Starting phenix.real_space_refine
on Tue Mar  3 10:59:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q3u_13795/03_2026/7q3u_13795.cif"
  }
  resolution = 3.7
  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=   0.002
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      35      5.16       5
     C    1400      2.51       5
     N     450      2.21       5
     O     470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 2355
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 471
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 2, 'TRANS': 68}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.37, per 1000 atoms: 0.16
  Number of scatterers: 2355
  At special positions: 0
  Unit cell: (55.12, 68.9, 41.34, 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      35     16.00
     O     470      8.00
     N     450      7.00
     C    1400      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.13
  Conformation dependent library (CDL) restraints added in 70.3 milliseconds
  

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  510

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 2 sheets defined
      0.0% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 311 through 312
    Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.565A  pdb=" N   SER A 317 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER B 317 " --> pdb=" O   ILE D 318 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   SER D 317 " --> pdb=" O   ILE E 318 " (cutoff:3.500A)

    8 hydrogen bonds defined for protein.
    21 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: 0.26

  Time building geometry restraints manager: 0.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 775
        1.33 -     1.45: 396
        1.45 -     1.57: 1149
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 2390
  Sorted by residual:
  bond pdb=" CG  GLN A 343 "
       pdb=" CD  GLN A 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.475  0.041 2.50e-02 1.60e+03 2.68e+00
  bond pdb=" CG  GLN E 343 "
       pdb=" CD  GLN E 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.475  0.041 2.50e-02 1.60e+03 2.68e+00
  bond pdb=" CG  GLN C 343 "
       pdb=" CD  GLN C 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.476  0.040 2.50e-02 1.60e+03 2.59e+00
  bond pdb=" CG  GLN D 343 "
       pdb=" CD  GLN D 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.476  0.040 2.50e-02 1.60e+03 2.59e+00
  bond pdb=" CG  GLN B 343 "
       pdb=" CD  GLN B 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.476  0.040 2.50e-02 1.60e+03 2.56e+00
  ... (remaining 2385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 2940
        1.91 -     3.83: 155
        3.83 -     5.74: 70
        5.74 -     7.66: 5
        7.66 -     9.57: 5
  Bond angle restraints: 3175
  Sorted by residual:
  angle pdb=" N   MET C 307 "
        pdb=" CA  MET C 307 "
        pdb=" C   MET C 307 "
      ideal   model   delta    sigma   weight residual
     111.30  106.42    4.88 1.43e+00 4.89e-01 1.16e+01
  angle pdb=" N   MET A 307 "
        pdb=" CA  MET A 307 "
        pdb=" C   MET A 307 "
      ideal   model   delta    sigma   weight residual
     111.30  106.44    4.86 1.43e+00 4.89e-01 1.16e+01
  angle pdb=" N   MET E 307 "
        pdb=" CA  MET E 307 "
        pdb=" C   MET E 307 "
      ideal   model   delta    sigma   weight residual
     111.30  106.45    4.85 1.43e+00 4.89e-01 1.15e+01
  angle pdb=" N   MET D 307 "
        pdb=" CA  MET D 307 "
        pdb=" C   MET D 307 "
      ideal   model   delta    sigma   weight residual
     111.30  106.47    4.83 1.43e+00 4.89e-01 1.14e+01
  angle pdb=" N   MET B 307 "
        pdb=" CA  MET B 307 "
        pdb=" C   MET B 307 "
      ideal   model   delta    sigma   weight residual
     111.30  106.48    4.82 1.43e+00 4.89e-01 1.14e+01
  ... (remaining 3170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 1165
       17.75 -    35.50: 145
       35.50 -    53.25: 10
       53.25 -    71.00: 5
       71.00 -    88.75: 10
  Dihedral angle restraints: 1335
    sinusoidal: 475
      harmonic: 860
  Sorted by residual:
  dihedral pdb=" CA  MET C 337 "
           pdb=" C   MET C 337 "
           pdb=" N   GLY C 338 "
           pdb=" CA  GLY C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.31  -24.69     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  MET B 337 "
           pdb=" C   MET B 337 "
           pdb=" N   GLY B 338 "
           pdb=" CA  GLY B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.31  -24.69     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  MET D 337 "
           pdb=" C   MET D 337 "
           pdb=" N   GLY D 338 "
           pdb=" CA  GLY D 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.34  -24.66     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 1332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.036: 158
       0.036 -    0.072: 80
       0.072 -    0.108: 32
       0.108 -    0.144: 0
       0.144 -    0.180: 5
  Chirality restraints: 275
  Sorted by residual:
  chirality pdb=" CB  ILE B 318 "
            pdb=" CA  ILE B 318 "
            pdb=" CG1 ILE B 318 "
            pdb=" CG2 ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CB  ILE A 318 "
            pdb=" CA  ILE A 318 "
            pdb=" CG1 ILE A 318 "
            pdb=" CG2 ILE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CB  ILE E 318 "
            pdb=" CA  ILE E 318 "
            pdb=" CG1 ILE E 318 "
            pdb=" CG2 ILE E 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.94e-01
  ... (remaining 272 not shown)

  Planarity restraints: 465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 348 "   -0.030 5.00e-02 4.00e+02   4.57e-02 3.35e+00
        pdb=" N   PRO A 349 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 349 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 349 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 348 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO B 349 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 349 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 349 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 348 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO E 349 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO E 349 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 349 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 462 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 93
        2.68 -     3.23: 2401
        3.23 -     3.79: 3973
        3.79 -     4.34: 5200
        4.34 -     4.90: 9748
  Nonbonded interactions: 21415
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 331 "
            pdb=" OG  SER D 347 "
     model   vdw
     2.120 3.120
  nonbonded pdb=" OG  SER B 347 "
            pdb=" NE2 GLN C 331 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OD1 ASN B 301 "
            pdb=" N   ASN B 302 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" OD1 ASN E 301 "
            pdb=" N   ASN E 302 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" OD1 ASN D 301 "
            pdb=" N   ASN D 302 "
     model   vdw
     2.355 3.120
  ... (remaining 21410 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.760
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4561
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      :  0.005   0.041   2390  Z= 0.246
  Angle     :  1.167   9.569   3175  Z= 0.647
  Chirality :  0.049   0.180    275
  Planarity :  0.006   0.046    465
  Dihedral  : 16.840  88.755    825
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 36.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.72 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -5.79 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.41 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.002   ARG B 293 
 PHE   0.004   0.001   PHE E 316 
 TRP   0.017   0.004   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 2390)
  covalent geometry    : angle       1.16684 ( 3175)
  hydrogen bonds       : bond        0.26988 (    8)
  hydrogen bonds       : angle      12.59090 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.048 
Fit side-chains
   revert: symmetry clash
REVERT: B  306 ASN cc_start: 0.7212 (m110) cc_final: 0.6822 (m110)
REVERT: C  311 MET cc_start: 0.5155 (mtp) cc_final: 0.4871 (mtt)
REVERT: C  323 MET cc_start: 0.6237 (ptm) cc_final: 0.5684 (mtm)
REVERT: E  336 MET cc_start: 0.4106 (ptt) cc_final: 0.3128 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0384
  time to fit residues: 2.9277
Evaluate side-chains
  46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0040
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 345 ASN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 331 GLN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 345 ASN
** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.271797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.229885 restraints weight = 2282.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5071 r_free = 0.5071 target = 0.238228 restraints weight = 1400.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.5128 r_free = 0.5128 target = 0.244491 restraints weight = 945.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.5168 r_free = 0.5168 target = 0.249053 restraints weight = 679.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5189 r_free = 0.5189 target = 0.251720 restraints weight = 514.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.5176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5026
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2390  Z= 0.158
  Angle     :  0.780   6.659   3175  Z= 0.426
  Chirality :  0.041   0.125    275
  Planarity :  0.005   0.041    465
  Dihedral  :  5.895  21.113    355
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.67 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.70 (0.21), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.16), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 293 
 PHE   0.015   0.002   PHE E 313 
 TRP   0.010   0.002   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 2390)
  covalent geometry    : angle       0.77992 ( 3175)
  hydrogen bonds       : bond        0.05498 (    8)
  hydrogen bonds       : angle       4.18040 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.073 
Fit side-chains
REVERT: C  311 MET cc_start: 0.5710 (mtp) cc_final: 0.5439 (mtt)
REVERT: C  323 MET cc_start: 0.6354 (ptm) cc_final: 0.5860 (mtm)
REVERT: C  333 SER cc_start: 0.6835 (t) cc_final: 0.6568 (p)
REVERT: C  337 MET cc_start: 0.4855 (ptt) cc_final: 0.4511 (mtm)
REVERT: D  323 MET cc_start: 0.4189 (ptm) cc_final: 0.3470 (ppp)
REVERT: E  311 MET cc_start: 0.4163 (tmm) cc_final: 0.3158 (mtt)
REVERT: E  337 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.4482 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 57
  average time/residue: 0.0365
  time to fit residues: 2.6768
Evaluate side-chains
  49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain E residue  333 SER
Chi-restraints excluded: chain E residue  337 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 ASN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
C 302 ASN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 285 ASN
** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5281 r_free = 0.5281 target = 0.272591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5024 r_free = 0.5024 target = 0.236492 restraints weight = 2416.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.243745 restraints weight = 1538.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5124 r_free = 0.5124 target = 0.249122 restraints weight = 1032.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5156 r_free = 0.5156 target = 0.253059 restraints weight = 725.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.5178 r_free = 0.5178 target = 0.255732 restraints weight = 537.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.5191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5165
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2390  Z= 0.126
  Angle     :  0.685   6.813   3175  Z= 0.362
  Chirality :  0.038   0.116    275
  Planarity :  0.004   0.038    465
  Dihedral  :  5.554  17.222    355
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.67 %
    Favored  : 79.52 %
  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: -5.70 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.16), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 293 
 PHE   0.006   0.001   PHE E 313 
 TRP   0.008   0.002   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2390)
  covalent geometry    : angle       0.68490 ( 3175)
  hydrogen bonds       : bond        0.04058 (    8)
  hydrogen bonds       : angle       4.09440 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 MET cc_start: 0.5319 (ptt) cc_final: 0.5009 (ptt)
REVERT: C  337 MET cc_start: 0.3912 (ptt) cc_final: 0.3400 (mtm)
REVERT: D  316 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7203 (t80)
REVERT: D  323 MET cc_start: 0.4592 (ptm) cc_final: 0.3957 (ppp)
REVERT: D  336 MET cc_start: 0.5562 (ptt) cc_final: 0.4387 (tpp)
REVERT: D  339 MET cc_start: 0.5912 (ptp) cc_final: 0.5590 (pmm)
REVERT: E  311 MET cc_start: 0.4429 (tmm) cc_final: 0.3007 (mtt)
REVERT: E  319 ASN cc_start: 0.7158 (m-40) cc_final: 0.6504 (p0)
  outliers start: 8
  outliers final: 4
  residues processed: 56
  average time/residue: 0.0281
  time to fit residues: 2.0891
Evaluate side-chains
  52 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain D residue  316 PHE
Chi-restraints excluded: chain D residue  318 ILE
Chi-restraints excluded: chain E residue  333 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5242 r_free = 0.5242 target = 0.263177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.230520 restraints weight = 2439.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5062 r_free = 0.5062 target = 0.236584 restraints weight = 1611.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5099 r_free = 0.5099 target = 0.241310 restraints weight = 1117.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5127 r_free = 0.5127 target = 0.244680 restraints weight = 787.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5149 r_free = 0.5149 target = 0.247225 restraints weight = 581.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.5152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5381
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2390  Z= 0.140
  Angle     :  0.692   5.500   3175  Z= 0.370
  Chirality :  0.037   0.114    275
  Planarity :  0.004   0.038    465
  Dihedral  :  5.616  19.399    355
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.52 %
    Favored  : 77.14 %
  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: -5.78 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.40 (0.16), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 293 
 PHE   0.006   0.001   PHE E 283 
 TRP   0.011   0.002   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2390)
  covalent geometry    : angle       0.69191 ( 3175)
  hydrogen bonds       : bond        0.04844 (    8)
  hydrogen bonds       : angle       4.08213 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6757 (mp10)
REVERT: B  336 MET cc_start: 0.6004 (ptt) cc_final: 0.5713 (ptt)
REVERT: C  323 MET cc_start: 0.7556 (mtm) cc_final: 0.6032 (ttt)
REVERT: C  336 MET cc_start: 0.6791 (ptt) cc_final: 0.6363 (ptp)
REVERT: C  337 MET cc_start: 0.4075 (ptt) cc_final: 0.3172 (mtm)
REVERT: D  319 ASN cc_start: 0.7186 (t0) cc_final: 0.6771 (m-40)
REVERT: D  323 MET cc_start: 0.5900 (ptm) cc_final: 0.5210 (ppp)
REVERT: D  336 MET cc_start: 0.5692 (ptt) cc_final: 0.4495 (tpp)
REVERT: E  311 MET cc_start: 0.4967 (tmm) cc_final: 0.2990 (mtt)
REVERT: E  319 ASN cc_start: 0.7183 (m-40) cc_final: 0.6319 (p0)
  outliers start: 7
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0248
  time to fit residues: 1.7160
Evaluate side-chains
  50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain E residue  345 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0970
   chunk 20 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5139 r_free = 0.5139 target = 0.248417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.220535 restraints weight = 2481.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.224991 restraints weight = 1662.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5006 r_free = 0.5006 target = 0.228259 restraints weight = 1183.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.230824 restraints weight = 892.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.5046 r_free = 0.5046 target = 0.232743 restraints weight = 704.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.5070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5696
moved from start:          0.6451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2390  Z= 0.189
  Angle     :  0.793   9.291   3175  Z= 0.419
  Chirality :  0.044   0.328    275
  Planarity :  0.005   0.041    465
  Dihedral  :  6.111  22.715    355
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 23.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.72 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 18.10 %
    Favored  : 76.19 %
  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: -5.94 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.52 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.010   0.002   PHE E 283 
 TRP   0.006   0.002   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 2390)
  covalent geometry    : angle       0.79293 ( 3175)
  hydrogen bonds       : bond        0.05015 (    8)
  hydrogen bonds       : angle       3.79978 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: C  323 MET cc_start: 0.7458 (mtm) cc_final: 0.6238 (ttt)
REVERT: C  336 MET cc_start: 0.6872 (ptt) cc_final: 0.6459 (ptp)
REVERT: C  337 MET cc_start: 0.5135 (ptt) cc_final: 0.4063 (mtm)
REVERT: D  323 MET cc_start: 0.6634 (ptm) cc_final: 0.5885 (ppp)
REVERT: D  336 MET cc_start: 0.5872 (ptt) cc_final: 0.5072 (tpp)
REVERT: E  319 ASN cc_start: 0.7453 (m-40) cc_final: 0.6216 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 60
  average time/residue: 0.0411
  time to fit residues: 3.0731
Evaluate side-chains
  48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain E residue  307 MET
Chi-restraints excluded: chain E residue  345 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   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 285 ASN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5165 r_free = 0.5165 target = 0.250020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.221156 restraints weight = 2525.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4999 r_free = 0.4999 target = 0.225614 restraints weight = 1700.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.228936 restraints weight = 1216.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5045 r_free = 0.5045 target = 0.231085 restraints weight = 918.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5061 r_free = 0.5061 target = 0.233032 restraints weight = 741.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.5075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5730
moved from start:          0.7009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2390  Z= 0.162
  Angle     :  0.757   7.229   3175  Z= 0.398
  Chirality :  0.044   0.286    275
  Planarity :  0.004   0.039    465
  Dihedral  :  5.839  20.878    355
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 22.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 24.29 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -6.00 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.57 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG B 293 
 PHE   0.007   0.001   PHE E 283 
 TRP   0.009   0.002   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2390)
  covalent geometry    : angle       0.75658 ( 3175)
  hydrogen bonds       : bond        0.04418 (    8)
  hydrogen bonds       : angle       3.93211 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: B  285 ASN cc_start: 0.7883 (m110) cc_final: 0.7573 (m110)
REVERT: C  323 MET cc_start: 0.7369 (mtm) cc_final: 0.6234 (ttt)
REVERT: C  336 MET cc_start: 0.6944 (ptt) cc_final: 0.6571 (ptp)
REVERT: D  323 MET cc_start: 0.6753 (ptm) cc_final: 0.6078 (ppp)
REVERT: D  336 MET cc_start: 0.5860 (ptt) cc_final: 0.5224 (tpp)
  outliers start: 4
  outliers final: 3
  residues processed: 52
  average time/residue: 0.0353
  time to fit residues: 2.3813
Evaluate side-chains
  46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  322 MET
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain E residue  345 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0170
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5253 r_free = 0.5253 target = 0.257057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5061 r_free = 0.5061 target = 0.225760 restraints weight = 2452.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.5097 r_free = 0.5097 target = 0.230117 restraints weight = 1663.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5119 r_free = 0.5119 target = 0.233210 restraints weight = 1225.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5137 r_free = 0.5137 target = 0.235706 restraints weight = 961.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.5148 r_free = 0.5148 target = 0.237375 restraints weight = 788.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.5163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5692
moved from start:          0.7487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2390  Z= 0.137
  Angle     :  0.711   6.317   3175  Z= 0.372
  Chirality :  0.040   0.210    275
  Planarity :  0.004   0.036    465
  Dihedral  :  5.593  18.294    355
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.62 %
    Favored  : 70.00 %
  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: -5.97 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.55 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 293 
 PHE   0.005   0.001   PHE E 283 
 TRP   0.009   0.001   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2390)
  covalent geometry    : angle       0.71149 ( 3175)
  hydrogen bonds       : bond        0.04521 (    8)
  hydrogen bonds       : angle       3.90722 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7327 (mtm) cc_final: 0.6224 (ttt)
REVERT: C  336 MET cc_start: 0.7007 (ptt) cc_final: 0.6670 (ptp)
REVERT: D  323 MET cc_start: 0.6652 (ptm) cc_final: 0.5964 (ppp)
REVERT: D  336 MET cc_start: 0.5903 (ptt) cc_final: 0.5196 (tpp)
REVERT: E  285 ASN cc_start: 0.6154 (m110) cc_final: 0.5851 (m-40)
REVERT: E  336 MET cc_start: 0.5110 (tpt) cc_final: 0.4757 (tpt)
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0311
  time to fit residues: 2.0948
Evaluate side-chains
  46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  322 MET
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain E residue  345 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 346 GLN
** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5182 r_free = 0.5182 target = 0.247651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.216415 restraints weight = 2425.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.220383 restraints weight = 1706.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5042 r_free = 0.5042 target = 0.223303 restraints weight = 1284.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5056 r_free = 0.5056 target = 0.225161 restraints weight = 1021.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5070 r_free = 0.5070 target = 0.226932 restraints weight = 861.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.5087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5850
moved from start:          0.7862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2390  Z= 0.172
  Angle     :  0.753   6.637   3175  Z= 0.396
  Chirality :  0.042   0.201    275
  Planarity :  0.004   0.037    465
  Dihedral  :  5.896  18.756    355
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 21.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.46 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 27.14 %
    Favored  : 69.52 %
  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: -5.98 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.55 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG B 293 
 PHE   0.007   0.001   PHE B 283 
 TRP   0.010   0.002   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2390)
  covalent geometry    : angle       0.75302 ( 3175)
  hydrogen bonds       : bond        0.04653 (    8)
  hydrogen bonds       : angle       4.05161 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.078 
Fit side-chains
REVERT: C  323 MET cc_start: 0.7251 (mtm) cc_final: 0.6267 (ttt)
REVERT: C  336 MET cc_start: 0.6984 (ptt) cc_final: 0.6638 (ptp)
REVERT: D  323 MET cc_start: 0.6899 (ptm) cc_final: 0.6243 (ppp)
REVERT: D  336 MET cc_start: 0.6282 (ptt) cc_final: 0.5398 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0431
  time to fit residues: 2.6339
Evaluate side-chains
  49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 MET
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain C residue  322 MET
Chi-restraints excluded: chain C residue  333 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
C 285 ASN
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5252 r_free = 0.5252 target = 0.254838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5046 r_free = 0.5046 target = 0.221738 restraints weight = 2466.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.225781 restraints weight = 1720.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5107 r_free = 0.5107 target = 0.228947 restraints weight = 1296.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.5123 r_free = 0.5123 target = 0.231157 restraints weight = 1031.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5135 r_free = 0.5135 target = 0.232945 restraints weight = 860.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.5144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5735
moved from start:          0.8149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2390  Z= 0.121
  Angle     :  0.667   5.881   3175  Z= 0.351
  Chirality :  0.039   0.155    275
  Planarity :  0.004   0.034    465
  Dihedral  :  5.432  18.030    355
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 28.57 %
    Favored  : 69.52 %
  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: -5.92 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.51 (0.15), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 293 
 PHE   0.005   0.001   PHE B 283 
 TRP   0.009   0.001   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2390)
  covalent geometry    : angle       0.66701 ( 3175)
  hydrogen bonds       : bond        0.04128 (    8)
  hydrogen bonds       : angle       4.11687 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  307 MET cc_start: 0.6709 (ttt) cc_final: 0.6424 (ttt)
REVERT: C  323 MET cc_start: 0.7293 (mtm) cc_final: 0.6242 (ttt)
REVERT: C  336 MET cc_start: 0.6998 (ptt) cc_final: 0.6658 (ptp)
REVERT: D  323 MET cc_start: 0.6790 (ptm) cc_final: 0.6086 (ppp)
REVERT: D  336 MET cc_start: 0.6183 (ptt) cc_final: 0.5318 (tpp)
REVERT: E  311 MET cc_start: 0.4541 (tmm) cc_final: 0.4114 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0370
  time to fit residues: 2.3722
Evaluate side-chains
  47 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  322 MET
Chi-restraints excluded: chain C residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0010
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 343 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 = 0.5180 r_free = 0.5180 target = 0.246895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4985 r_free = 0.4985 target = 0.214799 restraints weight = 2521.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.218830 restraints weight = 1767.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.221741 restraints weight = 1326.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.5057 r_free = 0.5057 target = 0.224079 restraints weight = 1055.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5069 r_free = 0.5069 target = 0.225724 restraints weight = 875.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.5083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5848
moved from start:          0.8445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2390  Z= 0.156
  Angle     :  0.719   8.915   3175  Z= 0.375
  Chirality :  0.040   0.177    275
  Planarity :  0.004   0.038    465
  Dihedral  :  5.787  21.043    355
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 20.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.49 %
    Favored  : 85.51 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.14 %
    Favored  : 70.48 %
  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: -5.93 (0.20), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.52 (0.16), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 293 
 PHE   0.007   0.001   PHE E 283 
 TRP   0.011   0.001   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 2390)
  covalent geometry    : angle       0.71941 ( 3175)
  hydrogen bonds       : bond        0.04296 (    8)
  hydrogen bonds       : angle       4.24183 (   21)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.116 
Fit side-chains
REVERT: C  307 MET cc_start: 0.5910 (tpt) cc_final: 0.3179 (ptp)
REVERT: C  336 MET cc_start: 0.7004 (ptt) cc_final: 0.6667 (ptp)
REVERT: D  323 MET cc_start: 0.6937 (ptm) cc_final: 0.6186 (ppp)
REVERT: D  336 MET cc_start: 0.6497 (ptt) cc_final: 0.5559 (tpp)
  outliers start: 5
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0357
  time to fit residues: 2.1448
Evaluate side-chains
  49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  322 MET
Chi-restraints excluded: chain C residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0370
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 343 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 = 0.5255 r_free = 0.5255 target = 0.254395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5046 r_free = 0.5046 target = 0.221636 restraints weight = 2494.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.225720 restraints weight = 1740.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5108 r_free = 0.5108 target = 0.229004 restraints weight = 1302.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5125 r_free = 0.5125 target = 0.231209 restraints weight = 1025.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.5139 r_free = 0.5139 target = 0.233063 restraints weight = 850.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.5154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5762
moved from start:          0.8654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2390  Z= 0.127
  Angle     :  0.667   8.169   3175  Z= 0.349
  Chirality :  0.039   0.141    275
  Planarity :  0.004   0.040    465
  Dihedral  :  5.535  20.465    355
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 27.14 %
    Favored  : 70.95 %
  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: -5.86 (0.21), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.46 (0.16), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 293 
 PHE   0.006   0.001   PHE E 283 
 TRP   0.010   0.001   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2390)
  covalent geometry    : angle       0.66652 ( 3175)
  hydrogen bonds       : bond        0.03908 (    8)
  hydrogen bonds       : angle       4.11116 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 654.67 seconds
wall clock time: 11 minutes 57.51 seconds (717.51 seconds total)