Starting phenix.real_space_refine
on Tue Mar  3 10:47:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2026/7da4_30622.cif"
  }
  resolution = 4.24
  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: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C     315      2.51       5
     N      84      2.21       5
     O     102      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: 507
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 169
          Classifications: {'peptide': 22}
          Link IDs: {'TRANS': 21}
  Restraints were copied for chains:
    A, C
  Time building chain proxies: 0.12, per 1000 atoms: 0.24
  Number of scatterers: 507
  At special positions: 0
  Unit cell: (42.4, 38.16, 29.68, 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       6     16.00
     O     102      8.00
     N      84      7.00
     C     315      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 18.7 milliseconds
  

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  120

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 0.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 171
        1.34 -     1.46: 88
        1.46 -     1.57: 245
        1.57 -     1.69: 0
        1.69 -     1.81: 9
  Bond restraints: 513
  Sorted by residual:
  bond pdb=" CA  ASN A 464 "
       pdb=" CB  ASN A 464 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.69e-02 3.50e+03 6.73e+00
  bond pdb=" CA  ASN B 464 "
       pdb=" CB  ASN B 464 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.044 1.69e-02 3.50e+03 6.68e+00
  bond pdb=" CA  ASN C 464 "
       pdb=" CB  ASN C 464 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.043 1.69e-02 3.50e+03 6.61e+00
  bond pdb=" CB  VAL B 458 "
       pdb=" CG1 VAL B 458 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.53e+00
  bond pdb=" CB  VAL C 458 "
       pdb=" CG1 VAL C 458 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  ... (remaining 508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 575
        1.66 -     3.32: 91
        3.32 -     4.98: 12
        4.98 -     6.64: 12
        6.64 -     8.30: 6
  Bond angle restraints: 696
  Sorted by residual:
  angle pdb=" C   ASN A 464 "
        pdb=" N   TYR A 465 "
        pdb=" CA  TYR A 465 "
      ideal   model   delta    sigma   weight residual
     121.54  129.84   -8.30 1.91e+00 2.74e-01 1.89e+01
  angle pdb=" C   ASN B 464 "
        pdb=" N   TYR B 465 "
        pdb=" CA  TYR B 465 "
      ideal   model   delta    sigma   weight residual
     121.54  129.83   -8.29 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" C   ASN C 464 "
        pdb=" N   TYR C 465 "
        pdb=" CA  TYR C 465 "
      ideal   model   delta    sigma   weight residual
     121.54  129.78   -8.24 1.91e+00 2.74e-01 1.86e+01
  angle pdb=" N   TYR C 465 "
        pdb=" CA  TYR C 465 "
        pdb=" CB  TYR C 465 "
      ideal   model   delta    sigma   weight residual
     110.49  104.05    6.44 1.69e+00 3.50e-01 1.45e+01
  angle pdb=" N   TYR A 465 "
        pdb=" CA  TYR A 465 "
        pdb=" CB  TYR A 465 "
      ideal   model   delta    sigma   weight residual
     110.49  104.09    6.40 1.69e+00 3.50e-01 1.44e+01
  ... (remaining 691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.76: 264
       17.76 -    35.52: 36
       35.52 -    53.27: 0
       53.27 -    71.03: 0
       71.03 -    88.78: 3
  Dihedral angle restraints: 303
    sinusoidal: 114
      harmonic: 189
  Sorted by residual:
  dihedral pdb=" CA  VAL B 460 "
           pdb=" C   VAL B 460 "
           pdb=" N   GLY B 461 "
           pdb=" CA  GLY B 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.48   25.52     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  VAL C 460 "
           pdb=" C   VAL C 460 "
           pdb=" N   GLY C 461 "
           pdb=" CA  GLY C 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.48   25.52     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  VAL A 460 "
           pdb=" C   VAL A 460 "
           pdb=" N   GLY A 461 "
           pdb=" CA  GLY A 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.51   25.49     0      5.00e+00 4.00e-02 2.60e+01
  ... (remaining 300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.065: 66
       0.065 -    0.129: 12
       0.129 -    0.193: 0
       0.193 -    0.257: 0
       0.257 -    0.321: 3
  Chirality restraints: 81
  Sorted by residual:
  chirality pdb=" CA  ASN A 464 "
            pdb=" N   ASN A 464 "
            pdb=" C   ASN A 464 "
            pdb=" CB  ASN A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  ASN C 464 "
            pdb=" N   ASN C 464 "
            pdb=" C   ASN C 464 "
            pdb=" CB  ASN C 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ASN B 464 "
            pdb=" N   ASN B 464 "
            pdb=" C   ASN B 464 "
            pdb=" CB  ASN B 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.51e+00
  ... (remaining 78 not shown)

  Planarity restraints: 90
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 464 "    0.008 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   ASN C 464 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN C 464 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR C 465 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 464 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.89e+00
        pdb=" C   ASN A 464 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A 464 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A 465 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 464 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   ASN B 464 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASN B 464 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TYR B 465 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 87 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 158
        2.78 -     3.31: 608
        3.31 -     3.84: 849
        3.84 -     4.37: 978
        4.37 -     4.90: 1760
  Nonbonded interactions: 4353
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 454 "
            pdb=" O   SER B 456 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" ND2 ASN A 454 "
            pdb=" O   SER A 456 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" ND2 ASN C 454 "
            pdb=" O   SER C 456 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" CG  ASN B 464 "
            pdb=" N   ASN C 464 "
     model   vdw
     2.485 3.350
  nonbonded pdb=" N   ASN C 463 "
            pdb=" OD1 ASN C 463 "
     model   vdw
     2.497 3.120
  ... (remaining 4348 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:                    0.010
  Process input model:                     1.950
  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:0.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    3.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
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      :  0.010   0.053    513  Z= 0.484
  Angle     :  1.542   8.296    696  Z= 0.836
  Chirality :  0.076   0.321     81
  Planarity :  0.006   0.017     90
  Dihedral  : 17.158  88.782    183
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 79.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 50.00 %
    Favored  : 50.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 30.00 %
    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: -8.65 (0.56), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.59 (0.42), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.005   TYR B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00992 (  513)
  covalent geometry    : angle       1.54213 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.011 
Fit side-chains
REVERT: B  465 TYR cc_start: 0.8246 (p90) cc_final: 0.7728 (p90)
REVERT: A  453 TYR cc_start: 0.5826 (p90) cc_final: 0.5542 (p90)
REVERT: C  468 MET cc_start: 0.7834 (ttp) cc_final: 0.7462 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0134
  time to fit residues: 0.4565
Evaluate side-chains
  25 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  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:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 451 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.161103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.118501 restraints weight = 745.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.123092 restraints weight = 486.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.126619 restraints weight = 374.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.129105 restraints weight = 315.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.130889 restraints weight = 277.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6055
moved from start:          0.5664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026    513  Z= 0.196
  Angle     :  0.891   5.551    696  Z= 0.475
  Chirality :  0.042   0.143     81
  Planarity :  0.004   0.012     90
  Dihedral  :  7.445  20.299     69
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 31.67 %
    Favored  : 68.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  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: -7.41 (0.62), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.64 (0.47), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.004   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (  513)
  covalent geometry    : angle       0.89070 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.011 
Fit side-chains
   revert: symmetry clash
REVERT: A  451 ASN cc_start: 0.8098 (m-40) cc_final: 0.7813 (p0)
REVERT: C  453 TYR cc_start: 0.5803 (p90) cc_final: 0.5339 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0117
  time to fit residues: 0.4601
Evaluate side-chains
  32 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.3610

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

Flipped N/Q/H residues before XYZ refinement:
C 459 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.329694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5563 r_free = 0.5563 target = 0.262171 restraints weight = 955.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.261252 restraints weight = 1064.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.261252 restraints weight = 1121.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.261252 restraints weight = 1121.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.261252 restraints weight = 1121.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.4981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          0.7201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024    513  Z= 0.152
  Angle     :  0.748   4.386    696  Z= 0.395
  Chirality :  0.038   0.116     81
  Planarity :  0.003   0.012     90
  Dihedral  :  6.650  17.369     69
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.33 %
    Favored  : 71.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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: -6.49 (0.75), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.94 (0.57), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (  513)
  covalent geometry    : angle       0.74816 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.011 
Fit side-chains
   revert: symmetry clash
REVERT: A  463 ASN cc_start: 0.5876 (p0) cc_final: 0.5535 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0111
  time to fit residues: 0.4231
Evaluate side-chains
  30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0870
   overall best weight:    0.3573

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN
C 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.171299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.126231 restraints weight = 776.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.130307 restraints weight = 547.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.134181 restraints weight = 431.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.136486 restraints weight = 361.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.138996 restraints weight = 316.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6107
moved from start:          0.8208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019    513  Z= 0.142
  Angle     :  0.733   5.277    696  Z= 0.389
  Chirality :  0.039   0.131     81
  Planarity :  0.003   0.013     90
  Dihedral  :  6.156  15.011     69
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 31.67 %
    Favored  : 68.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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: -6.35 (0.79), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.83 (0.61), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (  513)
  covalent geometry    : angle       0.73345 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.011 
Fit side-chains
REVERT: A  463 ASN cc_start: 0.5946 (p0) cc_final: 0.5616 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0118
  time to fit residues: 0.4583
Evaluate side-chains
  28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 2 optimal weight:    0.2980
   chunk 3 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.3313

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.182799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.132985 restraints weight = 669.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.138124 restraints weight = 459.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.142491 restraints weight = 358.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.144958 restraints weight = 299.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.148190 restraints weight = 265.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6013
moved from start:          0.8629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026    513  Z= 0.159
  Angle     :  0.766   4.929    696  Z= 0.407
  Chirality :  0.042   0.129     81
  Planarity :  0.003   0.010     90
  Dihedral  :  6.260  14.537     69
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 31.67 %
    Favored  : 68.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  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: -6.16 (0.77), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.69 (0.59), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (  513)
  covalent geometry    : angle       0.76620 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.012 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0116
  time to fit residues: 0.4830
Evaluate side-chains
  29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0570
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.1807

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN
A 464 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.316616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.189897 restraints weight = 982.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.195533 restraints weight = 779.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.198137 restraints weight = 661.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.202076 restraints weight = 587.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.205215 restraints weight = 535.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6013
moved from start:          0.9648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020    513  Z= 0.155
  Angle     :  0.804   5.695    696  Z= 0.419
  Chirality :  0.041   0.128     81
  Planarity :  0.002   0.008     90
  Dihedral  :  5.986  15.501     69
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.33 %
    Favored  : 71.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -6.01 (0.75), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.58 (0.57), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (  513)
  covalent geometry    : angle       0.80391 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.011 
Fit side-chains
REVERT: A  451 ASN cc_start: 0.6502 (p0) cc_final: 0.6275 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0117
  time to fit residues: 0.4438
Evaluate side-chains
  27 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0470
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.3143

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN
A 464 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.308070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.183157 restraints weight = 1038.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.188503 restraints weight = 789.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.191678 restraints weight = 657.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.196298 restraints weight = 578.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.198667 restraints weight = 516.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
moved from start:          0.9836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022    513  Z= 0.159
  Angle     :  0.771   4.919    696  Z= 0.401
  Chirality :  0.040   0.116     81
  Planarity :  0.002   0.006     90
  Dihedral  :  5.819  14.241     69
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.00 %
    Favored  : 75.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -5.90 (0.72), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.49 (0.55), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (  513)
  covalent geometry    : angle       0.77077 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.011 
Fit side-chains
   revert: symmetry clash
REVERT: B  451 ASN cc_start: 0.8190 (m110) cc_final: 0.7432 (t0)
REVERT: B  467 THR cc_start: 0.9068 (t) cc_final: 0.8407 (m)
REVERT: C  456 SER cc_start: 0.7544 (t) cc_final: 0.7262 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0114
  time to fit residues: 0.3973
Evaluate side-chains
  29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   overall best weight:    0.5310

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

Flipped N/Q/H residues before XYZ refinement:
B 459 GLN
A 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.293854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.183133 restraints weight = 1011.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.188915 restraints weight = 826.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.192263 restraints weight = 674.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.196413 restraints weight = 593.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.196858 restraints weight = 525.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5996
moved from start:          1.0090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026    513  Z= 0.167
  Angle     :  0.777   4.932    696  Z= 0.406
  Chirality :  0.042   0.115     81
  Planarity :  0.002   0.007     90
  Dihedral  :  6.222  14.499     69
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.33 %
    Favored  : 71.67 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  0.00 %
    Favored  : 98.33 %
  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: -5.90 (0.74), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.49 (0.56), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (  513)
  covalent geometry    : angle       0.77692 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.014 
Fit side-chains
REVERT: B  451 ASN cc_start: 0.7939 (m110) cc_final: 0.6734 (t0)
REVERT: B  453 TYR cc_start: 0.5826 (p90) cc_final: 0.5506 (p90)
REVERT: B  465 TYR cc_start: 0.6896 (p90) cc_final: 0.6601 (p90)
REVERT: B  467 THR cc_start: 0.9035 (t) cc_final: 0.8257 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0152
  time to fit residues: 0.5428
Evaluate side-chains
  28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5313

-------------------------------------------------------------------------------
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 = 0.4985 r_free = 0.4985 target = 0.188337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.133331 restraints weight = 762.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.136241 restraints weight = 599.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.137890 restraints weight = 507.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.139652 restraints weight = 455.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.140470 restraints weight = 416.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6170
moved from start:          1.0287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030    513  Z= 0.187
  Angle     :  0.832   5.381    696  Z= 0.435
  Chirality :  0.045   0.156     81
  Planarity :  0.003   0.017     90
  Dihedral  :  6.283  15.355     69
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.00 %
    Favored  : 75.00 %
  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: -5.71 (0.75), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.57), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (  513)
  covalent geometry    : angle       0.83191 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.013 
Fit side-chains
REVERT: B  449 LEU cc_start: 0.8445 (pt) cc_final: 0.8205 (pt)
REVERT: B  451 ASN cc_start: 0.8064 (m110) cc_final: 0.6851 (t0)
REVERT: B  453 TYR cc_start: 0.5811 (p90) cc_final: 0.5358 (p90)
REVERT: B  466 LEU cc_start: 0.8138 (pp) cc_final: 0.7897 (pp)
REVERT: B  467 THR cc_start: 0.9174 (t) cc_final: 0.8380 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0316
  time to fit residues: 1.0377
Evaluate side-chains
  28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4313

-------------------------------------------------------------------------------
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 = 0.4980 r_free = 0.4980 target = 0.213853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.151612 restraints weight = 724.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.155313 restraints weight = 562.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.158477 restraints weight = 472.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.160671 restraints weight = 417.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.160671 restraints weight = 380.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.4493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6042
moved from start:          1.0552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020    513  Z= 0.165
  Angle     :  0.774   4.745    696  Z= 0.407
  Chirality :  0.043   0.127     81
  Planarity :  0.002   0.012     90
  Dihedral  :  5.879  15.222     69
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.67 %
    Favored  : 73.33 %
  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: -5.70 (0.74), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.57), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (  513)
  covalent geometry    : angle       0.77436 (  696)

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

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

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  120 Ramachandran restraints generated.
    60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.023 
Fit side-chains
REVERT: B  451 ASN cc_start: 0.8066 (m110) cc_final: 0.6811 (t0)
REVERT: B  453 TYR cc_start: 0.5724 (p90) cc_final: 0.5264 (p90)
REVERT: B  465 TYR cc_start: 0.6626 (p90) cc_final: 0.6395 (p90)
REVERT: B  467 THR cc_start: 0.9049 (t) cc_final: 0.8260 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0144
  time to fit residues: 0.5143
Evaluate side-chains
  28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0870
   overall best weight:    0.2673

-------------------------------------------------------------------------------
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 = 0.5361 r_free = 0.5361 target = 0.340209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.273245 restraints weight = 1015.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.273245 restraints weight = 1066.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.273245 restraints weight = 1066.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.273245 restraints weight = 1066.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.273245 restraints weight = 1066.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.5245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5984
moved from start:          1.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025    513  Z= 0.159
  Angle     :  0.775   4.703    696  Z= 0.406
  Chirality :  0.044   0.153     81
  Planarity :  0.003   0.017     90
  Dihedral  :  5.448  17.022     69
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  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: -5.55 (0.74), residues: 60
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.22 (0.57), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.001   TYR B 453 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (  513)
  covalent geometry    : angle       0.77479 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 247.64 seconds
wall clock time: 4 minutes 57.50 seconds (297.50 seconds total)