Starting phenix.real_space_refine
on Fri Sep 11 01:43:24 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l48_0832/09_2026/6l48_0832.map"
  }
  resolution = 3.5
  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=   0.004
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      36      5.16       5
     C    4482      2.51       5
     N    1000      2.21       5
     O    1010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6528
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3236
          Classifications: {'peptide': 397}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 17, 'TRANS': 379}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 104
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.84, per 1000 atoms: 0.44
  Number of scatterers: 6528
  At special positions: 0
  Unit cell: (141.075, 74.195, 72.105, 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      36     16.00
     O    1010      8.00
     N    1000      7.00
     C    4482      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: 0.62
  Conformation dependent library (CDL) restraints added in 407.5 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1532

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      81.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.552A  pdb=" N   GLU A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 165
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 3.625A  pdb=" N   SER A 175 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 213
      Proline residue:  A 199  - end of helix
      removed outlier: 4.113A  pdb=" N   THR A 208 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY A 209 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 4.116A  pdb=" N   ARG A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
      Proline residue:  A 239  - end of helix
      removed outlier: 3.702A  pdb=" N   VAL A 243 " --> pdb=" O   PRO A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 284
      removed outlier: 3.858A  pdb=" N   ILE A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 319 through 344
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.521A  pdb=" N   PHE A 349 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 369 through 395
    Processing helix  chain 'A' and resid 412 through 418
      removed outlier: 3.782A  pdb=" N   ARG A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 444 through 469
      removed outlier: 4.030A  pdb=" N   ALA A 448 " --> pdb=" O   PHE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 487
      removed outlier: 3.672A  pdb=" N   PHE A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 526
    Processing helix  chain 'B' and resid 127 through 133
      removed outlier: 3.552A  pdb=" N   GLU B 131 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 165
    Processing helix  chain 'B' and resid 171 through 178
      removed outlier: 3.625A  pdb=" N   SER B 175 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 213
      Proline residue:  B 199  - end of helix
      removed outlier: 4.113A  pdb=" N   THR B 208 " --> pdb=" O   GLN B 204 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY B 209 " --> pdb=" O   HIS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 232
      removed outlier: 4.116A  pdb=" N   ARG B 219 " --> pdb=" O   HIS B 215 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B 221 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
      Proline residue:  B 239  - end of helix
      removed outlier: 3.701A  pdb=" N   VAL B 243 " --> pdb=" O   PRO B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 284
      removed outlier: 3.858A  pdb=" N   ILE B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 293 through 301
    Processing helix  chain 'B' and resid 319 through 344
    Processing helix  chain 'B' and resid 345 through 350
      removed outlier: 3.520A  pdb=" N   PHE B 349 " --> pdb=" O   CYS B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
    Processing helix  chain 'B' and resid 369 through 395
    Processing helix  chain 'B' and resid 412 through 418
      removed outlier: 3.781A  pdb=" N   ARG B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 444 through 469
      removed outlier: 4.029A  pdb=" N   ALA B 448 " --> pdb=" O   PHE B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 487
      removed outlier: 3.672A  pdb=" N   PHE B 486 " --> pdb=" O   PHE B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 526

    472 hydrogen bonds defined for protein.
    1416 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: 1.10

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1831
        1.34 -     1.46: 2056
        1.46 -     1.58: 2835
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6780
  Sorted by residual:
  bond pdb=" CA  ARG B 309 "
       pdb=" C   ARG B 309 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.30e-02 5.92e+03 4.39e+00
  bond pdb=" CA  ARG A 309 "
       pdb=" C   ARG A 309 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.30e-02 5.92e+03 4.38e+00
  bond pdb=" C13 CLR B2001 "
       pdb=" C14 CLR B2001 "
    ideal  model  delta    sigma   weight residual
    1.537  1.509  0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C13 CLR A2001 "
       pdb=" C14 CLR A2001 "
    ideal  model  delta    sigma   weight residual
    1.537  1.510  0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" N   ASP A 310 "
       pdb=" CA  ASP A 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.64e+00
  ... (remaining 6775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 9011
        1.90 -     3.80: 194
        3.80 -     5.69: 47
        5.69 -     7.59: 10
        7.59 -     9.49: 10
  Bond angle restraints: 9272
  Sorted by residual:
  angle pdb=" N   ARG B 309 "
        pdb=" CA  ARG B 309 "
        pdb=" C   ARG B 309 "
      ideal   model   delta    sigma   weight residual
     111.28  104.58    6.70 1.09e+00 8.42e-01 3.78e+01
  angle pdb=" N   ARG A 309 "
        pdb=" CA  ARG A 309 "
        pdb=" C   ARG A 309 "
      ideal   model   delta    sigma   weight residual
     111.28  104.59    6.69 1.09e+00 8.42e-01 3.76e+01
  angle pdb=" C   TRP A 388 "
        pdb=" N   LEU A 389 "
        pdb=" CA  LEU A 389 "
      ideal   model   delta    sigma   weight residual
     122.38  113.90    8.48 1.81e+00 3.05e-01 2.19e+01
  angle pdb=" C   TRP B 388 "
        pdb=" N   LEU B 389 "
        pdb=" CA  LEU B 389 "
      ideal   model   delta    sigma   weight residual
     122.38  113.92    8.46 1.81e+00 3.05e-01 2.19e+01
  angle pdb=" N   ASP A 310 "
        pdb=" CA  ASP A 310 "
        pdb=" C   ASP A 310 "
      ideal   model   delta    sigma   weight residual
     110.80  119.11   -8.31 2.13e+00 2.20e-01 1.52e+01
  ... (remaining 9267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.42: 3364
       14.42 -    28.84: 287
       28.84 -    43.26: 81
       43.26 -    57.67: 10
       57.67 -    72.09: 2
  Dihedral angle restraints: 3744
    sinusoidal: 1370
      harmonic: 2374
  Sorted by residual:
  dihedral pdb=" N   ASP A 310 "
           pdb=" C   ASP A 310 "
           pdb=" CA  ASP A 310 "
           pdb=" CB  ASP A 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.29  -11.49     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" N   ASP B 310 "
           pdb=" C   ASP B 310 "
           pdb=" CA  ASP B 310 "
           pdb=" CB  ASP B 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.29  -11.49     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" CA  GLN A 354 "
           pdb=" C   GLN A 354 "
           pdb=" N   GLU A 355 "
           pdb=" CA  GLU A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.66  -22.34     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 3741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 988
       0.100 -    0.201: 30
       0.201 -    0.301: 2
       0.301 -    0.401: 0
       0.401 -    0.502: 2
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  ASP A 310 "
            pdb=" N   ASP A 310 "
            pdb=" C   ASP A 310 "
            pdb=" CB  ASP A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.29e+00
  chirality pdb=" CA  ASP B 310 "
            pdb=" N   ASP B 310 "
            pdb=" C   ASP B 310 "
            pdb=" CB  ASP B 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.28e+00
  chirality pdb=" CA  ARG B 309 "
            pdb=" N   ARG B 309 "
            pdb=" C   ARG B 309 "
            pdb=" CB  ARG B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1019 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 308 "   -0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   TYR B 308 "    0.069 2.00e-02 2.50e+03
        pdb=" O   TYR B 308 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ARG B 309 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 308 "    0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   TYR A 308 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   TYR A 308 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ARG A 309 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 389 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   LEU A 389 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   LEU A 389 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASN A 390 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 848
        2.75 -     3.29: 6781
        3.29 -     3.83: 11195
        3.83 -     4.36: 12372
        4.36 -     4.90: 21540
  Nonbonded interactions: 52736
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 130 "
            pdb=" OH  TYR B 322 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OD2 ASP A 130 "
            pdb=" OH  TYR A 322 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR B 299 "
            pdb=" O   LEU B 396 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A 299 "
            pdb=" O   LEU A 396 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   PHE A 237 "
            pdb=" N   TYR A 241 "
     model   vdw
     2.284 3.120
  ... (remaining 52731 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  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:                    0.010
  Process input model:                     9.190
  Find NCS groups from input model:        0.060
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
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      :  0.003   0.035   6780  Z= 0.174
  Angle     :  0.762   9.490   9272  Z= 0.404
  Chirality :  0.050   0.502   1022
  Planarity :  0.006   0.040   1100
  Dihedral  : 12.132  72.093   2212
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  7.34 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.26 %
  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: -3.38 (0.26), residues: 782
  helix: -1.58 (0.18), residues: 600
  sheet:  None (None), residues: 0
  loop : -4.04 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 350 
 TYR   0.013   0.001   TYR B 433 
 PHE   0.015   0.001   PHE A 331 
 TRP   0.011   0.001   TRP B 504 
 HIS   0.008   0.001   HIS A 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.17 ( 6780)
  covalent geometry    : angle       0.76160 /  0.40 ( 9272)
  hydrogen bonds       : bond        0.09525 /  6.17 (  472)
  hydrogen bonds       : angle       7.79531 /  5.39 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 217
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7028 (pmt170) cc_final: 0.6719 (ptt-90)
REVERT: A  151 LEU cc_start: 0.8834 (tt) cc_final: 0.8447 (mt)
REVERT: A  205 HIS cc_start: 0.8220 (t70) cc_final: 0.7766 (t-170)
REVERT: A  241 TYR cc_start: 0.7991 (t80) cc_final: 0.7616 (t80)
REVERT: A  246 TYR cc_start: 0.8110 (m-10) cc_final: 0.7796 (m-80)
REVERT: A  273 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7002 (tm-30)
REVERT: A  293 THR cc_start: 0.8402 (p) cc_final: 0.7688 (t)
REVERT: A  468 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7697 (mm)
REVERT: A  511 ASN cc_start: 0.8285 (t0) cc_final: 0.7909 (m-40)
REVERT: A  522 TRP cc_start: 0.7287 (t-100) cc_final: 0.5239 (t60)
REVERT: B  125 ARG cc_start: 0.6984 (pmt170) cc_final: 0.6125 (ptt180)
REVERT: B  241 TYR cc_start: 0.8001 (t80) cc_final: 0.7584 (t80)
REVERT: B  246 TYR cc_start: 0.8094 (m-10) cc_final: 0.7786 (m-80)
REVERT: B  273 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7178 (tm-30)
REVERT: B  275 VAL cc_start: 0.8169 (t) cc_final: 0.7931 (t)
REVERT: B  468 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7655 (mm)
REVERT: B  522 TRP cc_start: 0.7409 (t-100) cc_final: 0.5196 (t60)
  outliers start: 16
  outliers final: 6
  residues processed: 233
  average time/residue: 0.0825
  time to fit residues: 25.3674
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 268 HIS
B 268 HIS
B 296 GLN
B 511 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.204141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.177885 restraints weight = 7689.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182408 restraints weight = 4290.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.185455 restraints weight = 2991.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.187389 restraints weight = 2353.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.188580 restraints weight = 2003.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6780  Z= 0.164
  Angle     :  0.694  13.039   9272  Z= 0.349
  Chirality :  0.042   0.164   1022
  Planarity :  0.005   0.038   1100
  Dihedral  :  7.024  48.798    904
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 14.68 %
    Favored  : 79.36 %
  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: -1.87 (0.29), residues: 782
  helix: -0.39 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.77 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 350 
 TYR   0.012   0.002   TYR A 336 
 PHE   0.016   0.002   PHE B 254 
 TRP   0.012   0.001   TRP A 188 
 HIS   0.006   0.001   HIS B 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 ( 6780)
  covalent geometry    : angle       0.69382 /  0.35 ( 9272)
  hydrogen bonds       : bond        0.04174 /  2.77 (  472)
  hydrogen bonds       : angle       6.15943 /  4.27 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6861 (pmt170) cc_final: 0.6505 (ptt-90)
REVERT: A  129 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7596 (mt)
REVERT: A  151 LEU cc_start: 0.8580 (tt) cc_final: 0.8046 (mt)
REVERT: A  161 TYR cc_start: 0.6944 (t80) cc_final: 0.6566 (t80)
REVERT: A  273 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6820 (tm-30)
REVERT: A  291 ILE cc_start: 0.7676 (mp) cc_final: 0.7371 (tp)
REVERT: A  297 TYR cc_start: 0.8532 (t80) cc_final: 0.7911 (t80)
REVERT: A  439 PHE cc_start: 0.4570 (m-10) cc_final: 0.4355 (m-10)
REVERT: A  522 TRP cc_start: 0.7133 (t-100) cc_final: 0.5237 (t60)
REVERT: B  125 ARG cc_start: 0.6828 (pmt170) cc_final: 0.6137 (ptt180)
REVERT: B  129 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7596 (mt)
REVERT: B  161 TYR cc_start: 0.6912 (t80) cc_final: 0.6623 (t80)
REVERT: B  273 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6963 (mm-30)
REVERT: B  297 TYR cc_start: 0.8485 (t80) cc_final: 0.7921 (t80)
REVERT: B  439 PHE cc_start: 0.4686 (m-10) cc_final: 0.4428 (m-10)
REVERT: B  522 TRP cc_start: 0.7322 (t-100) cc_final: 0.5404 (t60)
  outliers start: 39
  outliers final: 25
  residues processed: 176
  average time/residue: 0.0673
  time to fit residues: 16.5755
Evaluate side-chains
  152 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 GLN
A 511 ASN
B 204 GLN
B 260 GLN
B 511 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.210124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.185601 restraints weight = 7487.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.189655 restraints weight = 4336.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.191924 restraints weight = 3074.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.193929 restraints weight = 2489.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.194956 restraints weight = 2105.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6780  Z= 0.146
  Angle     :  0.672  12.714   9272  Z= 0.330
  Chirality :  0.042   0.195   1022
  Planarity :  0.005   0.061   1100
  Dihedral  :  6.483  51.813    900
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 17.43 %
    Favored  : 76.61 %
  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: -1.09 (0.30), residues: 782
  helix:  0.18 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -3.52 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 350 
 TYR   0.011   0.001   TYR B 404 
 PHE   0.020   0.001   PHE B 481 
 TRP   0.014   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.15 ( 6780)
  covalent geometry    : angle       0.67180 /  0.33 ( 9272)
  hydrogen bonds       : bond        0.03957 /  2.62 (  472)
  hydrogen bonds       : angle       5.89621 /  4.08 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6524 (pmt170) cc_final: 0.5852 (ptt180)
REVERT: A  129 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7680 (mt)
REVERT: A  161 TYR cc_start: 0.6981 (t80) cc_final: 0.6573 (t80)
REVERT: A  291 ILE cc_start: 0.7466 (mp) cc_final: 0.7252 (tp)
REVERT: A  297 TYR cc_start: 0.8533 (t80) cc_final: 0.8044 (t80)
REVERT: A  299 TYR cc_start: 0.7002 (t80) cc_final: 0.6785 (t80)
REVERT: A  478 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7214 (tm)
REVERT: A  522 TRP cc_start: 0.7225 (t-100) cc_final: 0.5353 (t60)
REVERT: B  125 ARG cc_start: 0.6661 (pmt170) cc_final: 0.6013 (ptt180)
REVERT: B  129 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7697 (mt)
REVERT: B  273 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6802 (mm-30)
REVERT: B  297 TYR cc_start: 0.8572 (t80) cc_final: 0.8109 (t80)
REVERT: B  299 TYR cc_start: 0.6724 (t80) cc_final: 0.6454 (t80)
REVERT: B  436 PHE cc_start: 0.7164 (m-10) cc_final: 0.6943 (m-10)
REVERT: B  522 TRP cc_start: 0.7232 (t-100) cc_final: 0.5297 (t60)
  outliers start: 39
  outliers final: 27
  residues processed: 172
  average time/residue: 0.0693
  time to fit residues: 16.4369
Evaluate side-chains
  161 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 65 optimal weight:    0.1980
   chunk 36 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.213573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.188101 restraints weight = 7602.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.192324 restraints weight = 4413.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.195117 restraints weight = 3116.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.196924 restraints weight = 2470.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.197814 restraints weight = 2107.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6780  Z= 0.131
  Angle     :  0.663  12.665   9272  Z= 0.319
  Chirality :  0.041   0.161   1022
  Planarity :  0.005   0.046   1100
  Dihedral  :  6.346  53.841    900
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 18.81 %
    Favored  : 75.54 %
  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: -0.70 (0.31), residues: 782
  helix:  0.42 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.57 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 319 
 TYR   0.013   0.001   TYR B 430 
 PHE   0.021   0.001   PHE A 254 
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 6780)
  covalent geometry    : angle       0.66305 /  0.32 ( 9272)
  hydrogen bonds       : bond        0.03768 /  2.49 (  472)
  hydrogen bonds       : angle       5.63907 /  3.90 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6398 (pmt170) cc_final: 0.5664 (ptt180)
REVERT: A  129 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7520 (mt)
REVERT: A  273 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6991 (mm-30)
REVERT: A  297 TYR cc_start: 0.8468 (t80) cc_final: 0.8027 (t80)
REVERT: A  436 PHE cc_start: 0.7196 (m-10) cc_final: 0.6977 (m-10)
REVERT: A  478 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7065 (tm)
REVERT: A  482 PHE cc_start: 0.6577 (m-80) cc_final: 0.6262 (m-80)
REVERT: A  522 TRP cc_start: 0.7274 (t-100) cc_final: 0.5308 (t60)
REVERT: B  125 ARG cc_start: 0.6450 (pmt170) cc_final: 0.5818 (ptt180)
REVERT: B  129 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7510 (mt)
REVERT: B  297 TYR cc_start: 0.8530 (t80) cc_final: 0.8067 (t80)
REVERT: B  522 TRP cc_start: 0.7292 (t-100) cc_final: 0.5222 (t60)
  outliers start: 37
  outliers final: 29
  residues processed: 169
  average time/residue: 0.0650
  time to fit residues: 15.3701
Evaluate side-chains
  166 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0370
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.7660

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.210376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.185830 restraints weight = 7676.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.189745 restraints weight = 4588.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.192172 restraints weight = 3312.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.193970 restraints weight = 2678.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.194923 restraints weight = 2307.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6780  Z= 0.143
  Angle     :  0.679  12.780   9272  Z= 0.326
  Chirality :  0.042   0.213   1022
  Planarity :  0.005   0.040   1100
  Dihedral  :  5.886  52.237    900
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 19.88 %
    Favored  : 74.31 %
  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: -0.51 (0.31), residues: 782
  helix:  0.51 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.33 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.020   0.001   TYR A 210 
 PHE   0.022   0.001   PHE A 481 
 TRP   0.009   0.001   TRP B 188 
 HIS   0.005   0.001   HIS A 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 6780)
  covalent geometry    : angle       0.67899 /  0.33 ( 9272)
  hydrogen bonds       : bond        0.03787 /  2.51 (  472)
  hydrogen bonds       : angle       5.62329 /  3.90 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6348 (pmt170) cc_final: 0.5600 (ptt180)
REVERT: A  129 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7502 (mt)
REVERT: A  273 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6665 (mm-30)
REVERT: A  297 TYR cc_start: 0.8501 (t80) cc_final: 0.8045 (t80)
REVERT: A  468 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: A  478 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7417 (tm)
REVERT: A  522 TRP cc_start: 0.7278 (t-100) cc_final: 0.5292 (t60)
REVERT: B  125 ARG cc_start: 0.6364 (pmt170) cc_final: 0.5693 (ptt180)
REVERT: B  129 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7621 (mt)
REVERT: B  297 TYR cc_start: 0.8646 (t80) cc_final: 0.8411 (t80)
REVERT: B  522 TRP cc_start: 0.7293 (t-100) cc_final: 0.5228 (t60)
  outliers start: 38
  outliers final: 29
  residues processed: 167
  average time/residue: 0.0685
  time to fit residues: 16.0528
Evaluate side-chains
  170 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    0.2980
   chunk 43 optimal weight:    0.0370
   chunk 13 optimal weight:    0.0980
   chunk 74 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0370
   overall best weight:    0.2938

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.215823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.191476 restraints weight = 7593.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.195405 restraints weight = 4479.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.198115 restraints weight = 3214.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.199781 restraints weight = 2561.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.200986 restraints weight = 2198.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6780  Z= 0.119
  Angle     :  0.643  12.825   9272  Z= 0.306
  Chirality :  0.041   0.206   1022
  Planarity :  0.005   0.039   1100
  Dihedral  :  5.619  57.147    900
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 21.25 %
    Favored  : 73.55 %
  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: -0.05 (0.32), residues: 782
  helix:  0.79 (0.22), residues: 610
  sheet:  None (None), residues: 0
  loop : -2.98 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 210 
 PHE   0.022   0.001   PHE A 254 
 TRP   0.008   0.001   TRP B 427 
 HIS   0.003   0.001   HIS A 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 6780)
  covalent geometry    : angle       0.64298 /  0.31 ( 9272)
  hydrogen bonds       : bond        0.03558 /  2.35 (  472)
  hydrogen bonds       : angle       5.40506 /  3.74 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6240 (pmt170) cc_final: 0.5453 (ptt180)
REVERT: A  129 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7403 (mt)
REVERT: A  297 TYR cc_start: 0.8384 (t80) cc_final: 0.8092 (t80)
REVERT: A  478 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7360 (tm)
REVERT: A  482 PHE cc_start: 0.6594 (m-80) cc_final: 0.6363 (m-80)
REVERT: A  522 TRP cc_start: 0.7323 (t-100) cc_final: 0.5254 (t60)
REVERT: B  125 ARG cc_start: 0.6245 (pmt170) cc_final: 0.5504 (ptt180)
REVERT: B  129 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7397 (mt)
REVERT: B  297 TYR cc_start: 0.8508 (t80) cc_final: 0.8162 (t80)
REVERT: B  522 TRP cc_start: 0.7346 (t-100) cc_final: 0.5187 (t60)
  outliers start: 34
  outliers final: 27
  residues processed: 177
  average time/residue: 0.0564
  time to fit residues: 14.5762
Evaluate side-chains
  164 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.0370
   chunk 32 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0670
   chunk 74 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 386 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.213892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.189297 restraints weight = 7564.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.193337 restraints weight = 4473.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.196004 restraints weight = 3198.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.197449 restraints weight = 2564.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.198710 restraints weight = 2239.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6780  Z= 0.124
  Angle     :  0.645  12.828   9272  Z= 0.307
  Chirality :  0.041   0.184   1022
  Planarity :  0.005   0.040   1100
  Dihedral  :  5.543  59.011    898
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 21.71 %
    Favored  : 73.39 %
  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: -0.01 (0.31), residues: 782
  helix:  0.77 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -2.87 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 272 
 TYR   0.015   0.001   TYR B 210 
 PHE   0.024   0.001   PHE A 481 
 TRP   0.007   0.001   TRP B 188 
 HIS   0.005   0.001   HIS A 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6780)
  covalent geometry    : angle       0.64519 /  0.31 ( 9272)
  hydrogen bonds       : bond        0.03559 /  2.34 (  472)
  hydrogen bonds       : angle       5.34848 /  3.72 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6336 (pmt170) cc_final: 0.5430 (ptt180)
REVERT: A  129 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7323 (mt)
REVERT: A  273 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6850 (mt-10)
REVERT: A  297 TYR cc_start: 0.8471 (t80) cc_final: 0.7963 (t80)
REVERT: A  478 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7268 (tm)
REVERT: A  522 TRP cc_start: 0.7458 (t-100) cc_final: 0.5297 (t60)
REVERT: B  125 ARG cc_start: 0.6315 (pmt170) cc_final: 0.5494 (ptt180)
REVERT: B  129 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7267 (mt)
REVERT: B  297 TYR cc_start: 0.8569 (t80) cc_final: 0.8315 (t80)
REVERT: B  522 TRP cc_start: 0.7499 (t-100) cc_final: 0.5258 (t60)
  outliers start: 32
  outliers final: 24
  residues processed: 172
  average time/residue: 0.0586
  time to fit residues: 14.5816
Evaluate side-chains
  162 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.215035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.192989 restraints weight = 7661.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.196138 restraints weight = 4902.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.197810 restraints weight = 3688.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.199423 restraints weight = 3104.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.200205 restraints weight = 2723.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6780  Z= 0.163
  Angle     :  0.676  12.586   9272  Z= 0.331
  Chirality :  0.043   0.192   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.538  58.334    898
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.95 %
    Favored  : 73.70 %
  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: -0.26 (0.31), residues: 782
  helix:  0.64 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.00 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 219 
 TYR   0.016   0.002   TYR A 430 
 PHE   0.028   0.002   PHE A 334 
 TRP   0.009   0.001   TRP A 188 
 HIS   0.006   0.001   HIS B 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.16 ( 6780)
  covalent geometry    : angle       0.67626 /  0.33 ( 9272)
  hydrogen bonds       : bond        0.03818 /  2.52 (  472)
  hydrogen bonds       : angle       5.51048 /  3.84 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6466 (mt-10)
REVERT: A  297 TYR cc_start: 0.8654 (t80) cc_final: 0.8391 (t80)
REVERT: A  413 TYR cc_start: 0.6670 (OUTLIER) cc_final: 0.6256 (t80)
REVERT: A  478 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7440 (tm)
REVERT: A  522 TRP cc_start: 0.7364 (t-100) cc_final: 0.5409 (t60)
REVERT: B  125 ARG cc_start: 0.6412 (pmt170) cc_final: 0.5839 (ptt180)
REVERT: B  297 TYR cc_start: 0.8662 (t80) cc_final: 0.8375 (t80)
REVERT: B  522 TRP cc_start: 0.7429 (t-100) cc_final: 0.5364 (t60)
  outliers start: 35
  outliers final: 28
  residues processed: 165
  average time/residue: 0.0583
  time to fit residues: 14.0975
Evaluate side-chains
  154 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0040
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.218946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.197139 restraints weight = 7658.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.200324 restraints weight = 4909.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.202202 restraints weight = 3689.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.203760 restraints weight = 3071.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.204189 restraints weight = 2690.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.4691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6780  Z= 0.131
  Angle     :  0.645  12.850   9272  Z= 0.312
  Chirality :  0.041   0.173   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.378  56.945    898
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.64 %
    Favored  : 74.16 %
  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:  0.04 (0.31), residues: 782
  helix:  0.81 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.74 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.014   0.001   TYR A 210 
 PHE   0.030   0.001   PHE A 334 
 TRP   0.008   0.001   TRP B 188 
 HIS   0.004   0.001   HIS A 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 6780)
  covalent geometry    : angle       0.64504 /  0.31 ( 9272)
  hydrogen bonds       : bond        0.03605 /  2.37 (  472)
  hydrogen bonds       : angle       5.42823 /  3.78 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5898 (ptt-90) cc_final: 0.5257 (ptt180)
REVERT: A  212 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7627 (mttt)
REVERT: A  273 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6446 (mt-10)
REVERT: A  297 TYR cc_start: 0.8504 (t80) cc_final: 0.8184 (t80)
REVERT: A  413 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.6194 (t80)
REVERT: A  449 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.3967 (tpt)
REVERT: A  522 TRP cc_start: 0.7374 (t-100) cc_final: 0.5393 (t60)
REVERT: B  125 ARG cc_start: 0.6327 (pmt170) cc_final: 0.5755 (ptt180)
REVERT: B  297 TYR cc_start: 0.8566 (t80) cc_final: 0.8215 (t80)
REVERT: B  522 TRP cc_start: 0.7340 (t-100) cc_final: 0.5311 (t60)
  outliers start: 34
  outliers final: 27
  residues processed: 159
  average time/residue: 0.0600
  time to fit residues: 13.9647
Evaluate side-chains
  158 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.6738

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.218110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.196047 restraints weight = 7606.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.199227 restraints weight = 4908.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.201323 restraints weight = 3712.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.202689 restraints weight = 3060.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.203456 restraints weight = 2698.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6780  Z= 0.138
  Angle     :  0.668  13.740   9272  Z= 0.322
  Chirality :  0.042   0.174   1022
  Planarity :  0.005   0.043   1100
  Dihedral  :  5.369  55.966    898
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 21.41 %
    Favored  : 74.01 %
  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:  0.07 (0.31), residues: 782
  helix:  0.82 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.68 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.014   0.001   TYR A 210 
 PHE   0.029   0.001   PHE A 334 
 TRP   0.007   0.001   TRP B 504 
 HIS   0.004   0.001   HIS A 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 6780)
  covalent geometry    : angle       0.66767 /  0.32 ( 9272)
  hydrogen bonds       : bond        0.03635 /  2.39 (  472)
  hydrogen bonds       : angle       5.44294 /  3.80 ( 1416)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5934 (ptt-90) cc_final: 0.5316 (ptt180)
REVERT: A  212 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7628 (mttt)
REVERT: A  273 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6404 (mt-10)
REVERT: A  297 TYR cc_start: 0.8550 (t80) cc_final: 0.8110 (t80)
REVERT: A  413 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.6155 (t80)
REVERT: A  449 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.3980 (tpt)
REVERT: A  522 TRP cc_start: 0.7374 (t-100) cc_final: 0.5368 (t60)
REVERT: B  297 TYR cc_start: 0.8597 (t80) cc_final: 0.8315 (t80)
REVERT: B  402 MET cc_start: 0.5921 (ptt) cc_final: 0.5587 (ptt)
REVERT: B  522 TRP cc_start: 0.7334 (t-100) cc_final: 0.5281 (t60)
  outliers start: 30
  outliers final: 26
  residues processed: 155
  average time/residue: 0.0604
  time to fit residues: 13.6729
Evaluate side-chains
  153 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.214334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.191989 restraints weight = 7621.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.195271 restraints weight = 4769.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.197553 restraints weight = 3572.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.198602 restraints weight = 2923.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.199798 restraints weight = 2614.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6780  Z= 0.160
  Angle     :  0.694  13.534   9272  Z= 0.336
  Chirality :  0.044   0.173   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.407  51.306    898
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 21.25 %
    Favored  : 74.01 %
  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: -0.09 (0.31), residues: 782
  helix:  0.71 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.69 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.014   0.001   TYR A 430 
 PHE   0.025   0.002   PHE A 334 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.009   0.001   HIS B 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 6780)
  covalent geometry    : angle       0.69373 /  0.34 ( 9272)
  hydrogen bonds       : bond        0.03805 /  2.52 (  472)
  hydrogen bonds       : angle       5.53744 /  3.86 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1162.71 seconds
wall clock time: 20 minutes 49.82 seconds (1249.82 seconds total)