Starting phenix.real_space_refine
on Tue Mar  3 11:27:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wrl_32732/03_2026/7wrl_32732.cif"
  }
  resolution = 3.51
  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=   0.043
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      15      5.16       5
     C    2052      2.51       5
     N     548      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3251
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 971
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 776
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "R"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1504
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Chain breaks: 1
  Time building chain proxies: 0.85, per 1000 atoms: 0.26
  Number of scatterers: 3251
  At special positions: 0
  Unit cell: (63.72, 82.08, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     636      8.00
     N     548      7.00
     C    2052      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.03

  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: 0.20
  Conformation dependent library (CDL) restraints added in 125.0 milliseconds
  

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 11 sheets defined
      5.0% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 3.969A  pdb=" N   GLN A  65 " --> pdb=" O   ASP A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.608A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 384 through 390
      removed outlier: 3.578A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN R 388 " --> pdb=" O   THR R 385 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASP R 389 " --> pdb=" O   LYS R 386 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU R 390 " --> pdb=" O   LEU R 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 384 through 390'
    Processing helix  chain 'R' and resid 498 through 502
      removed outlier: 3.785A  pdb=" N   TYR R 501 " --> pdb=" O   ARG R 498 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLY R 502 " --> pdb=" O   PRO R 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 498 through 502'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39
      removed outlier: 6.876A  pdb=" N   SER A  34 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ARG A  50 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73
      removed outlier: 3.508A  pdb=" N   ASP A  73 " --> pdb=" O   THR A  78 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR A  78 " --> pdb=" O   ASP A  73 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 101
      removed outlier: 4.703A  pdb=" N   VAL A 119 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   VAL A 100 " --> pdb=" O   MET A 117 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   MET A 117 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22
      removed outlier: 3.831A  pdb=" N   SER B  65 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50
      removed outlier: 6.537A  pdb=" N   TRP B  37 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 356 through 358
    Processing sheet with id=AB1, first strand: chain 'R' and resid 361 through 362
      removed outlier: 6.995A  pdb=" N   CYS R 361 " --> pdb=" O   CYS R 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454

    51 hydrogen bonds defined for protein.
    117 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.41

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1017
        1.34 -     1.46: 739
        1.46 -     1.57: 1558
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3332
  Sorted by residual:
  bond pdb=" C   ASP A 109 "
       pdb=" N   PHE A 110 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.030 1.49e-02 4.50e+03 3.93e+00
  bond pdb=" CB  CYS B  90 "
       pdb=" SG  CYS B  90 "
    ideal  model  delta    sigma   weight residual
    1.808  1.757  0.051 3.30e-02 9.18e+02 2.39e+00
  bond pdb=" C   LYS A  13 "
       pdb=" N   PRO A  14 "
    ideal  model  delta    sigma   weight residual
    1.330  1.349 -0.019 1.25e-02 6.40e+03 2.35e+00
  bond pdb=" N   ALA R 411 "
       pdb=" CA  ALA R 411 "
    ideal  model  delta    sigma   weight residual
    1.457  1.436  0.021 1.41e-02 5.03e+03 2.13e+00
  bond pdb=" C   ALA R 372 "
       pdb=" N   PRO R 373 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 2.04e+00
  ... (remaining 3327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 4176
        1.79 -     3.58: 285
        3.58 -     5.37: 55
        5.37 -     7.16: 9
        7.16 -     8.95: 4
  Bond angle restraints: 4529
  Sorted by residual:
  angle pdb=" N   VAL R 483 "
        pdb=" CA  VAL R 483 "
        pdb=" C   VAL R 483 "
      ideal   model   delta    sigma   weight residual
     106.21  110.82   -4.61 1.07e+00 8.73e-01 1.86e+01
  angle pdb=" C   GLY R 485 "
        pdb=" N   PHE R 486 "
        pdb=" CA  PHE R 486 "
      ideal   model   delta    sigma   weight residual
     121.54  129.41   -7.87 1.91e+00 2.74e-01 1.70e+01
  angle pdb=" N   VAL R 367 "
        pdb=" CA  VAL R 367 "
        pdb=" C   VAL R 367 "
      ideal   model   delta    sigma   weight residual
     112.29  108.61    3.68 9.40e-01 1.13e+00 1.53e+01
  angle pdb=" OG1 THR B  94 "
        pdb=" CB  THR B  94 "
        pdb=" CG2 THR B  94 "
      ideal   model   delta    sigma   weight residual
     109.30  102.03    7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" C   TYR B  51 "
        pdb=" N   ASP B  52 "
        pdb=" CA  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     121.71  116.85    4.86 1.39e+00 5.18e-01 1.22e+01
  ... (remaining 4524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 1709
       17.40 -    34.79: 196
       34.79 -    52.19: 33
       52.19 -    69.59: 5
       69.59 -    86.98: 1
  Dihedral angle restraints: 1944
    sinusoidal: 734
      harmonic: 1210
  Sorted by residual:
  dihedral pdb=" CA  LYS A  13 "
           pdb=" C   LYS A  13 "
           pdb=" N   PRO A  14 "
           pdb=" CA  PRO A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.72  -34.28     0      5.00e+00 4.00e-02 4.70e+01
  dihedral pdb=" CA  TYR A  60 "
           pdb=" C   TYR A  60 "
           pdb=" N   ALA A  61 "
           pdb=" CA  ALA A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.47   23.53     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  ARG R 466 "
           pdb=" C   ARG R 466 "
           pdb=" N   ASP R 467 "
           pdb=" CA  ASP R 467 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.19   21.81     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 1941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 307
       0.047 -    0.094: 120
       0.094 -    0.141: 43
       0.141 -    0.188: 11
       0.188 -    0.235: 4
  Chirality restraints: 485
  Sorted by residual:
  chirality pdb=" CB  ILE A  51 "
            pdb=" CA  ILE A  51 "
            pdb=" CG1 ILE A  51 "
            pdb=" CG2 ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  TYR B  51 "
            pdb=" N   TYR B  51 "
            pdb=" C   TYR B  51 "
            pdb=" CB  TYR B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  VAL R 483 "
            pdb=" CA  VAL R 483 "
            pdb=" CG1 VAL R 483 "
            pdb=" CG2 VAL R 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.85    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 482 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS R 462 "    0.050 5.00e-02 4.00e+02   7.53e-02 9.08e+00
        pdb=" N   PRO R 463 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO R 463 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 463 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 338 "   -0.014 2.00e-02 2.50e+03   1.75e-02 5.37e+00
        pdb=" CG  PHE R 338 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 338 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 338 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 338 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 338 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 338 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  56 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.00e+00
        pdb=" N   PRO B  57 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B  57 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  57 "    0.031 5.00e-02 4.00e+02
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 986
        2.81 -     3.33: 2686
        3.33 -     3.86: 5412
        3.86 -     4.38: 6037
        4.38 -     4.90: 10870
  Nonbonded interactions: 25991
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R 415 "
            pdb=" OD2 ASP R 420 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR B  32 "
            pdb=" OD2 ASP R 405 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN B  54 "
            pdb=" O   GLY B  66 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   SER A  25 "
            pdb=" OG  SER A  25 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OD2 ASP R 398 "
            pdb=" OH  TYR R 423 "
     model   vdw
     2.327 3.040
  ... (remaining 25986 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.690
  Find NCS groups from input model:        0.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
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      :  0.006   0.054   3335  Z= 0.273
  Angle     :  1.031   8.952   4535  Z= 0.594
  Chirality :  0.060   0.235    485
  Planarity :  0.008   0.075    586
  Dihedral  : 14.713  86.983   1171
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.38 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.19 (0.37), residues: 411
  helix: -4.93 (0.34), residues: 27
  sheet: -2.41 (0.46), residues: 118
  loop : -2.86 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A  84 
 TYR   0.032   0.003   TYR B  51 
 PHE   0.040   0.003   PHE R 338 
 TRP   0.014   0.003   TRP A  47 
 HIS   0.002   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 3332)
  covalent geometry    : angle       1.03124 ( 4529)
  SS BOND              : bond        0.00123 (    3)
  SS BOND              : angle       0.52933 (    6)
  hydrogen bonds       : bond        0.24310 (   51)
  hydrogen bonds       : angle      10.83828 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.074 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0654
  time to fit residues: 5.4338
Evaluate side-chains
  50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
B  54 ASN
** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.142378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114456 restraints weight = 5256.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.117846 restraints weight = 3372.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.120147 restraints weight = 2523.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.121784 restraints weight = 2086.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.122577 restraints weight = 1825.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   3335  Z= 0.167
  Angle     :  0.644   5.954   4535  Z= 0.354
  Chirality :  0.045   0.173    485
  Planarity :  0.006   0.063    586
  Dihedral  :  6.506  25.660    466
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.42 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.37), residues: 411
  helix: -4.50 (0.56), residues: 27
  sheet: -1.75 (0.46), residues: 116
  loop : -2.94 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 457 
 TYR   0.020   0.002   TYR B  51 
 PHE   0.020   0.002   PHE R 338 
 TRP   0.013   0.002   TRP A 120 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3332)
  covalent geometry    : angle       0.64340 ( 4529)
  SS BOND              : bond        0.00138 (    3)
  SS BOND              : angle       0.73177 (    6)
  hydrogen bonds       : bond        0.03518 (   51)
  hydrogen bonds       : angle       8.16144 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.102 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0731
  time to fit residues: 5.7322
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  100 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
R 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.114307 restraints weight = 5242.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.117758 restraints weight = 3266.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120120 restraints weight = 2431.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.121452 restraints weight = 2001.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.122573 restraints weight = 1777.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3335  Z= 0.155
  Angle     :  0.608   5.905   4535  Z= 0.333
  Chirality :  0.045   0.163    485
  Planarity :  0.005   0.058    586
  Dihedral  :  5.920  22.745    466
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.68 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.78 (0.37), residues: 411
  helix: -4.43 (0.58), residues: 27
  sheet: -1.56 (0.48), residues: 116
  loop : -2.91 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 454 
 TYR   0.021   0.002   TYR B  51 
 PHE   0.011   0.001   PHE R 347 
 TRP   0.011   0.002   TRP A 120 
 HIS   0.000   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3332)
  covalent geometry    : angle       0.60783 ( 4529)
  SS BOND              : bond        0.00051 (    3)
  SS BOND              : angle       0.86133 (    6)
  hydrogen bonds       : bond        0.03073 (   51)
  hydrogen bonds       : angle       7.61465 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 LYS cc_start: 0.7250 (mptt) cc_final: 0.6233 (ptmm)
REVERT: B   81 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7942 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.0611
  time to fit residues: 5.3132
Evaluate side-chains
  65 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.0270
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0670
   chunk 5 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0170
   overall best weight:    0.2814

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
R 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.144861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.116813 restraints weight = 5110.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120564 restraints weight = 3128.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123030 restraints weight = 2297.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124729 restraints weight = 1875.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125686 restraints weight = 1625.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3335  Z= 0.101
  Angle     :  0.551   5.798   4535  Z= 0.298
  Chirality :  0.043   0.149    485
  Planarity :  0.004   0.056    586
  Dihedral  :  5.257  17.819    466
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.06 %
    Favored  : 81.97 %
  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: -3.51 (0.38), residues: 411
  helix: -4.25 (0.65), residues: 27
  sheet: -1.23 (0.48), residues: 122
  loop : -2.82 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  84 
 TYR   0.019   0.001   TYR B  51 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.007   0.001   TRP A 120 
 HIS   0.000   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3332)
  covalent geometry    : angle       0.55013 ( 4529)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       1.14383 (    6)
  hydrogen bonds       : bond        0.02506 (   51)
  hydrogen bonds       : angle       6.98375 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7368 (mtm110)
REVERT: B   44 LYS cc_start: 0.6876 (mptt) cc_final: 0.6204 (ptmm)
REVERT: R  498 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6812 (mtt90)
  outliers start: 7
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0747
  time to fit residues: 6.5227
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.0370
   chunk 22 optimal weight:    0.0050
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0020
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.1278

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
R 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.147024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.119125 restraints weight = 5104.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.122937 restraints weight = 3091.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125448 restraints weight = 2249.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.127170 restraints weight = 1830.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.128195 restraints weight = 1582.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   3335  Z= 0.094
  Angle     :  0.550   6.499   4535  Z= 0.294
  Chirality :  0.043   0.148    485
  Planarity :  0.004   0.054    586
  Dihedral  :  4.990  19.968    466
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.18 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.39), residues: 411
  helix: -4.10 (0.72), residues: 27
  sheet: -0.98 (0.49), residues: 124
  loop : -2.78 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.018   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A 110 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.000   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3332)
  covalent geometry    : angle       0.55042 ( 4529)
  SS BOND              : bond        0.00089 (    3)
  SS BOND              : angle       0.46772 (    6)
  hydrogen bonds       : bond        0.02372 (   51)
  hydrogen bonds       : angle       6.68692 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7375 (mtm110)
REVERT: A   89 GLU cc_start: 0.5919 (pp20) cc_final: 0.5537 (mm-30)
REVERT: R  444 LYS cc_start: 0.6036 (tppt) cc_final: 0.5291 (pttt)
REVERT: R  498 ARG cc_start: 0.7136 (mtt90) cc_final: 0.6887 (mtt90)
  outliers start: 10
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0691
  time to fit residues: 5.9361
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.0470
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    0.1980
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.116254 restraints weight = 5104.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.119776 restraints weight = 3172.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122114 restraints weight = 2361.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.123683 restraints weight = 1950.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124605 restraints weight = 1711.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3335  Z= 0.122
  Angle     :  0.567   7.118   4535  Z= 0.303
  Chirality :  0.043   0.152    485
  Planarity :  0.004   0.054    586
  Dihedral  :  4.924  19.107    466
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.46 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.18 %
    Favored  : 79.72 %
  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: -3.19 (0.39), residues: 411
  helix: -4.17 (0.71), residues: 27
  sheet: -0.82 (0.50), residues: 117
  loop : -2.67 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  56 
 TYR   0.019   0.001   TYR B  51 
 PHE   0.009   0.001   PHE R 347 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.000   0.000   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3332)
  covalent geometry    : angle       0.56612 ( 4529)
  SS BOND              : bond        0.00758 (    3)
  SS BOND              : angle       1.14547 (    6)
  hydrogen bonds       : bond        0.02517 (   51)
  hydrogen bonds       : angle       6.58702 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7417 (mtm110)
REVERT: B   44 LYS cc_start: 0.7031 (mptt) cc_final: 0.6175 (ptmm)
REVERT: R  444 LYS cc_start: 0.6221 (tppt) cc_final: 0.5447 (pttt)
REVERT: R  498 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6787 (mtt90)
  outliers start: 11
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0685
  time to fit residues: 5.4896
Evaluate side-chains
  71 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.114944 restraints weight = 5261.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.118609 restraints weight = 3216.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.121041 restraints weight = 2370.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.122678 restraints weight = 1947.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123638 restraints weight = 1704.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3335  Z= 0.128
  Angle     :  0.566   6.540   4535  Z= 0.303
  Chirality :  0.043   0.152    485
  Planarity :  0.004   0.053    586
  Dihedral  :  4.862  19.064    466
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.03 %
    Favored  : 78.87 %
  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: -3.23 (0.39), residues: 411
  helix: -4.16 (0.73), residues: 27
  sheet: -0.89 (0.49), residues: 117
  loop : -2.67 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.019   0.001   TYR B  51 
 PHE   0.009   0.001   PHE B 101 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.000   0.000   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3332)
  covalent geometry    : angle       0.56494 ( 4529)
  SS BOND              : bond        0.00735 (    3)
  SS BOND              : angle       1.13703 (    6)
  hydrogen bonds       : bond        0.02561 (   51)
  hydrogen bonds       : angle       6.53162 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 LYS cc_start: 0.7114 (mptt) cc_final: 0.6720 (ptpp)
REVERT: R  444 LYS cc_start: 0.6229 (tppt) cc_final: 0.5526 (pttt)
REVERT: R  498 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6815 (mtt90)
  outliers start: 11
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0691
  time to fit residues: 5.7668
Evaluate side-chains
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Chi-restraints excluded: chain R residue  501 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0470
   chunk 29 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.143756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.115011 restraints weight = 5264.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.118749 restraints weight = 3246.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121329 restraints weight = 2375.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123059 restraints weight = 1925.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.124039 restraints weight = 1665.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3335  Z= 0.124
  Angle     :  0.568   6.884   4535  Z= 0.304
  Chirality :  0.043   0.152    485
  Planarity :  0.004   0.053    586
  Dihedral  :  4.778  18.647    466
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.15 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.39), residues: 411
  helix: -4.13 (0.73), residues: 27
  sheet: -0.87 (0.49), residues: 117
  loop : -2.66 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.019   0.001   TYR B  51 
 PHE   0.009   0.001   PHE B 101 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.000   0.000   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3332)
  covalent geometry    : angle       0.56539 ( 4529)
  SS BOND              : bond        0.00608 (    3)
  SS BOND              : angle       1.63025 (    6)
  hydrogen bonds       : bond        0.02470 (   51)
  hydrogen bonds       : angle       6.51363 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  444 LYS cc_start: 0.6316 (tppt) cc_final: 0.5617 (pttt)
REVERT: R  498 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6434 (mtt90)
REVERT: R  501 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6405 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0751
  time to fit residues: 5.5570
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  382 VAL
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Chi-restraints excluded: chain R residue  501 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0040
   chunk 39 optimal weight:    0.3980
   chunk 25 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.145772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117942 restraints weight = 5152.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.121534 restraints weight = 3203.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.123993 restraints weight = 2358.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125443 restraints weight = 1926.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126724 restraints weight = 1692.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3335  Z= 0.104
  Angle     :  0.562   7.082   4535  Z= 0.298
  Chirality :  0.042   0.148    485
  Planarity :  0.004   0.053    586
  Dihedral  :  4.574  18.850    466
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.56 %
    Favored  : 76.34 %
  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: -3.01 (0.40), residues: 411
  helix: -4.08 (0.75), residues: 27
  sheet: -0.56 (0.51), residues: 117
  loop : -2.62 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  56 
 TYR   0.018   0.001   TYR B  51 
 PHE   0.008   0.001   PHE A 110 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.000   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3332)
  covalent geometry    : angle       0.56000 ( 4529)
  SS BOND              : bond        0.00483 (    3)
  SS BOND              : angle       1.26729 (    6)
  hydrogen bonds       : bond        0.02302 (   51)
  hydrogen bonds       : angle       6.25138 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7327 (mtm110)
REVERT: R  444 LYS cc_start: 0.6185 (tppt) cc_final: 0.5556 (pttt)
REVERT: R  498 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6319 (mtt90)
REVERT: R  501 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6586 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0758
  time to fit residues: 5.3302
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  465 GLU
Chi-restraints excluded: chain R residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.142504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114348 restraints weight = 5233.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.117825 restraints weight = 3273.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120142 restraints weight = 2436.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121734 restraints weight = 2006.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.122717 restraints weight = 1764.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3335  Z= 0.146
  Angle     :  0.587   7.693   4535  Z= 0.314
  Chirality :  0.043   0.149    485
  Planarity :  0.004   0.053    586
  Dihedral  :  4.736  18.671    466
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.85 %
    Favored  : 76.06 %
  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: -3.06 (0.40), residues: 411
  helix: -4.12 (0.73), residues: 27
  sheet: -0.69 (0.50), residues: 120
  loop : -2.61 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.019   0.002   TYR B  51 
 PHE   0.010   0.001   PHE B 101 
 TRP   0.009   0.002   TRP A 120 
 HIS   0.000   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3332)
  covalent geometry    : angle       0.58529 ( 4529)
  SS BOND              : bond        0.00495 (    3)
  SS BOND              : angle       1.31560 (    6)
  hydrogen bonds       : bond        0.02671 (   51)
  hydrogen bonds       : angle       6.45822 (  117)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   84 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7380 (mtm110)
REVERT: B   44 LYS cc_start: 0.6985 (mptt) cc_final: 0.6295 (ptmm)
REVERT: R  444 LYS cc_start: 0.6348 (tppt) cc_final: 0.5663 (pttt)
REVERT: R  501 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6591 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 58
  average time/residue: 0.0760
  time to fit residues: 5.3474
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain R residue  341 VAL
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  393 THR
Chi-restraints excluded: chain R residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112718 restraints weight = 5297.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.116137 restraints weight = 3351.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.118441 restraints weight = 2504.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.120071 restraints weight = 2072.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.120965 restraints weight = 1813.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3335  Z= 0.179
  Angle     :  0.627   7.966   4535  Z= 0.338
  Chirality :  0.045   0.152    485
  Planarity :  0.004   0.051    586
  Dihedral  :  5.030  21.976    466
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.97 %
    Favored  : 75.49 %
  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: -3.23 (0.39), residues: 411
  helix: -4.19 (0.69), residues: 27
  sheet: -0.96 (0.50), residues: 120
  loop : -2.64 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 454 
 TYR   0.019   0.002   TYR B  51 
 PHE   0.014   0.002   PHE B 101 
 TRP   0.011   0.002   TRP A 120 
 HIS   0.000   0.000   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 3332)
  covalent geometry    : angle       0.62568 ( 4529)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       1.30731 (    6)
  hydrogen bonds       : bond        0.02844 (   51)
  hydrogen bonds       : angle       6.58141 (  117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 886.98 seconds
wall clock time: 15 minutes 51.30 seconds (951.30 seconds total)