Starting phenix.real_space_refine
on Fri Aug 22 18:57:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvh_42620/08_2025/8uvh_42620.map"
  }
  resolution = 2.33
  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=   0.003 sd=   0.066
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      60      5.16       5
     C    4786      2.51       5
     N    1126      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7158
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3579
          Classifications: {'peptide': 459}
          Link IDs: {'PTRANS': 29, 'TRANS': 429}
          Chain breaks: 5
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.21, per 1000 atoms: 0.31
  Number of scatterers: 7158
  At special positions: 0
  Unit cell: (76.725, 99.825, 79.2, 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      60     16.00
     O    1186      8.00
     N    1126      7.00
     C    4786      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: 0.52
  Conformation dependent library (CDL) restraints added in 274.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      84.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 20
      removed outlier: 3.610A  pdb=" N   LEU A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
      removed outlier: 4.421A  pdb=" N   LEU A  25 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 52
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 61 through 70
      removed outlier: 3.515A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 84 through 103
    Processing helix  chain 'A' and resid 104 through 118
      removed outlier: 3.588A  pdb=" N   ARG A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 137
    Processing helix  chain 'A' and resid 140 through 158
      Proline residue:  A 150  - end of helix
    Processing helix  chain 'A' and resid 202 through 220
      removed outlier: 3.520A  pdb=" N   ILE A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   CYS A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 241
      removed outlier: 3.593A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 276
      Proline residue:  A 259  - end of helix
    Processing helix  chain 'A' and resid 292 through 308
    Processing helix  chain 'A' and resid 313 through 334
      removed outlier: 4.135A  pdb=" N   ASP A 334 " --> pdb=" O   TRP A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 368
    Processing helix  chain 'A' and resid 398 through 406
    Processing helix  chain 'A' and resid 407 through 427
    Processing helix  chain 'A' and resid 428 through 437
    Processing helix  chain 'A' and resid 438 through 441
    Processing helix  chain 'A' and resid 444 through 460
    Processing helix  chain 'A' and resid 464 through 483
      Proline residue:  A 474  - end of helix
    Processing helix  chain 'A' and resid 486 through 498
      removed outlier: 3.654A  pdb=" N   ILE A 490 " --> pdb=" O   ASN A 486 " (cutoff:3.500A)
      Proline residue:  A 493  - end of helix
    Processing helix  chain 'A' and resid 508 through 517
      removed outlier: 4.026A  pdb=" N   TYR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 547
      removed outlier: 3.878A  pdb=" N   ILE A 531 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 553
    Processing helix  chain 'A' and resid 558 through 562
    Processing helix  chain 'B' and resid 14 through 20
    Processing helix  chain 'B' and resid 21 through 25
      removed outlier: 4.421A  pdb=" N   LEU B  25 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 52
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.515A  pdb=" N   LEU B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 74 through 80
    Processing helix  chain 'B' and resid 84 through 103
    Processing helix  chain 'B' and resid 104 through 118
      removed outlier: 3.588A  pdb=" N   ARG B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 137
    Processing helix  chain 'B' and resid 140 through 158
      Proline residue:  B 150  - end of helix
    Processing helix  chain 'B' and resid 202 through 220
      removed outlier: 3.520A  pdb=" N   ILE B 212 " --> pdb=" O   MET B 208 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   CYS B 213 " --> pdb=" O   THR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 241
      removed outlier: 3.592A  pdb=" N   VAL B 231 " --> pdb=" O   THR B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 276
      Proline residue:  B 259  - end of helix
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 313 through 334
      removed outlier: 4.135A  pdb=" N   ASP B 334 " --> pdb=" O   TRP B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 368
    Processing helix  chain 'B' and resid 398 through 406
    Processing helix  chain 'B' and resid 407 through 427
    Processing helix  chain 'B' and resid 428 through 437
    Processing helix  chain 'B' and resid 438 through 441
    Processing helix  chain 'B' and resid 444 through 460
    Processing helix  chain 'B' and resid 464 through 483
      Proline residue:  B 474  - end of helix
    Processing helix  chain 'B' and resid 486 through 498
      removed outlier: 3.654A  pdb=" N   ILE B 490 " --> pdb=" O   ASN B 486 " (cutoff:3.500A)
      Proline residue:  B 493  - end of helix
    Processing helix  chain 'B' and resid 508 through 517
      removed outlier: 4.025A  pdb=" N   TYR B 517 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 547
      removed outlier: 3.878A  pdb=" N   ILE B 531 " --> pdb=" O   LYS B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 553
    Processing helix  chain 'B' and resid 558 through 562

    512 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1131
        1.33 -     1.45: 1881
        1.45 -     1.57: 4234
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 7346
  Sorted by residual:
  bond pdb=" C   PRO B 444 "
       pdb=" O   PRO B 444 "
    ideal  model  delta    sigma   weight residual
    1.240  1.205  0.035 1.12e-02 7.97e+03 9.79e+00
  bond pdb=" C   PRO A 444 "
       pdb=" O   PRO A 444 "
    ideal  model  delta    sigma   weight residual
    1.240  1.206  0.035 1.12e-02 7.97e+03 9.54e+00
  bond pdb=" CA  SER B  60 "
       pdb=" CB  SER B  60 "
    ideal  model  delta    sigma   weight residual
    1.529  1.485  0.044 1.74e-02 3.30e+03 6.30e+00
  bond pdb=" N   LEU B 440 "
       pdb=" CA  LEU B 440 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.26e+00
  bond pdb=" CA  SER A  60 "
       pdb=" CB  SER A  60 "
    ideal  model  delta    sigma   weight residual
    1.529  1.486  0.043 1.74e-02 3.30e+03 6.21e+00
  ... (remaining 7341 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 9657
        1.41 -     2.82: 260
        2.82 -     4.23: 69
        4.23 -     5.64: 28
        5.64 -     7.05: 4
  Bond angle restraints: 10018
  Sorted by residual:
  angle pdb=" N   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" C   HIS A 441 "
      ideal   model   delta    sigma   weight residual
     113.20  107.59    5.61 1.21e+00 6.83e-01 2.15e+01
  angle pdb=" N   HIS B 441 "
        pdb=" CA  HIS B 441 "
        pdb=" C   HIS B 441 "
      ideal   model   delta    sigma   weight residual
     113.20  107.60    5.60 1.21e+00 6.83e-01 2.15e+01
  angle pdb=" N   LEU A 440 "
        pdb=" CA  LEU A 440 "
        pdb=" C   LEU A 440 "
      ideal   model   delta    sigma   weight residual
     113.02  107.80    5.22 1.20e+00 6.94e-01 1.89e+01
  angle pdb=" N   LEU B 440 "
        pdb=" CA  LEU B 440 "
        pdb=" C   LEU B 440 "
      ideal   model   delta    sigma   weight residual
     113.02  107.80    5.22 1.20e+00 6.94e-01 1.89e+01
  angle pdb=" CA  PRO A 444 "
        pdb=" C   PRO A 444 "
        pdb=" N   PRO A 445 "
      ideal   model   delta    sigma   weight residual
     117.93  122.31   -4.38 1.20e+00 6.94e-01 1.33e+01
  ... (remaining 10013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 4018
       16.77 -    33.55: 258
       33.55 -    50.32: 34
       50.32 -    67.10: 10
       67.10 -    83.87: 6
  Dihedral angle restraints: 4326
    sinusoidal: 1656
      harmonic: 2670
  Sorted by residual:
  dihedral pdb=" CA  PHE A  18 "
           pdb=" C   PHE A  18 "
           pdb=" N   VAL A  19 "
           pdb=" CA  VAL A  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.76  -19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PHE B  18 "
           pdb=" C   PHE B  18 "
           pdb=" N   VAL B  19 "
           pdb=" CA  VAL B  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  LEU B  65 "
           pdb=" C   LEU B  65 "
           pdb=" N   LEU B  66 "
           pdb=" CA  LEU B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.25  -17.75     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 4323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 973
       0.050 -    0.101: 200
       0.101 -    0.151: 35
       0.151 -    0.201: 0
       0.201 -    0.251: 4
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" CA  TYR A  82 "
            pdb=" N   TYR A  82 "
            pdb=" C   TYR A  82 "
            pdb=" CB  TYR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  TYR B  82 "
            pdb=" N   TYR B  82 "
            pdb=" C   TYR B  82 "
            pdb=" CB  TYR B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  LEU A 440 "
            pdb=" N   LEU A 440 "
            pdb=" C   LEU A 440 "
            pdb=" CB  LEU A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1209 not shown)

  Planarity restraints: 1200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 437 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   MET A 437 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   MET A 437 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A 438 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 437 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   MET B 437 "    0.060 2.00e-02 2.50e+03
        pdb=" O   MET B 437 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU B 438 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B  82 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.14e+00
        pdb=" C   TYR B  82 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   TYR B  82 "    0.019 2.00e-02 2.50e+03
        pdb=" N   MET B  83 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1197 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1625
        2.78 -     3.31: 7503
        3.31 -     3.84: 12860
        3.84 -     4.37: 15004
        4.37 -     4.90: 25992
  Nonbonded interactions: 62984
  Sorted by model distance:
  nonbonded pdb=" O   MET B 137 "
            pdb=" OG1 THR B 223 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   MET A 137 "
            pdb=" OG1 THR A 223 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   SER B  60 "
            pdb=" OH  TYR B  82 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   SER A  60 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER B 464 "
            pdb=" OG1 THR B 468 "
     model   vdw
     2.284 3.040
  ... (remaining 62979 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             1.260
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.420
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7346  Z= 0.201
  Angle     :  0.640   7.046  10018  Z= 0.365
  Chirality :  0.043   0.251   1212
  Planarity :  0.006   0.048   1200
  Dihedral  : 11.896  83.869   2582
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.28), residues: 894
  helix:  2.04 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.20 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  76 
 TYR   0.025   0.002   TYR B 214 
 PHE   0.010   0.001   PHE A  18 
 TRP   0.040   0.003   TRP B  49 
 HIS   0.003   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7346)
  covalent geometry    : angle       0.64030 (10018)
  hydrogen bonds       : bond        0.13043 (  512)
  hydrogen bonds       : angle       5.05632 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   16 ILE cc_start: 0.7210 (tp) cc_final: 0.6979 (pp)
REVERT: A  123 ARG cc_start: 0.5443 (ptp-110) cc_final: 0.5044 (ttm110)
REVERT: A  455 LEU cc_start: 0.6828 (mt) cc_final: 0.6215 (tp)
REVERT: A  532 MET cc_start: 0.7610 (mmt) cc_final: 0.7172 (mmm)
REVERT: B   16 ILE cc_start: 0.7225 (tp) cc_final: 0.7011 (pp)
REVERT: B  123 ARG cc_start: 0.5376 (ptp-110) cc_final: 0.4870 (ptp-170)
REVERT: B  125 MET cc_start: 0.8134 (ttm) cc_final: 0.7923 (ttp)
REVERT: B  261 MET cc_start: 0.7772 (tmm) cc_final: 0.7538 (tmm)
REVERT: B  455 LEU cc_start: 0.7003 (mt) cc_final: 0.6473 (tp)
REVERT: B  491 MET cc_start: 0.7493 (mtp) cc_final: 0.6995 (mtp)
REVERT: B  534 ILE cc_start: 0.7404 (mt) cc_final: 0.7118 (tp)
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.4539
  time to fit residues: 70.2131
Evaluate side-chains
  120 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain B residue   60 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0030
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 230 ASN
** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.186517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.141703 restraints weight = 6316.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.77
r_work: 0.3521 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7346  Z= 0.136
  Angle     :  0.567   5.916  10018  Z= 0.292
  Chirality :  0.042   0.154   1212
  Planarity :  0.006   0.050   1200
  Dihedral  :  4.322  21.198    952
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  5.36 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.28), residues: 894
  helix:  2.21 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop : -0.11 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 112 
 TYR   0.009   0.001   TYR B  48 
 PHE   0.013   0.001   PHE A  35 
 TRP   0.016   0.002   TRP A 103 
 HIS   0.006   0.002   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7346)
  covalent geometry    : angle       0.56707 (10018)
  hydrogen bonds       : bond        0.04363 (  512)
  hydrogen bonds       : angle       4.07145 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   16 ILE cc_start: 0.7445 (tp) cc_final: 0.7125 (pt)
REVERT: A  123 ARG cc_start: 0.5164 (ptp-110) cc_final: 0.4549 (ptp-170)
REVERT: A  267 PHE cc_start: 0.7757 (m-80) cc_final: 0.7488 (m-10)
REVERT: A  308 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7725 (mttm)
REVERT: A  425 GLU cc_start: 0.7388 (tp30) cc_final: 0.7137 (mm-30)
REVERT: A  455 LEU cc_start: 0.6756 (mt) cc_final: 0.6036 (tp)
REVERT: A  545 ASN cc_start: 0.7907 (m-40) cc_final: 0.7456 (m110)
REVERT: B  123 ARG cc_start: 0.5155 (ptp-110) cc_final: 0.4572 (ptp-170)
REVERT: B  208 MET cc_start: 0.7316 (mmm) cc_final: 0.6932 (mmp)
REVERT: B  261 MET cc_start: 0.7981 (tmm) cc_final: 0.7769 (tmm)
REVERT: B  308 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7599 (mttp)
REVERT: B  455 LEU cc_start: 0.6667 (mt) cc_final: 0.6093 (tp)
REVERT: B  491 MET cc_start: 0.7559 (mtp) cc_final: 0.7123 (mtp)
REVERT: B  534 ILE cc_start: 0.7251 (mt) cc_final: 0.6967 (tp)
REVERT: B  545 ASN cc_start: 0.7989 (m-40) cc_final: 0.7753 (m110)
  outliers start: 7
  outliers final: 2
  residues processed: 132
  average time/residue: 0.4818
  time to fit residues: 67.4919
Evaluate side-chains
  118 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  449 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 84 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.185935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.140894 restraints weight = 6303.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 1.79
r_work: 0.3520 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7346  Z= 0.127
  Angle     :  0.540   6.055  10018  Z= 0.277
  Chirality :  0.041   0.132   1212
  Planarity :  0.006   0.052   1200
  Dihedral  :  4.242  26.140    950
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.91 %
    Favored  : 91.45 %
  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 aren not related in a simple way.
  whole:  2.74 (0.29), residues: 894
  helix:  2.24 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop :  0.05 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 112 
 TYR   0.007   0.001   TYR B  48 
 PHE   0.012   0.001   PHE A  35 
 TRP   0.018   0.002   TRP B 399 
 HIS   0.004   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7346)
  covalent geometry    : angle       0.53999 (10018)
  hydrogen bonds       : bond        0.03993 (  512)
  hydrogen bonds       : angle       3.91259 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   16 ILE cc_start: 0.7455 (tp) cc_final: 0.7112 (pt)
REVERT: A  123 ARG cc_start: 0.5185 (ptp-110) cc_final: 0.4567 (ptp-170)
REVERT: A  267 PHE cc_start: 0.7762 (m-80) cc_final: 0.7485 (m-10)
REVERT: A  308 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7702 (mttt)
REVERT: A  425 GLU cc_start: 0.7403 (tp30) cc_final: 0.7112 (mm-30)
REVERT: A  455 LEU cc_start: 0.6785 (mt) cc_final: 0.6070 (tp)
REVERT: A  459 PHE cc_start: 0.6407 (t80) cc_final: 0.5897 (t80)
REVERT: A  545 ASN cc_start: 0.7896 (m-40) cc_final: 0.7517 (m110)
REVERT: A  553 ASP cc_start: 0.7685 (t0) cc_final: 0.7080 (t70)
REVERT: B  123 ARG cc_start: 0.5161 (ptp-110) cc_final: 0.4469 (ptp-170)
REVERT: B  261 MET cc_start: 0.7984 (tmm) cc_final: 0.7739 (tmm)
REVERT: B  308 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7619 (mttp)
REVERT: B  425 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7218 (mp0)
REVERT: B  455 LEU cc_start: 0.6644 (mt) cc_final: 0.6126 (tp)
REVERT: B  491 MET cc_start: 0.7519 (mtp) cc_final: 0.6976 (mtp)
  outliers start: 5
  outliers final: 3
  residues processed: 131
  average time/residue: 0.4413
  time to fit residues: 61.3688
Evaluate side-chains
  124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  71 GLN
B  77 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.187938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.143804 restraints weight = 6307.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.74
r_work: 0.3578 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7346  Z= 0.164
  Angle     :  0.599   6.346  10018  Z= 0.305
  Chirality :  0.043   0.141   1212
  Planarity :  0.006   0.055   1200
  Dihedral  :  4.380  29.408    950
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.18 %
    Favored  : 89.67 %
  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 aren not related in a simple way.
  whole:  2.48 (0.29), residues: 894
  helix:  2.04 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.02 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.015   0.001   TYR B 489 
 PHE   0.017   0.001   PHE A  35 
 TRP   0.020   0.002   TRP B 399 
 HIS   0.007   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7346)
  covalent geometry    : angle       0.59887 (10018)
  hydrogen bonds       : bond        0.04304 (  512)
  hydrogen bonds       : angle       4.03143 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  123 ARG cc_start: 0.5189 (ptp-110) cc_final: 0.4808 (ttm110)
REVERT: A  267 PHE cc_start: 0.7721 (m-80) cc_final: 0.7453 (m-10)
REVERT: A  308 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7725 (mttt)
REVERT: A  373 GLN cc_start: 0.7832 (mt0) cc_final: 0.7510 (mt0)
REVERT: A  425 GLU cc_start: 0.7328 (tp30) cc_final: 0.7091 (mp0)
REVERT: A  455 LEU cc_start: 0.6768 (mt) cc_final: 0.6058 (tp)
REVERT: A  459 PHE cc_start: 0.6308 (t80) cc_final: 0.5772 (t80)
REVERT: A  553 ASP cc_start: 0.7745 (t0) cc_final: 0.7144 (t70)
REVERT: B  120 LYS cc_start: 0.4466 (tmtt) cc_final: 0.3824 (pttt)
REVERT: B  261 MET cc_start: 0.7981 (tmm) cc_final: 0.7691 (tmm)
REVERT: B  308 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7720 (mttp)
REVERT: B  425 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7225 (mp0)
REVERT: B  455 LEU cc_start: 0.6702 (mt) cc_final: 0.6178 (tp)
REVERT: B  491 MET cc_start: 0.7610 (mtp) cc_final: 0.7112 (mtp)
  outliers start: 9
  outliers final: 3
  residues processed: 128
  average time/residue: 0.4480
  time to fit residues: 60.8697
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 7 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  71 GLN
B  77 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.184673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139738 restraints weight = 6339.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.75
r_work: 0.3512 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7346  Z= 0.126
  Angle     :  0.534   5.811  10018  Z= 0.275
  Chirality :  0.040   0.144   1212
  Planarity :  0.006   0.054   1200
  Dihedral  :  4.253  26.723    950
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.95 %
    Favored  : 89.03 %
  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 aren not related in a simple way.
  whole:  2.60 (0.29), residues: 894
  helix:  2.14 (0.20), residues: 720
  sheet:  None (None), residues: 0
  loop : -0.02 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 112 
 TYR   0.008   0.001   TYR A  48 
 PHE   0.011   0.001   PHE A  35 
 TRP   0.021   0.002   TRP B 399 
 HIS   0.004   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7346)
  covalent geometry    : angle       0.53437 (10018)
  hydrogen bonds       : bond        0.03887 (  512)
  hydrogen bonds       : angle       3.88203 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  123 ARG cc_start: 0.5227 (ptp-110) cc_final: 0.4859 (ttm110)
REVERT: A  267 PHE cc_start: 0.7775 (m-80) cc_final: 0.7472 (m-10)
REVERT: A  308 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7669 (mttt)
REVERT: A  455 LEU cc_start: 0.6841 (mt) cc_final: 0.6159 (tp)
REVERT: A  459 PHE cc_start: 0.6413 (t80) cc_final: 0.5823 (t80)
REVERT: A  553 ASP cc_start: 0.7728 (t0) cc_final: 0.7157 (t70)
REVERT: B   52 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6657 (mt-10)
REVERT: B  120 LYS cc_start: 0.4385 (tmtt) cc_final: 0.3703 (pttt)
REVERT: B  261 MET cc_start: 0.8023 (tmm) cc_final: 0.7798 (tmm)
REVERT: B  425 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7136 (mp0)
REVERT: B  455 LEU cc_start: 0.6655 (mt) cc_final: 0.6156 (tp)
REVERT: B  491 MET cc_start: 0.7534 (mtp) cc_final: 0.7112 (mtp)
  outliers start: 8
  outliers final: 3
  residues processed: 127
  average time/residue: 0.4820
  time to fit residues: 65.1381
Evaluate side-chains
  120 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0770
   chunk 33 optimal weight:    0.3980
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.184247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.139205 restraints weight = 6340.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 1.75
r_work: 0.3505 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7346  Z= 0.133
  Angle     :  0.552   6.026  10018  Z= 0.282
  Chirality :  0.041   0.142   1212
  Planarity :  0.006   0.055   1200
  Dihedral  :  4.246  25.926    950
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.20 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.29), residues: 894
  helix:  2.10 (0.19), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.02 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.008   0.001   TYR A  48 
 PHE   0.013   0.001   PHE A  35 
 TRP   0.020   0.002   TRP B 399 
 HIS   0.005   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7346)
  covalent geometry    : angle       0.55171 (10018)
  hydrogen bonds       : bond        0.03956 (  512)
  hydrogen bonds       : angle       3.88971 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  123 ARG cc_start: 0.5237 (ptp-110) cc_final: 0.4986 (ttm110)
REVERT: A  308 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7661 (mttt)
REVERT: A  373 GLN cc_start: 0.7871 (mt0) cc_final: 0.7558 (mt0)
REVERT: A  455 LEU cc_start: 0.6814 (mt) cc_final: 0.6134 (tp)
REVERT: A  459 PHE cc_start: 0.6453 (t80) cc_final: 0.5863 (t80)
REVERT: A  553 ASP cc_start: 0.7745 (t0) cc_final: 0.7183 (t70)
REVERT: B   52 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6655 (mt-10)
REVERT: B  123 ARG cc_start: 0.5337 (ptp-110) cc_final: 0.4602 (ptp-170)
REVERT: B  425 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7157 (mp0)
REVERT: B  455 LEU cc_start: 0.6610 (mt) cc_final: 0.6110 (tp)
REVERT: B  491 MET cc_start: 0.7545 (mtp) cc_final: 0.7129 (mtp)
  outliers start: 10
  outliers final: 4
  residues processed: 120
  average time/residue: 0.4763
  time to fit residues: 60.8586
Evaluate side-chains
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 87 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.182125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136994 restraints weight = 6296.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.75
r_work: 0.3483 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7346  Z= 0.164
  Angle     :  0.598   7.147  10018  Z= 0.304
  Chirality :  0.042   0.142   1212
  Planarity :  0.006   0.056   1200
  Dihedral  :  4.374  28.629    950
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.71 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.29), residues: 894
  helix:  1.97 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop :  0.06 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.017   0.001   TYR B 489 
 PHE   0.016   0.001   PHE A  35 
 TRP   0.019   0.002   TRP B 399 
 HIS   0.007   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 7346)
  covalent geometry    : angle       0.59828 (10018)
  hydrogen bonds       : bond        0.04229 (  512)
  hydrogen bonds       : angle       4.01260 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  123 ARG cc_start: 0.5276 (ptp-110) cc_final: 0.4866 (ttm110)
REVERT: A  308 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7709 (mttt)
REVERT: A  373 GLN cc_start: 0.7865 (mt0) cc_final: 0.7552 (mt0)
REVERT: A  425 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7132 (tm-30)
REVERT: A  455 LEU cc_start: 0.6793 (mt) cc_final: 0.6148 (tp)
REVERT: A  459 PHE cc_start: 0.6458 (t80) cc_final: 0.5841 (t80)
REVERT: A  553 ASP cc_start: 0.7812 (t0) cc_final: 0.7208 (t70)
REVERT: B   52 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6725 (mt-10)
REVERT: B  120 LYS cc_start: 0.3817 (tmtt) cc_final: 0.3172 (pttt)
REVERT: B  425 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7138 (mp0)
REVERT: B  455 LEU cc_start: 0.6653 (mt) cc_final: 0.6154 (tp)
REVERT: B  491 MET cc_start: 0.7572 (mtp) cc_final: 0.7058 (mtp)
  outliers start: 9
  outliers final: 5
  residues processed: 123
  average time/residue: 0.4276
  time to fit residues: 56.1373
Evaluate side-chains
  126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  71 GLN
B  77 GLN
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.182315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.137445 restraints weight = 6301.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 1.72
r_work: 0.3488 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7346  Z= 0.153
  Angle     :  0.594   7.460  10018  Z= 0.301
  Chirality :  0.042   0.140   1212
  Planarity :  0.006   0.056   1200
  Dihedral  :  4.358  28.089    950
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.71 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.28), residues: 894
  helix:  1.95 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop :  0.07 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  76 
 TYR   0.009   0.001   TYR B 214 
 PHE   0.015   0.001   PHE A  35 
 TRP   0.021   0.002   TRP B 399 
 HIS   0.007   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7346)
  covalent geometry    : angle       0.59429 (10018)
  hydrogen bonds       : bond        0.04158 (  512)
  hydrogen bonds       : angle       3.97876 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7615 (mttt)
REVERT: A  373 GLN cc_start: 0.7868 (mt0) cc_final: 0.7557 (mt0)
REVERT: A  425 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7131 (tm-30)
REVERT: A  455 LEU cc_start: 0.6798 (mt) cc_final: 0.6159 (tp)
REVERT: A  459 PHE cc_start: 0.6470 (t80) cc_final: 0.5855 (t80)
REVERT: A  553 ASP cc_start: 0.7808 (t0) cc_final: 0.7206 (t70)
REVERT: B   52 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6707 (mt-10)
REVERT: B  123 ARG cc_start: 0.5384 (ptp-110) cc_final: 0.4533 (ptp-170)
REVERT: B  425 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7123 (mp0)
REVERT: B  455 LEU cc_start: 0.6655 (mt) cc_final: 0.6166 (tp)
REVERT: B  491 MET cc_start: 0.7558 (mtp) cc_final: 0.7046 (mtp)
  outliers start: 9
  outliers final: 5
  residues processed: 120
  average time/residue: 0.3845
  time to fit residues: 49.2983
Evaluate side-chains
  126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0870
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.184523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139782 restraints weight = 6297.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.73
r_work: 0.3516 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7346  Z= 0.125
  Angle     :  0.567   8.246  10018  Z= 0.287
  Chirality :  0.041   0.141   1212
  Planarity :  0.005   0.056   1200
  Dihedral  :  4.320  30.389    950
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.22 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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 aren not related in a simple way.
  whole:  2.51 (0.29), residues: 894
  helix:  2.05 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.03 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  76 
 TYR   0.020   0.001   TYR B 489 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.023   0.002   TRP B 399 
 HIS   0.005   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7346)
  covalent geometry    : angle       0.56682 (10018)
  hydrogen bonds       : bond        0.03879 (  512)
  hydrogen bonds       : angle       3.88758 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7698 (mttt)
REVERT: A  425 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7135 (tm-30)
REVERT: A  455 LEU cc_start: 0.6819 (mt) cc_final: 0.6174 (tp)
REVERT: A  459 PHE cc_start: 0.6461 (t80) cc_final: 0.5833 (t80)
REVERT: A  553 ASP cc_start: 0.7729 (t0) cc_final: 0.7152 (t70)
REVERT: B   52 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6659 (mt-10)
REVERT: B  123 ARG cc_start: 0.5337 (ptp-110) cc_final: 0.4506 (ptp-170)
REVERT: B  308 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7676 (mttp)
REVERT: B  425 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7150 (mp0)
REVERT: B  455 LEU cc_start: 0.6679 (mt) cc_final: 0.6165 (tp)
REVERT: B  491 MET cc_start: 0.7518 (mtp) cc_final: 0.7095 (mtp)
REVERT: B  525 MET cc_start: 0.6016 (ttm) cc_final: 0.5476 (ttt)
  outliers start: 8
  outliers final: 4
  residues processed: 126
  average time/residue: 0.4274
  time to fit residues: 57.3977
Evaluate side-chains
  124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    0.0000
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0270
   chunk 69 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.5444

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
B 104 ASN
B 465 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.186090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.141503 restraints weight = 6332.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 1.73
r_work: 0.3534 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7346  Z= 0.120
  Angle     :  0.556   8.418  10018  Z= 0.281
  Chirality :  0.040   0.158   1212
  Planarity :  0.005   0.055   1200
  Dihedral  :  4.243  30.051    950
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.73 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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 aren not related in a simple way.
  whole:  2.57 (0.29), residues: 894
  helix:  2.10 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.04 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 112 
 TYR   0.008   0.001   TYR A  40 
 PHE   0.010   0.001   PHE A  35 
 TRP   0.022   0.002   TRP B 399 
 HIS   0.005   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7346)
  covalent geometry    : angle       0.55550 (10018)
  hydrogen bonds       : bond        0.03770 (  512)
  hydrogen bonds       : angle       3.85458 ( 1512)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7766 (mt0) cc_final: 0.7546 (mt0)
REVERT: A  308 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7657 (mttt)
REVERT: A  425 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7133 (tm-30)
REVERT: A  455 LEU cc_start: 0.6813 (mt) cc_final: 0.6153 (tp)
REVERT: A  459 PHE cc_start: 0.6499 (t80) cc_final: 0.5857 (t80)
REVERT: A  553 ASP cc_start: 0.7726 (t0) cc_final: 0.7158 (t70)
REVERT: B   52 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6606 (mt-10)
REVERT: B  123 ARG cc_start: 0.5354 (ptp-110) cc_final: 0.4506 (ptp-170)
REVERT: B  308 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7532 (mtmm)
REVERT: B  425 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7086 (mp0)
REVERT: B  455 LEU cc_start: 0.6666 (mt) cc_final: 0.6140 (tp)
REVERT: B  491 MET cc_start: 0.7504 (mtp) cc_final: 0.6999 (mtp)
REVERT: B  525 MET cc_start: 0.5970 (ttm) cc_final: 0.5437 (ttt)
  outliers start: 7
  outliers final: 1
  residues processed: 130
  average time/residue: 0.4873
  time to fit residues: 67.8061
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain B residue  425 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0970
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  77 GLN
B 465 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.186056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.141227 restraints weight = 6336.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.73
r_work: 0.3531 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7346  Z= 0.124
  Angle     :  0.563   7.486  10018  Z= 0.284
  Chirality :  0.040   0.147   1212
  Planarity :  0.005   0.055   1200
  Dihedral  :  4.223  29.605    950
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 12.24 %
    Favored  : 87.12 %
  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 aren not related in a simple way.
  whole:  2.57 (0.29), residues: 894
  helix:  2.10 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop :  0.02 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 112 
 TYR   0.023   0.001   TYR B 489 
 PHE   0.011   0.001   PHE A  35 
 TRP   0.020   0.002   TRP B 399 
 HIS   0.005   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7346)
  covalent geometry    : angle       0.56346 (10018)
  hydrogen bonds       : bond        0.03807 (  512)
  hydrogen bonds       : angle       3.85173 ( 1512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3266.66 seconds
wall clock time: 56 minutes 16.52 seconds (3376.52 seconds total)