Starting phenix.real_space_refine
on Tue Mar  3 10:47:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mc2_63785/03_2026/9mc2_63785.map"
  }
  resolution = 3.55
  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=   0.001
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: 3
    Type Number    sf(0)   Gaussians
     C     336      2.51       5
     N      84      2.21       5
     O      78      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 498
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 83
          Classifications: {'peptide': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 9}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.08, per 1000 atoms: 0.16
  Number of scatterers: 498
  At special positions: 0
  Unit cell: (43.46, 44.52, 29.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O      78      8.00
     N      84      7.00
     C     336      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: 0.02
  Conformation dependent library (CDL) restraints added in 13.9 milliseconds
  

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  108

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 1 sheets defined
      0.0% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.01
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.656A  pdb=" N   VAL D 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   VAL E 309 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE D 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)

    4 hydrogen bonds defined for protein.
    12 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: 0.03

  Time building geometry restraints manager: 0.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 72
        1.29 -     1.35: 66
        1.35 -     1.41: 42
        1.41 -     1.48: 78
        1.48 -     1.54: 246
  Bond restraints: 504
  Sorted by residual:
  bond pdb=" CB  ILE A 308 "
       pdb=" CG1 ILE A 308 "
    ideal  model  delta    sigma   weight residual
    1.530  1.510  0.020 2.00e-02 2.50e+03 9.61e-01
  bond pdb=" CB  LYS F 274 "
       pdb=" CG  LYS F 274 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.14e-01
  bond pdb=" CB  LYS A 274 "
       pdb=" CG  LYS A 274 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.12e-01
  bond pdb=" CB  ILE B 308 "
       pdb=" CG1 ILE B 308 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.019 2.00e-02 2.50e+03 9.07e-01
  bond pdb=" CB  ILE D 308 "
       pdb=" CG1 ILE D 308 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.019 2.00e-02 2.50e+03 8.92e-01
  ... (remaining 499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.73: 520
        0.73 -     1.45: 116
        1.45 -     2.18: 18
        2.18 -     2.90: 6
        2.90 -     3.63: 12
  Bond angle restraints: 672
  Sorted by residual:
  angle pdb=" C   GLN A 307 "
        pdb=" N   ILE A 308 "
        pdb=" CA  ILE A 308 "
      ideal   model   delta    sigma   weight residual
     122.57  120.26    2.31 1.65e+00 3.67e-01 1.96e+00
  angle pdb=" C   GLN D 307 "
        pdb=" N   ILE D 308 "
        pdb=" CA  ILE D 308 "
      ideal   model   delta    sigma   weight residual
     122.57  120.31    2.26 1.65e+00 3.67e-01 1.87e+00
  angle pdb=" C   GLN F 307 "
        pdb=" N   ILE F 308 "
        pdb=" CA  ILE F 308 "
      ideal   model   delta    sigma   weight residual
     122.57  120.35    2.22 1.65e+00 3.67e-01 1.81e+00
  angle pdb=" C   GLN B 307 "
        pdb=" N   ILE B 308 "
        pdb=" CA  ILE B 308 "
      ideal   model   delta    sigma   weight residual
     122.57  120.35    2.22 1.65e+00 3.67e-01 1.81e+00
  angle pdb=" C   GLN E 307 "
        pdb=" N   ILE E 308 "
        pdb=" CA  ILE E 308 "
      ideal   model   delta    sigma   weight residual
     122.57  120.36    2.21 1.65e+00 3.67e-01 1.79e+00
  ... (remaining 667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -     4.83: 192
        4.83 -     9.65: 42
        9.65 -    14.46: 36
       14.46 -    19.28: 6
       19.28 -    24.10: 24
  Dihedral angle restraints: 300
    sinusoidal: 126
      harmonic: 174
  Sorted by residual:
  dihedral pdb=" CA  LYS F 311 "
           pdb=" C   LYS F 311 "
           pdb=" N   PRO F 312 "
           pdb=" CA  PRO F 312 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -168.98  -11.02     0      5.00e+00 4.00e-02 4.85e+00
  dihedral pdb=" CA  LYS B 311 "
           pdb=" C   LYS B 311 "
           pdb=" N   PRO B 312 "
           pdb=" CA  PRO B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -168.99  -11.01     0      5.00e+00 4.00e-02 4.85e+00
  dihedral pdb=" CA  LYS D 311 "
           pdb=" C   LYS D 311 "
           pdb=" N   PRO D 312 "
           pdb=" CA  PRO D 312 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -169.03  -10.97     0      5.00e+00 4.00e-02 4.82e+00
  ... (remaining 297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.030: 31
       0.030 -    0.058: 17
       0.058 -    0.086: 12
       0.086 -    0.114: 6
       0.114 -    0.142: 12
  Chirality restraints: 78
  Sorted by residual:
  chirality pdb=" CA  PRO E 312 "
            pdb=" N   PRO E 312 "
            pdb=" C   PRO E 312 "
            pdb=" CB  PRO E 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  PRO C 312 "
            pdb=" N   PRO C 312 "
            pdb=" C   PRO C 312 "
            pdb=" CB  PRO C 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  PRO D 312 "
            pdb=" N   PRO D 312 "
            pdb=" C   PRO D 312 "
            pdb=" CB  PRO D 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 75 not shown)

  Planarity restraints: 78
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 311 "   -0.003 2.00e-02 2.50e+03   5.98e-03 3.58e-01
        pdb=" C   LYS A 311 "    0.010 2.00e-02 2.50e+03
        pdb=" O   LYS A 311 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   PRO A 312 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 311 "   -0.003 2.00e-02 2.50e+03   5.91e-03 3.49e-01
        pdb=" C   LYS C 311 "    0.010 2.00e-02 2.50e+03
        pdb=" O   LYS C 311 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   PRO C 312 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 311 "   -0.003 2.00e-02 2.50e+03   5.83e-03 3.39e-01
        pdb=" C   LYS D 311 "    0.010 2.00e-02 2.50e+03
        pdb=" O   LYS D 311 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   PRO D 312 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 75 not shown)

  Histogram of nonbonded interaction distances:
        2.65 -     3.10: 352
        3.10 -     3.55: 436
        3.55 -     4.00: 612
        4.00 -     4.45: 687
        4.45 -     4.90: 1313
  Nonbonded interactions: 3400
  Sorted by model distance:
  nonbonded pdb=" N   LYS E 274 "
            pdb=" O   LYS E 274 "
     model   vdw
     2.654 2.496
  nonbonded pdb=" N   LYS B 274 "
            pdb=" O   LYS B 274 "
     model   vdw
     2.654 2.496
  nonbonded pdb=" N   LYS A 274 "
            pdb=" O   LYS A 274 "
     model   vdw
     2.654 2.496
  nonbonded pdb=" N   LYS D 274 "
            pdb=" O   LYS D 274 "
     model   vdw
     2.654 2.496
  nonbonded pdb=" N   LYS F 274 "
            pdb=" O   LYS F 274 "
     model   vdw
     2.655 2.496
  ... (remaining 3395 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'
  selection = chain 'F'
}

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:             0.710
  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:          0.010
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     1.530
  Find NCS groups from input model:        0.010
  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:0.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    2.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
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      :  0.009   0.036    504  Z= 0.386
  Angle     :  0.787   3.625    672  Z= 0.399
  Chirality :  0.070   0.142     78
  Planarity :  0.002   0.006     78
  Dihedral  : 10.273  24.101    192
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 34.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -4.34 (0.55), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.42), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00916 (  504)
  covalent geometry    : angle       0.78683 (  672)
  hydrogen bonds       : bond        0.17239 (    4)
  hydrogen bonds       : angle      10.10895 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0556
  time to fit residues: 0.8169
Evaluate side-chains
  11 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0770
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5577

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
D 307 GLN
E 307 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.074655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.060154 restraints weight = 941.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.063458 restraints weight = 446.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.065911 restraints weight = 263.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.067529 restraints weight = 176.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.069102 restraints weight = 130.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018    504  Z= 0.132
  Angle     :  0.507   2.804    672  Z= 0.264
  Chirality :  0.061   0.132     78
  Planarity :  0.005   0.024     78
  Dihedral  :  3.521   7.877     66
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  9.26 %
    Allowed  : 18.52 %
    Favored  : 72.22 %
  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: -2.06 (0.85), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.65), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR C 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (  504)
  covalent geometry    : angle       0.50706 (  672)
  hydrogen bonds       : bond        0.04154 (    4)
  hydrogen bonds       : angle       6.78075 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 14
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 14
  average time/residue: 0.0439
  time to fit residues: 0.6511
Evaluate side-chains
  16 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7313

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

Flipped N/Q/H residues before XYZ refinement:
F 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.080010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.065354 restraints weight = 804.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.069205 restraints weight = 357.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.072221 restraints weight = 198.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.074328 restraints weight = 122.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.075758 restraints weight = 81.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.015    504  Z= 0.147
  Angle     :  0.514   2.666    672  Z= 0.264
  Chirality :  0.060   0.126     78
  Planarity :  0.005   0.022     78
  Dihedral  :  2.946   7.321     66
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  9.26 %
    Allowed  : 29.63 %
    Favored  : 61.11 %
  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: -0.99 (0.96), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.75 (0.73), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.004   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (  504)
  covalent geometry    : angle       0.51362 (  672)
  hydrogen bonds       : bond        0.03866 (    4)
  hydrogen bonds       : angle       6.56058 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.011 
Fit side-chains
REVERT: C  311 LYS cc_start: 0.7615 (mttt) cc_final: 0.7362 (mttp)
  outliers start: 5
  outliers final: 5
  residues processed: 13
  average time/residue: 0.0459
  time to fit residues: 0.6311
Evaluate side-chains
  16 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.8647

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.071482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.059973 restraints weight = 1018.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.062837 restraints weight = 419.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.064986 restraints weight = 234.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.066504 restraints weight = 152.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.067534 restraints weight = 107.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.017    504  Z= 0.163
  Angle     :  0.508   2.678    672  Z= 0.262
  Chirality :  0.061   0.126     78
  Planarity :  0.005   0.024     78
  Dihedral  :  3.041   7.478     66
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 25.93 %
    Favored  : 62.96 %
  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: -0.79 (0.97), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.59 (0.74), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.004   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (  504)
  covalent geometry    : angle       0.50771 (  672)
  hydrogen bonds       : bond        0.03360 (    4)
  hydrogen bonds       : angle       6.45317 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 13
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 14
  average time/residue: 0.0270
  time to fit residues: 0.4131
Evaluate side-chains
  19 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 13
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0030
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.3997

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.075695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062852 restraints weight = 969.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.065840 restraints weight = 418.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.068191 restraints weight = 239.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.069900 restraints weight = 157.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.071174 restraints weight = 111.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6635
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010    504  Z= 0.096
  Angle     :  0.434   2.671    672  Z= 0.221
  Chirality :  0.059   0.120     78
  Planarity :  0.005   0.025     78
  Dihedral  :  2.534   6.198     66
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 25.93 %
    Favored  : 62.96 %
  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: -0.97 (0.97), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.73 (0.74), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (  504)
  covalent geometry    : angle       0.43416 (  672)
  hydrogen bonds       : bond        0.02852 (    4)
  hydrogen bonds       : angle       6.16790 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 15
  average time/residue: 0.0326
  time to fit residues: 0.5254
Evaluate side-chains
  20 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.071378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.059726 restraints weight = 973.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.062612 restraints weight = 412.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.064819 restraints weight = 233.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.066386 restraints weight = 151.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.067476 restraints weight = 107.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015    504  Z= 0.135
  Angle     :  0.468   2.767    672  Z= 0.238
  Chirality :  0.060   0.123     78
  Planarity :  0.005   0.026     78
  Dihedral  :  2.751   6.652     66
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 25.93 %
    Favored  : 62.96 %
  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: -0.92 (0.98), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.69 (0.74), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (  504)
  covalent geometry    : angle       0.46810 (  672)
  hydrogen bonds       : bond        0.02830 (    4)
  hydrogen bonds       : angle       6.17522 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 13
  average time/residue: 0.0202
  time to fit residues: 0.2957
Evaluate side-chains
  18 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0970
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6643

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.067742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.056725 restraints weight = 1081.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.059649 restraints weight = 431.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.061793 restraints weight = 235.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.063380 restraints weight = 149.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.064476 restraints weight = 103.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.4081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015    504  Z= 0.128
  Angle     :  0.458   2.750    672  Z= 0.233
  Chirality :  0.060   0.122     78
  Planarity :  0.005   0.027     78
  Dihedral  :  2.735   6.692     66
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 27.78 %
    Favored  : 61.11 %
  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: -0.96 (0.99), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.72 (0.76), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (  504)
  covalent geometry    : angle       0.45791 (  672)
  hydrogen bonds       : bond        0.02880 (    4)
  hydrogen bonds       : angle       6.11401 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.011 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 13
  average time/residue: 0.0078
  time to fit residues: 0.1347
Evaluate side-chains
  17 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.071231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.059749 restraints weight = 1051.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.062696 restraints weight = 425.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.064948 restraints weight = 235.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.066524 restraints weight = 150.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.067645 restraints weight = 104.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.017    504  Z= 0.152
  Angle     :  0.492   2.836    672  Z= 0.252
  Chirality :  0.060   0.124     78
  Planarity :  0.005   0.027     78
  Dihedral  :  2.866   7.048     66
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 29.63 %
    Favored  : 59.26 %
  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: -1.00 (0.98), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.75 (0.75), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.004   TYR F 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (  504)
  covalent geometry    : angle       0.49225 (  672)
  hydrogen bonds       : bond        0.02812 (    4)
  hydrogen bonds       : angle       6.10328 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.019 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 10
  average time/residue: 0.0157
  time to fit residues: 0.2041
Evaluate side-chains
  15 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0370
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.3777

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.074199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.061612 restraints weight = 995.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064677 restraints weight = 436.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.066953 restraints weight = 248.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.068710 restraints weight = 164.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.070015 restraints weight = 116.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010    504  Z= 0.095
  Angle     :  0.437   2.714    672  Z= 0.223
  Chirality :  0.059   0.120     78
  Planarity :  0.005   0.026     78
  Dihedral  :  2.526   6.396     66
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 29.63 %
    Favored  : 59.26 %
  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: -1.06 (1.00), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.80 (0.76), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (  504)
  covalent geometry    : angle       0.43656 (  672)
  hydrogen bonds       : bond        0.02477 (    4)
  hydrogen bonds       : angle       6.02321 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.022 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 13
  average time/residue: 0.0147
  time to fit residues: 0.2551
Evaluate side-chains
  18 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8647

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.060224 restraints weight = 995.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.063175 restraints weight = 408.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.065439 restraints weight = 227.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.066981 restraints weight = 144.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068117 restraints weight = 101.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.4203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018    504  Z= 0.158
  Angle     :  0.498   2.809    672  Z= 0.255
  Chirality :  0.060   0.124     78
  Planarity :  0.005   0.027     78
  Dihedral  :  2.865   6.995     66
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 29.63 %
    Favored  : 59.26 %
  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: -1.04 (0.97), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.78 (0.74), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.004   TYR E 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (  504)
  covalent geometry    : angle       0.49823 (  672)
  hydrogen bonds       : bond        0.02748 (    4)
  hydrogen bonds       : angle       6.11319 (   12)

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

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

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  108 Ramachandran restraints generated.
    54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.013 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 11
  average time/residue: 0.0107
  time to fit residues: 0.1614
Evaluate side-chains
  16 residues out of total 54 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain F residue  308 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.8313

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.071819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.060474 restraints weight = 950.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.063447 restraints weight = 401.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.065714 restraints weight = 223.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.067222 restraints weight = 143.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.068360 restraints weight = 101.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018    504  Z= 0.156
  Angle     :  0.490   2.815    672  Z= 0.252
  Chirality :  0.060   0.123     78
  Planarity :  0.005   0.027     78
  Dihedral  :  2.923   7.345     66
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 29.63 %
    Favored  : 59.26 %
  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: -1.07 (0.96), residues: 54
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.81 (0.73), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.004   TYR E 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (  504)
  covalent geometry    : angle       0.48991 (  672)
  hydrogen bonds       : bond        0.02811 (    4)
  hydrogen bonds       : angle       6.10683 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 243.87 seconds
wall clock time: 5 minutes 6.83 seconds (306.83 seconds total)