
  time to fit residues: 6.0414
Evaluate side-chains
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
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  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  274 CYS
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  305 ILE
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 34 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0470
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.233480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.199756 restraints weight = 4686.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.206185 restraints weight = 2964.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.210494 restraints weight = 2072.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.212976 restraints weight = 1574.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.214928 restraints weight = 1297.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   2940  Z= 0.144
  Angle     :  0.925  13.530   4011  Z= 0.398
  Chirality :  0.048   0.375    502
  Planarity :  0.003   0.027    486
  Dihedral  : 14.338 105.588    511
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.38
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.53 (0.44), residues: 362
  helix:  2.79 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.77 (1.17), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 368 
 TYR   0.010   0.001   TYR A 296 
 PHE   0.011   0.001   PHE A 308 
 TRP   0.005   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2932)
  covalent geometry    : angle       0.88475 ( 3989)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.90916 (    4)
  hydrogen bonds       : bond        0.03351 (  280)
  hydrogen bonds       : angle       4.11151 (  834)
  link_BETA1-4         : bond        0.01001 (    4)
  link_BETA1-4         : angle       3.60056 (   12)
  link_NAG-ASN         : bond        0.00986 (    2)
  link_NAG-ASN         : angle       4.99499 (    6)

*********************** 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  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.7553 (t0) cc_final: 0.7293 (t0)
REVERT: A  177 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6145 (pmm)
REVERT: A  236 ARG cc_start: 0.5491 (tpp80) cc_final: 0.5134 (tpp-160)
  outliers start: 15
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0478
  time to fit residues: 5.5916
Evaluate side-chains
  95 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   59 ASN
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  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  365 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.233345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.200294 restraints weight = 4532.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.206621 restraints weight = 2871.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.210670 restraints weight = 2007.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.213410 restraints weight = 1535.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.215196 restraints weight = 1254.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.4525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start:          0.2810

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= 0.154
  Angle     :  0.938  13.347   4011  Z= 0.413
  Chirality :  0.048   0.294    502
  Planarity :  0.006   0.098    486
  Dihedral  : 13.630 102.725    511
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.34 (0.44), residues: 362
  helix:  2.65 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.69 (1.17), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 192 
 TYR   0.010   0.001   TYR A 296 
 PHE   0.031   0.002   PHE A 220 
 TRP   0.007   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2932)
  covalent geometry    : angle       0.89434 ( 3989)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       1.02249 (    4)
  hydrogen bonds       : bond        0.03443 (  280)
  hydrogen bonds       : angle       4.17987 (  834)
  link_BETA1-4         : bond        0.01076 (    4)
  link_BETA1-4         : angle       3.79877 (   12)
  link_NAG-ASN         : bond        0.00991 (    2)
  link_NAG-ASN         : angle       5.13197 (    6)

*********************** 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
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ASN cc_start: 0.7518 (m-40) cc_final: 0.7272 (m-40)
REVERT: A  132 PHE cc_start: 0.7553 (m-80) cc_final: 0.7207 (t80)
REVERT: A  177 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6194 (pmm)
REVERT: A  236 ARG cc_start: 0.5500 (tpp80) cc_final: 0.5187 (tpp-160)
  outliers start: 14
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0483
  time to fit residues: 5.3894
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  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   59 ASN
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  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  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 31 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4702 r_free = 0.4702 target = 0.232002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.196085 restraints weight = 4596.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.203250 restraints weight = 2805.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.207812 restraints weight = 1926.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.210948 restraints weight = 1458.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.212868 restraints weight = 1177.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.4509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2940  Z= 0.160
  Angle     :  0.953  13.953   4011  Z= 0.417
  Chirality :  0.047   0.304    502
  Planarity :  0.004   0.029    486
  Dihedral  : 13.032 100.105    511
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.62 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.22 (0.44), residues: 362
  helix:  2.57 (0.27), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.76 (1.15), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 192 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.028   0.002   PHE A 220 
 TRP   0.007   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2932)
  covalent geometry    : angle       0.90794 ( 3989)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       1.00110 (    4)
  hydrogen bonds       : bond        0.03421 (  280)
  hydrogen bonds       : angle       4.22701 (  834)
  link_BETA1-4         : bond        0.01128 (    4)
  link_BETA1-4         : angle       3.94414 (   12)
  link_NAG-ASN         : bond        0.00987 (    2)
  link_NAG-ASN         : angle       5.24940 (    6)

********************** 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
  96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.062 
Fit side-chains
REVERT: A  127 ASN cc_start: 0.7403 (m-40) cc_final: 0.6869 (m110)
REVERT: A  177 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6136 (pmm)
REVERT: A  236 ARG cc_start: 0.5606 (tpp80) cc_final: 0.5263 (tpp-160)
  outliers start: 14
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0444
  time to fit residues: 4.9730
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  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   59 ASN
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  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  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 12 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   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 = 0.4702 r_free = 0.4702 target = 0.231810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.196503 restraints weight = 4522.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.203640 restraints weight = 2784.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.208356 restraints weight = 1904.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.211404 restraints weight = 1424.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.213237 restraints weight = 1149.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2940  Z= 0.152
  Angle     :  0.954  14.132   4011  Z= 0.416
  Chirality :  0.048   0.297    502
  Planarity :  0.005   0.078    486
  Dihedral  : 12.484  96.965    511
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.24 (0.44), residues: 362
  helix:  2.60 (0.27), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.83 (1.12), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 192 
 TYR   0.009   0.001   TYR A 280 
 PHE   0.028   0.002   PHE A 220 
 TRP   0.007   0.001   TRP A 191 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 2932)
  covalent geometry    : angle       0.90653 ( 3989)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       0.95235 (    4)
  hydrogen bonds       : bond        0.03415 (  280)
  hydrogen bonds       : angle       4.21151 (  834)
  link_BETA1-4         : bond        0.01170 (    4)
  link_BETA1-4         : angle       4.08736 (   12)
  link_NAG-ASN         : bond        0.01015 (    2)
  link_NAG-ASN         : angle       5.33134 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 666.50 seconds
wall clock time: 12 minutes 6.89 seconds (726.89 seconds total)