Starting phenix.real_space_refine
on Sun Apr  5 00:32:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10tq_75463/04_2026/10tq_75463_neut.cif"
  }
  resolution = 3.1
  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=   0.010
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      20      5.16       5
     C    4266      2.51       5
     N    1046      2.21       5
     O    1070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6402
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3201
          Classifications: {'peptide': 428}
          Link IDs: {'PTRANS': 15, 'TRANS': 412}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.09, per 1000 atoms: 0.33
  Number of scatterers: 6402
  At special positions: 0
  Unit cell: (114.4, 87.75, 67.6, 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      20     16.00
     O    1070      8.00
     N    1046      7.00
     C    4266      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: 0.56
  Conformation dependent library (CDL) restraints added in 268.7 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      90.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 17
    Processing helix  chain 'A' and resid 18 through 22
    Processing helix  chain 'A' and resid 23 through 38
    Processing helix  chain 'A' and resid 44 through 73
      removed outlier: 4.296A  pdb=" N   VAL A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   ASN A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   ALA A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 87
    Processing helix  chain 'A' and resid 90 through 116
      removed outlier: 7.909A  pdb=" N   ASN A 111 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   ASP A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
      removed outlier: 3.771A  pdb=" N   ILE A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 150
      removed outlier: 3.994A  pdb=" N   ASP A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 158 through 168
    Processing helix  chain 'A' and resid 171 through 198
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 213 through 218
      removed outlier: 3.537A  pdb=" N   ILE A 218 " --> pdb=" O   ASN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 240
    Processing helix  chain 'A' and resid 247 through 267
      removed outlier: 3.572A  pdb=" N   VAL A 251 " --> pdb=" O   PRO A 247 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   HIS A 267 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 280 through 300
      removed outlier: 4.004A  pdb=" N   VAL A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 314
      removed outlier: 4.123A  pdb=" N   LEU A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 336
    Processing helix  chain 'A' and resid 336 through 351
      removed outlier: 3.750A  pdb=" N   THR A 340 " --> pdb=" O   ASN A 336 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 342 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 372
      removed outlier: 3.799A  pdb=" N   ASN A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 379
    Processing helix  chain 'A' and resid 380 through 393
    Processing helix  chain 'A' and resid 398 through 427
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'B' and resid 2 through 17
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 23 through 38
    Processing helix  chain 'B' and resid 44 through 73
      removed outlier: 4.296A  pdb=" N   VAL B  48 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   ASN B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   ALA B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE B  61 " --> pdb=" O   THR B  57 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 87
    Processing helix  chain 'B' and resid 90 through 116
      removed outlier: 7.908A  pdb=" N   ASN B 111 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   ASP B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
      removed outlier: 3.772A  pdb=" N   ILE B 121 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 150
      removed outlier: 3.994A  pdb=" N   ASP B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 157
    Processing helix  chain 'B' and resid 158 through 168
    Processing helix  chain 'B' and resid 171 through 198
      Proline residue:  B 181  - end of helix
    Processing helix  chain 'B' and resid 207 through 211
    Processing helix  chain 'B' and resid 213 through 218
      removed outlier: 3.538A  pdb=" N   ILE B 218 " --> pdb=" O   ASN B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 240
    Processing helix  chain 'B' and resid 247 through 267
      removed outlier: 3.572A  pdb=" N   VAL B 251 " --> pdb=" O   PRO B 247 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   HIS B 267 " --> pdb=" O   ALA B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 280 through 300
      removed outlier: 4.005A  pdb=" N   VAL B 284 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU B 287 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 314
      removed outlier: 4.124A  pdb=" N   LEU B 308 " --> pdb=" O   HIS B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 336
    Processing helix  chain 'B' and resid 336 through 351
      removed outlier: 3.751A  pdb=" N   THR B 340 " --> pdb=" O   ASN B 336 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU B 342 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 372
      removed outlier: 3.799A  pdb=" N   ASN B 359 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 379
    Processing helix  chain 'B' and resid 380 through 393
    Processing helix  chain 'B' and resid 398 through 427
      Proline residue:  B 412  - end of helix

    538 hydrogen bonds defined for protein.
    1566 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: 0.76 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: 1957
        1.34 -     1.46: 1032
        1.46 -     1.57: 3519
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 6548
  Sorted by residual:
  bond pdb=" N   ILE A  61 "
       pdb=" CA  ILE A  61 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.60e+00
  bond pdb=" N   ILE B  61 "
       pdb=" CA  ILE B  61 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.41e-02 5.03e+03 5.98e+00
  bond pdb=" N   THR B  59 "
       pdb=" CA  THR B  59 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.33e-02 5.65e+03 5.35e+00
  bond pdb=" N   THR A  59 "
       pdb=" CA  THR A  59 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.28e-02 6.10e+03 4.93e+00
  bond pdb=" N   PHE A  60 "
       pdb=" CA  PHE A  60 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.20e-02 6.94e+03 4.91e+00
  ... (remaining 6543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 8318
        1.19 -     2.37: 536
        2.37 -     3.56: 72
        3.56 -     4.74: 14
        4.74 -     5.93: 26
  Bond angle restraints: 8966
  Sorted by residual:
  angle pdb=" C   ALA A 107 "
        pdb=" N   LEU A 108 "
        pdb=" CA  LEU A 108 "
      ideal   model   delta    sigma   weight residual
     122.09  116.46    5.63 1.79e+00 3.12e-01 9.90e+00
  angle pdb=" C   ALA B 107 "
        pdb=" N   LEU B 108 "
        pdb=" CA  LEU B 108 "
      ideal   model   delta    sigma   weight residual
     122.09  116.49    5.60 1.79e+00 3.12e-01 9.80e+00
  angle pdb=" N   LEU A 152 "
        pdb=" CA  LEU A 152 "
        pdb=" C   LEU A 152 "
      ideal   model   delta    sigma   weight residual
     109.81  115.74   -5.93 2.21e+00 2.05e-01 7.20e+00
  angle pdb=" N   LEU B 152 "
        pdb=" CA  LEU B 152 "
        pdb=" C   LEU B 152 "
      ideal   model   delta    sigma   weight residual
     109.81  115.69   -5.88 2.21e+00 2.05e-01 7.07e+00
  angle pdb=" CA  ILE A  61 "
        pdb=" C   ILE A  61 "
        pdb=" O   ILE A  61 "
      ideal   model   delta    sigma   weight residual
     120.78  117.51    3.27 1.25e+00 6.40e-01 6.86e+00
  ... (remaining 8961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.50: 3374
       11.50 -    23.00: 290
       23.00 -    34.49: 80
       34.49 -    45.99: 9
       45.99 -    57.49: 7
  Dihedral angle restraints: 3760
    sinusoidal: 1324
      harmonic: 2436
  Sorted by residual:
  dihedral pdb=" CA  LEU B 152 "
           pdb=" C   LEU B 152 "
           pdb=" N   PRO B 153 "
           pdb=" CA  PRO B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.28  -26.72     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  LEU A 152 "
           pdb=" C   LEU A 152 "
           pdb=" N   PRO A 153 "
           pdb=" CA  PRO A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.32  -26.68     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  VAL A  53 "
           pdb=" C   VAL A  53 "
           pdb=" N   TRP A  54 "
           pdb=" CA  TRP A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.53  -20.47     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 3757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 644
       0.034 -    0.068: 352
       0.068 -    0.102: 95
       0.102 -    0.137: 30
       0.137 -    0.171: 7
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" CA  THR B 119 "
            pdb=" N   THR B 119 "
            pdb=" C   THR B 119 "
            pdb=" CB  THR B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.29e-01
  chirality pdb=" CA  THR A 119 "
            pdb=" N   THR A 119 "
            pdb=" C   THR A 119 "
            pdb=" CB  THR A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" CA  PRO B 153 "
            pdb=" N   PRO B 153 "
            pdb=" C   PRO B 153 "
            pdb=" CB  PRO B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.55e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  56 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.89e+00
        pdb=" C   ALA B  56 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ALA B  56 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR B  57 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  56 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ALA A  56 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ALA A  56 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR A  57 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B  54 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.67e+00
        pdb=" C   TRP B  54 "    0.033 2.00e-02 2.50e+03
        pdb=" O   TRP B  54 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  55 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1079 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1708
        2.79 -     3.32: 6678
        3.32 -     3.85: 10530
        3.85 -     4.37: 12895
        4.37 -     4.90: 21994
  Nonbonded interactions: 53805
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 107 "
            pdb=" OG  SER B 157 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ALA A 107 "
            pdb=" OG  SER A 157 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ALA B  84 "
            pdb=" OH  TYR B 206 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   ALA A  84 "
            pdb=" OH  TYR A 206 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OE1 GLU A  72 "
            pdb=" NH2 ARG A 219 "
     model   vdw
     2.359 3.120
  ... (remaining 53800 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:             5.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.140
  Find NCS groups from input model:        0.040
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
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      :  0.008   0.048   6548  Z= 0.319
  Angle     :  0.709   5.929   8966  Z= 0.386
  Chirality :  0.045   0.171   1128
  Planarity :  0.006   0.042   1082
  Dihedral  :  9.913  57.489   2196
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.00 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.23), residues: 852
  helix: -1.61 (0.14), residues: 712
  sheet:  None (None), residues: 0
  loop :  1.62 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 219 
 TYR   0.005   0.001   TYR A 206 
 PHE   0.010   0.002   PHE B  95 
 TRP   0.016   0.002   TRP A 228 
 HIS   0.005   0.002   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00763 ( 6548)
  covalent geometry    : angle       0.70943 ( 8966)
  hydrogen bonds       : bond        0.15045 (  538)
  hydrogen bonds       : angle       6.03572 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7105 (ptt90)
REVERT: A   57 THR cc_start: 0.8476 (m) cc_final: 0.8023 (p)
REVERT: A   60 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6495 (m-80)
REVERT: A   90 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7524 (mttt)
REVERT: A  196 PHE cc_start: 0.7795 (t80) cc_final: 0.7455 (t80)
REVERT: A  265 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.5765 (mmt180)
REVERT: A  276 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7329 (ttp80)
REVERT: A  349 ASP cc_start: 0.8445 (t70) cc_final: 0.8240 (t0)
REVERT: B   20 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7336 (ptt90)
REVERT: B   57 THR cc_start: 0.8439 (m) cc_final: 0.8005 (p)
REVERT: B   60 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6656 (m-80)
REVERT: B  112 ASP cc_start: 0.8688 (m-30) cc_final: 0.8476 (m-30)
REVERT: B  276 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7425 (mtm110)
REVERT: B  349 ASP cc_start: 0.8500 (t70) cc_final: 0.8278 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0974
  time to fit residues: 11.4639
Evaluate side-chains
  98 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain B residue   60 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.102817 restraints weight = 7637.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.88
r_work: 0.2977 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6548  Z= 0.159
  Angle     :  0.539   5.936   8966  Z= 0.284
  Chirality :  0.039   0.135   1128
  Planarity :  0.005   0.040   1082
  Dihedral  :  5.345  58.597    904
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  5.32 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 852
  helix:  0.68 (0.18), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.50 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 392 
 TYR   0.007   0.001   TYR A 294 
 PHE   0.010   0.001   PHE B  95 
 TRP   0.016   0.001   TRP B 228 
 HIS   0.005   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6548)
  covalent geometry    : angle       0.53881 ( 8966)
  hydrogen bonds       : bond        0.05296 (  538)
  hydrogen bonds       : angle       4.70857 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7284 (ptt90)
REVERT: A   60 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6418 (m-80)
REVERT: A  148 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.7922 (m-30)
REVERT: A  196 PHE cc_start: 0.7844 (t80) cc_final: 0.7563 (t80)
REVERT: A  200 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8004 (mtm180)
REVERT: A  265 ARG cc_start: 0.7241 (mtp-110) cc_final: 0.5628 (mmt180)
REVERT: A  276 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7750 (ttm-80)
REVERT: A  297 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7007 (tmm-80)
REVERT: B   20 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7340 (ptt90)
REVERT: B   60 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6497 (m-80)
REVERT: B  199 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6813 (ptp90)
REVERT: B  265 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.5629 (mmt180)
REVERT: B  276 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7521 (mtm110)
REVERT: B  297 ARG cc_start: 0.8314 (tmm-80) cc_final: 0.8017 (tmm160)
  outliers start: 9
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1600
  time to fit residues: 15.3033
Evaluate side-chains
  75 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue  207 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 66 optimal weight:    0.0370
   chunk 46 optimal weight:    0.0770
   chunk 50 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.098558 restraints weight = 7777.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.02
r_work: 0.3015 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6548  Z= 0.120
  Angle     :  0.478   5.700   8966  Z= 0.248
  Chirality :  0.037   0.128   1128
  Planarity :  0.004   0.043   1082
  Dihedral  :  4.974  56.214    904
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  6.38 %
    Favored  : 92.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.28), residues: 852
  helix:  1.58 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.35 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 392 
 TYR   0.010   0.001   TYR B 290 
 PHE   0.010   0.001   PHE B  95 
 TRP   0.013   0.001   TRP B 228 
 HIS   0.004   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6548)
  covalent geometry    : angle       0.47804 ( 8966)
  hydrogen bonds       : bond        0.04346 (  538)
  hydrogen bonds       : angle       4.34509 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7253 (ptt90)
REVERT: A   60 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6303 (m-80)
REVERT: A  196 PHE cc_start: 0.7856 (t80) cc_final: 0.7507 (t80)
REVERT: A  200 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8126 (mtm180)
REVERT: A  265 ARG cc_start: 0.7081 (mtp-110) cc_final: 0.5572 (mmt180)
REVERT: A  297 ARG cc_start: 0.8049 (tmm-80) cc_final: 0.7655 (tmm160)
REVERT: B   20 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7379 (ptt90)
REVERT: B  265 ARG cc_start: 0.7358 (mtp-110) cc_final: 0.5644 (mmt180)
  outliers start: 9
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1019
  time to fit residues: 9.5651
Evaluate side-chains
  69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3199 r_free = 0.3199 target = 0.111627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.092160 restraints weight = 7926.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.18
r_work: 0.2874 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6548  Z= 0.152
  Angle     :  0.502   5.509   8966  Z= 0.259
  Chirality :  0.038   0.134   1128
  Planarity :  0.004   0.041   1082
  Dihedral  :  4.507  55.336    902
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  6.53 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.28), residues: 852
  helix:  1.72 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.10 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.013   0.001   TRP B 228 
 HIS   0.004   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6548)
  covalent geometry    : angle       0.50154 ( 8966)
  hydrogen bonds       : bond        0.04624 (  538)
  hydrogen bonds       : angle       4.33523 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7199 (ptt90)
REVERT: A   60 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6205 (m-80)
REVERT: A  196 PHE cc_start: 0.7799 (t80) cc_final: 0.7452 (t80)
REVERT: A  200 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8024 (mtm180)
REVERT: A  220 ASP cc_start: 0.8177 (t0) cc_final: 0.7861 (t0)
REVERT: A  265 ARG cc_start: 0.7134 (mtp-110) cc_final: 0.5555 (mmt180)
REVERT: A  276 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7298 (mtm110)
REVERT: A  297 ARG cc_start: 0.8007 (tmm-80) cc_final: 0.7621 (tmm160)
REVERT: B   20 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7243 (ptt90)
REVERT: B  265 ARG cc_start: 0.7341 (mtp-110) cc_final: 0.5531 (mmt180)
REVERT: B  276 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7368 (mtm110)
  outliers start: 11
  outliers final: 3
  residues processed: 83
  average time/residue: 0.0971
  time to fit residues: 10.3989
Evaluate side-chains
  76 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.119167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.102060 restraints weight = 7748.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 1.86
r_work: 0.2836 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6548  Z= 0.181
  Angle     :  0.530   6.260   8966  Z= 0.272
  Chirality :  0.039   0.138   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  4.520  53.292    902
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.14 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 852
  helix:  1.73 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.09 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 294 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.004   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6548)
  covalent geometry    : angle       0.53030 ( 8966)
  hydrogen bonds       : bond        0.04839 (  538)
  hydrogen bonds       : angle       4.35794 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7156 (ptt90)
REVERT: A   60 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.5908 (m-80)
REVERT: A  196 PHE cc_start: 0.7588 (t80) cc_final: 0.7258 (t80)
REVERT: A  200 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7878 (mtm180)
REVERT: A  220 ASP cc_start: 0.7982 (t0) cc_final: 0.7453 (t70)
REVERT: A  265 ARG cc_start: 0.7019 (mtp-110) cc_final: 0.5376 (mmt180)
REVERT: A  276 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7075 (mtm110)
REVERT: B   20 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7186 (ptt90)
REVERT: B  265 ARG cc_start: 0.7135 (mtp-110) cc_final: 0.5283 (mmt180)
REVERT: B  276 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7123 (mtm110)
  outliers start: 7
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1022
  time to fit residues: 9.5888
Evaluate side-chains
  77 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.111658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.091996 restraints weight = 7962.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.19
r_work: 0.2851 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6548  Z= 0.129
  Angle     :  0.483   7.380   8966  Z= 0.249
  Chirality :  0.037   0.130   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  4.427  52.533    902
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.51 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.28), residues: 852
  helix:  1.95 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.02 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 297 
 TYR   0.006   0.001   TYR B 290 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.015   0.001   TRP B 228 
 HIS   0.003   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6548)
  covalent geometry    : angle       0.48296 ( 8966)
  hydrogen bonds       : bond        0.04328 (  538)
  hydrogen bonds       : angle       4.24312 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7241 (ptt90)
REVERT: A   60 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6178 (m-80)
REVERT: A  196 PHE cc_start: 0.7859 (t80) cc_final: 0.7548 (t80)
REVERT: A  200 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.8048 (mtm180)
REVERT: A  265 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.5609 (mmt180)
REVERT: B   20 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7271 (ptt90)
REVERT: B  265 ARG cc_start: 0.7337 (mtp-110) cc_final: 0.5587 (mmt180)
REVERT: B  276 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7308 (mtm110)
  outliers start: 6
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1034
  time to fit residues: 9.2898
Evaluate side-chains
  70 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.112019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.092853 restraints weight = 7914.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.12
r_work: 0.2850 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6548  Z= 0.140
  Angle     :  0.492   7.886   8966  Z= 0.253
  Chirality :  0.037   0.132   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  4.373  51.206    902
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  8.81 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.28), residues: 852
  helix:  2.01 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.03 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 363 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6548)
  covalent geometry    : angle       0.49235 ( 8966)
  hydrogen bonds       : bond        0.04411 (  538)
  hydrogen bonds       : angle       4.24126 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7225 (ptt90)
REVERT: A   60 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6206 (m-10)
REVERT: A  196 PHE cc_start: 0.7911 (t80) cc_final: 0.7613 (t80)
REVERT: A  200 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8072 (mtm180)
REVERT: A  265 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.5687 (mmt180)
REVERT: A  276 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7347 (mtm110)
REVERT: B   20 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7284 (ptt90)
REVERT: B   57 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8251 (p)
REVERT: B  265 ARG cc_start: 0.7352 (mtp-110) cc_final: 0.5596 (mmt180)
REVERT: B  276 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7341 (mtm110)
  outliers start: 9
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0948
  time to fit residues: 9.5348
Evaluate side-chains
  82 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  148 ASP
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 40 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.112929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.093391 restraints weight = 7884.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.15
r_work: 0.2873 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6548  Z= 0.122
  Angle     :  0.477   8.771   8966  Z= 0.245
  Chirality :  0.037   0.129   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  4.325  50.235    902
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  8.51 %
    Favored  : 90.12 %
  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 are not related in a simple way.
  whole:  2.70 (0.28), residues: 852
  helix:  2.14 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.18 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 200 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6548)
  covalent geometry    : angle       0.47735 ( 8966)
  hydrogen bonds       : bond        0.04164 (  538)
  hydrogen bonds       : angle       4.18317 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7194 (ptt90)
REVERT: A   57 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8204 (p)
REVERT: A   60 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6116 (m-80)
REVERT: A  196 PHE cc_start: 0.7893 (t80) cc_final: 0.7591 (t80)
REVERT: A  265 ARG cc_start: 0.7162 (mtp-110) cc_final: 0.5589 (mmt180)
REVERT: A  276 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7386 (mtm110)
REVERT: B   20 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7257 (ptt90)
REVERT: B   57 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8198 (p)
REVERT: B  265 ARG cc_start: 0.7272 (mtp-110) cc_final: 0.5550 (mmt180)
REVERT: B  276 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7339 (mtm110)
  outliers start: 9
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1031
  time to fit residues: 10.1700
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  148 ASP
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.094652 restraints weight = 8259.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.17
r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6548  Z= 0.128
  Angle     :  0.485   9.097   8966  Z= 0.248
  Chirality :  0.037   0.131   1128
  Planarity :  0.004   0.043   1082
  Dihedral  :  4.289  49.223    902
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.81 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.28), residues: 852
  helix:  2.19 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.21 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 363 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6548)
  covalent geometry    : angle       0.48542 ( 8966)
  hydrogen bonds       : bond        0.04223 (  538)
  hydrogen bonds       : angle       4.17480 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7251 (ptt90)
REVERT: A   57 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8298 (p)
REVERT: A   60 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6240 (m-80)
REVERT: A  148 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: A  196 PHE cc_start: 0.7950 (t80) cc_final: 0.7656 (t80)
REVERT: A  265 ARG cc_start: 0.7264 (mtp-110) cc_final: 0.5659 (mmt180)
REVERT: A  276 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7395 (mtm110)
REVERT: B   20 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7299 (ptt90)
REVERT: B   57 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8285 (p)
REVERT: B  265 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.5619 (mmt180)
REVERT: B  276 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7415 (mtm110)
  outliers start: 11
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0928
  time to fit residues: 8.9556
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 69 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0770
   chunk 7 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.125044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.107404 restraints weight = 7775.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.98
r_work: 0.3071 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6548  Z= 0.114
  Angle     :  0.474   9.078   8966  Z= 0.242
  Chirality :  0.036   0.127   1128
  Planarity :  0.004   0.043   1082
  Dihedral  :  4.253  48.434    902
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.66 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.28), residues: 852
  helix:  2.27 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.32 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6548)
  covalent geometry    : angle       0.47369 ( 8966)
  hydrogen bonds       : bond        0.04017 (  538)
  hydrogen bonds       : angle       4.13027 ( 1566)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7262 (ptt90)
REVERT: A   57 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8308 (p)
REVERT: A  196 PHE cc_start: 0.7997 (t80) cc_final: 0.7717 (t80)
REVERT: A  265 ARG cc_start: 0.7240 (mtp-110) cc_final: 0.5683 (mmt180)
REVERT: A  276 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7438 (mtm110)
REVERT: B   20 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7333 (ptt90)
REVERT: B   57 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8289 (p)
REVERT: B  265 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.5645 (mmt180)
REVERT: B  276 ARG cc_start: 0.7974 (ttm170) cc_final: 0.7464 (mtm110)
  outliers start: 10
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0923
  time to fit residues: 8.9957
Evaluate side-chains
  77 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  267 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 55 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0040
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.115156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.095934 restraints weight = 8035.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.14
r_work: 0.3010 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6548  Z= 0.119
  Angle     :  0.483   8.724   8966  Z= 0.245
  Chirality :  0.037   0.129   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  3.774  25.337    900
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.12 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.28), residues: 852
  helix:  2.29 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.30 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 297 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.014   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6548)
  covalent geometry    : angle       0.48328 ( 8966)
  hydrogen bonds       : bond        0.04060 (  538)
  hydrogen bonds       : angle       4.13486 ( 1566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1687.58 seconds
wall clock time: 29 minutes 35.01 seconds (1775.01 seconds total)