Starting phenix.real_space_refine
on Tue Mar  3 11:30:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yvj_34129/03_2026/7yvj_34129.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.024
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      16      5.16       5
     C    2073      2.51       5
     N     552      2.21       5
     O     626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 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: 3267
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 805
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "C"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 971
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 5, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 1491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1491
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
  Time building chain proxies: 0.65, per 1000 atoms: 0.20
  Number of scatterers: 3267
  At special positions: 0
  Unit cell: (72.16, 68.88, 82, 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      16     16.00
     O     626      8.00
     N     552      7.00
     C    2073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.04

  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: 0.24
  Conformation dependent library (CDL) restraints added in 76.0 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  772

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 7 sheets defined
      7.0% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   ASP C  31 " --> pdb=" O   MET C  28 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER C  32 " --> pdb=" O   ILE C  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 28 through 32'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.571A  pdb=" N   ASP C  90 " --> pdb=" O   ARG C  87 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   THR C  91 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 87 through 91'
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 5.578A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12
      removed outlier: 5.578A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22
    Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.863A  pdb=" N   MET C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   TYR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.057A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER B 514 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454

    97 hydrogen bonds defined for protein.
    216 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: 0.32

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 535
        1.31 -     1.44: 1009
        1.44 -     1.56: 1788
        1.56 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3352
  Sorted by residual:
  bond pdb=" CA  ASN B 437 "
       pdb=" C   ASN B 437 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.064 1.35e-02 5.49e+03 2.23e+01
  bond pdb=" CA  VAL B 350 "
       pdb=" C   VAL B 350 "
    ideal  model  delta    sigma   weight residual
    1.524  1.469  0.055 1.22e-02 6.72e+03 2.04e+01
  bond pdb=" C   VAL B 350 "
       pdb=" O   VAL B 350 "
    ideal  model  delta    sigma   weight residual
    1.237  1.192  0.044 1.13e-02 7.83e+03 1.54e+01
  bond pdb=" C   ASN B 437 "
       pdb=" O   ASN B 437 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.17e-02 7.31e+03 1.54e+01
  bond pdb=" CA  SER B 438 "
       pdb=" C   SER B 438 "
    ideal  model  delta    sigma   weight residual
    1.526  1.475  0.050 1.28e-02 6.10e+03 1.54e+01
  ... (remaining 3347 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 4249
        1.99 -     3.98: 272
        3.98 -     5.97: 29
        5.97 -     7.96: 7
        7.96 -     9.95: 3
  Bond angle restraints: 4560
  Sorted by residual:
  angle pdb=" C   ALA B 372 "
        pdb=" N   PRO B 373 "
        pdb=" CA  PRO B 373 "
      ideal   model   delta    sigma   weight residual
     119.64  125.83   -6.19 1.01e+00 9.80e-01 3.75e+01
  angle pdb=" N   TRP B 353 "
        pdb=" CA  TRP B 353 "
        pdb=" C   TRP B 353 "
      ideal   model   delta    sigma   weight residual
     110.24  117.26   -7.02 1.30e+00 5.92e-01 2.91e+01
  angle pdb=" N   ASN B 354 "
        pdb=" CA  ASN B 354 "
        pdb=" C   ASN B 354 "
      ideal   model   delta    sigma   weight residual
     109.59  118.06   -8.47 1.61e+00 3.86e-01 2.77e+01
  angle pdb=" N   ALA B 372 "
        pdb=" CA  ALA B 372 "
        pdb=" C   ALA B 372 "
      ideal   model   delta    sigma   weight residual
     109.81  119.76   -9.95 2.21e+00 2.05e-01 2.03e+01
  angle pdb=" N   TYR B 351 "
        pdb=" CA  TYR B 351 "
        pdb=" C   TYR B 351 "
      ideal   model   delta    sigma   weight residual
     113.19  118.37   -5.18 1.19e+00 7.06e-01 1.89e+01
  ... (remaining 4555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.89: 1720
       15.89 -    31.78: 196
       31.78 -    47.67: 38
       47.67 -    63.56: 5
       63.56 -    79.45: 2
  Dihedral angle restraints: 1961
    sinusoidal: 731
      harmonic: 1230
  Sorted by residual:
  dihedral pdb=" N   ASN B 439 "
           pdb=" C   ASN B 439 "
           pdb=" CA  ASN B 439 "
           pdb=" CB  ASN B 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.87    8.93     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" CA  GLN A  40 "
           pdb=" C   GLN A  40 "
           pdb=" N   HIS A  41 "
           pdb=" CA  HIS A  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.44   17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  THR A  72 "
           pdb=" C   THR A  72 "
           pdb=" N   ALA A  73 "
           pdb=" CA  ALA A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.13   16.87     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 1958 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 392
       0.080 -    0.160: 77
       0.160 -    0.239: 8
       0.239 -    0.319: 5
       0.319 -    0.399: 2
  Chirality restraints: 484
  Sorted by residual:
  chirality pdb=" CA  TYR C 104 "
            pdb=" N   TYR C 104 "
            pdb=" C   TYR C 104 "
            pdb=" CB  TYR C 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.98e+00
  chirality pdb=" CA  ALA B 372 "
            pdb=" N   ALA B 372 "
            pdb=" C   ALA B 372 "
            pdb=" CB  ALA B 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.16    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  TRP B 353 "
            pdb=" N   TRP B 353 "
            pdb=" C   TRP B 353 "
            pdb=" CB  TRP B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 481 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 420 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.91e+00
        pdb=" CG  ASP B 420 "   -0.052 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 420 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 420 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 436 "   -0.014 2.00e-02 2.50e+03   2.92e-02 8.53e+00
        pdb=" C   TRP B 436 "    0.050 2.00e-02 2.50e+03
        pdb=" O   TRP B 436 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN B 437 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 350 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   VAL B 350 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   VAL B 350 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR B 351 "    0.013 2.00e-02 2.50e+03
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 22
        2.42 -     3.04: 2156
        3.04 -     3.66: 4751
        3.66 -     4.28: 6698
        4.28 -     4.90: 11578
  Nonbonded interactions: 25205
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  16 "
            pdb=" CD1 LEU A  80 "
     model   vdw
     1.805 3.460
  nonbonded pdb=" OH  TYR C 105 "
            pdb=" ND2 ASN B 354 "
     model   vdw
     2.023 3.120
  nonbonded pdb=" O   GLY B 476 "
            pdb=" OD1 ASN B 477 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" O   SER C  30 "
            pdb=" OD1 ASP C  31 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   GLY B 446 "
            pdb=" OH  TYR B 449 "
     model   vdw
     2.190 3.040
  ... (remaining 25200 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:             12.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.760
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064   3358  Z= 0.524
  Angle     :  1.050   9.948   4572  Z= 0.678
  Chirality :  0.070   0.399    484
  Planarity :  0.005   0.037    594
  Dihedral  : 13.624  79.449   1171
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 24.91
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  :  8.29 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.80 %
    Favored  : 88.47 %
  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: -4.50 (0.32), residues: 422
  helix: -5.27 (0.23), residues: 29
  sheet: -2.27 (0.36), residues: 153
  loop : -3.28 (0.31), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.021   0.002   TYR C 104 
 PHE   0.008   0.001   PHE A 102 
 TRP   0.021   0.002   TRP B 353 
 HIS   0.003   0.002   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00823 ( 3352)
  covalent geometry    : angle       1.04874 ( 4560)
  SS BOND              : bond        0.00627 (    6)
  SS BOND              : angle       1.44425 (   12)
  hydrogen bonds       : bond        0.18634 (   93)
  hydrogen bonds       : angle       7.93732 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASN cc_start: 0.7487 (t0) cc_final: 0.7170 (t0)
REVERT: C   13 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8451 (mmmt)
REVERT: C   98 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7424 (tmt170)
REVERT: C  100 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7810 (tp-100)
REVERT: B  386 LYS cc_start: 0.7757 (mttt) cc_final: 0.7220 (pttt)
  outliers start: 6
  outliers final: 1
  residues processed: 124
  average time/residue: 0.0818
  time to fit residues: 11.6564
Evaluate side-chains
  99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  104 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  41 HIS
B 354 ASN
B 505 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.090131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.080162 restraints weight = 8505.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.082517 restraints weight = 3907.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.084095 restraints weight = 2213.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.085122 restraints weight = 1433.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.085823 restraints weight = 1027.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3358  Z= 0.196
  Angle     :  0.695   8.695   4572  Z= 0.359
  Chirality :  0.046   0.143    484
  Planarity :  0.005   0.044    594
  Dihedral  :  5.641  57.318    479
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  4.98 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.87 %
    Favored  : 78.39 %
  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: -3.60 (0.34), residues: 422
  helix: -5.18 (0.21), residues: 29
  sheet: -1.57 (0.37), residues: 155
  loop : -2.65 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 403 
 TYR   0.023   0.002   TYR B 508 
 PHE   0.016   0.002   PHE C  68 
 TRP   0.016   0.002   TRP B 353 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 3352)
  covalent geometry    : angle       0.69430 ( 4560)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       0.85073 (   12)
  hydrogen bonds       : bond        0.04155 (   93)
  hydrogen bonds       : angle       6.48525 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8084 (p90) cc_final: 0.7271 (p90)
REVERT: A   55 ASN cc_start: 0.7922 (t0) cc_final: 0.7338 (t0)
REVERT: C   13 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8508 (mmmt)
REVERT: B  386 LYS cc_start: 0.7471 (mttt) cc_final: 0.7050 (ttpt)
REVERT: B  403 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8430 (ttm-80)
REVERT: B  498 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7891 (mtt-85)
REVERT: B  508 TYR cc_start: 0.8453 (m-80) cc_final: 0.8171 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0784
  time to fit residues: 9.8741
Evaluate side-chains
  105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0270
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
B 360 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.090068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.080126 restraints weight = 8452.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.082490 restraints weight = 3893.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.084055 restraints weight = 2215.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.085090 restraints weight = 1441.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.085732 restraints weight = 1035.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3358  Z= 0.156
  Angle     :  0.655   7.523   4572  Z= 0.336
  Chirality :  0.044   0.146    484
  Planarity :  0.005   0.045    594
  Dihedral  :  5.378  55.145    479
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.45 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 20.75 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.35), residues: 422
  helix: -4.69 (0.40), residues: 16
  sheet: -1.14 (0.38), residues: 158
  loop : -2.40 (0.33), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  56 
 TYR   0.014   0.001   TYR B 365 
 PHE   0.015   0.001   PHE C  68 
 TRP   0.015   0.002   TRP B 353 
 HIS   0.001   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3352)
  covalent geometry    : angle       0.65422 ( 4560)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       0.75718 (   12)
  hydrogen bonds       : bond        0.03817 (   93)
  hydrogen bonds       : angle       6.23026 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8048 (p90) cc_final: 0.7480 (p90)
REVERT: A   55 ASN cc_start: 0.7844 (t0) cc_final: 0.7338 (t0)
REVERT: C   13 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8444 (mmmt)
REVERT: B  386 LYS cc_start: 0.7297 (mttt) cc_final: 0.6951 (ttpt)
REVERT: B  508 TYR cc_start: 0.8371 (m-80) cc_final: 0.8138 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 112
  average time/residue: 0.0783
  time to fit residues: 10.3218
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0050
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0570
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   overall best weight:    0.2512

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

Flipped N/Q/H residues before XYZ refinement:
B 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.093134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.083044 restraints weight = 8402.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.085451 restraints weight = 3853.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.086998 restraints weight = 2176.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.088065 restraints weight = 1420.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.088775 restraints weight = 1014.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3358  Z= 0.112
  Angle     :  0.652  10.174   4572  Z= 0.324
  Chirality :  0.043   0.145    484
  Planarity :  0.004   0.037    594
  Dihedral  :  5.008  52.052    479
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.45 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.61 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.37), residues: 422
  helix: -4.48 (0.56), residues: 16
  sheet: -0.59 (0.40), residues: 156
  loop : -2.13 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  56 
 TYR   0.019   0.001   TYR C  80 
 PHE   0.014   0.001   PHE B 400 
 TRP   0.015   0.001   TRP B 353 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3352)
  covalent geometry    : angle       0.65203 ( 4560)
  SS BOND              : bond        0.00349 (    6)
  SS BOND              : angle       0.68338 (   12)
  hydrogen bonds       : bond        0.03382 (   93)
  hydrogen bonds       : angle       5.91969 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7982 (p90) cc_final: 0.7324 (p90)
REVERT: A   55 ASN cc_start: 0.7789 (t0) cc_final: 0.7192 (t0)
REVERT: C   13 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8531 (mmmt)
REVERT: B  386 LYS cc_start: 0.7435 (mttt) cc_final: 0.7076 (ttpt)
REVERT: B  498 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7852 (mtt-85)
  outliers start: 16
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0749
  time to fit residues: 10.4625
Evaluate side-chains
  113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.090169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.080306 restraints weight = 8410.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.082637 restraints weight = 3874.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.084170 restraints weight = 2210.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.085191 restraints weight = 1446.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.085826 restraints weight = 1046.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3358  Z= 0.152
  Angle     :  0.663   8.692   4572  Z= 0.332
  Chirality :  0.044   0.138    484
  Planarity :  0.004   0.041    594
  Dihedral  :  5.013  51.718    479
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.69 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 23.92 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.38), residues: 422
  helix: -4.34 (0.68), residues: 16
  sheet: -0.27 (0.42), residues: 152
  loop : -2.09 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  56 
 TYR   0.026   0.001   TYR B 508 
 PHE   0.013   0.001   PHE C  68 
 TRP   0.011   0.001   TRP B 353 
 HIS   0.002   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3352)
  covalent geometry    : angle       0.66294 ( 4560)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       0.67965 (   12)
  hydrogen bonds       : bond        0.03659 (   93)
  hydrogen bonds       : angle       5.75696 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8068 (p90) cc_final: 0.7468 (p90)
REVERT: A   55 ASN cc_start: 0.7925 (t0) cc_final: 0.7339 (t0)
REVERT: C   13 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8515 (mmmt)
REVERT: C   43 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8755 (mmtp)
REVERT: B  386 LYS cc_start: 0.7245 (mttt) cc_final: 0.6872 (ttpt)
REVERT: B  466 ARG cc_start: 0.8245 (ptm-80) cc_final: 0.8030 (ptm-80)
REVERT: B  498 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7928 (mtt-85)
  outliers start: 17
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0752
  time to fit residues: 9.5039
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.092213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.082350 restraints weight = 8557.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.084713 restraints weight = 3944.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.086279 restraints weight = 2236.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.087252 restraints weight = 1449.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.087949 restraints weight = 1056.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3358  Z= 0.125
  Angle     :  0.657   8.698   4572  Z= 0.325
  Chirality :  0.043   0.147    484
  Planarity :  0.004   0.043    594
  Dihedral  :  4.842  50.147    479
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.21 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 23.92 %
    Favored  : 71.18 %
  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 (0.39), residues: 422
  helix: -4.14 (0.74), residues: 16
  sheet:  0.05 (0.42), residues: 152
  loop : -1.97 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  56 
 TYR   0.011   0.001   TYR B 508 
 PHE   0.013   0.001   PHE B 400 
 TRP   0.010   0.001   TRP B 353 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3352)
  covalent geometry    : angle       0.65734 ( 4560)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       0.68450 (   12)
  hydrogen bonds       : bond        0.03428 (   93)
  hydrogen bonds       : angle       5.62370 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8017 (p90) cc_final: 0.7398 (p90)
REVERT: A   55 ASN cc_start: 0.7950 (t0) cc_final: 0.7368 (t0)
REVERT: C   13 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8575 (mmmt)
REVERT: C   43 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8656 (mmtp)
REVERT: B  386 LYS cc_start: 0.7244 (mttt) cc_final: 0.6858 (ttpt)
REVERT: B  498 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7893 (mtt-85)
REVERT: B  508 TYR cc_start: 0.8347 (m-80) cc_final: 0.8141 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0725
  time to fit residues: 9.6920
Evaluate side-chains
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.085356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.075495 restraints weight = 8822.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.077833 restraints weight = 4051.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.079385 restraints weight = 2293.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.080359 restraints weight = 1484.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.081096 restraints weight = 1081.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3358  Z= 0.325
  Angle     :  0.792   9.479   4572  Z= 0.406
  Chirality :  0.048   0.150    484
  Planarity :  0.006   0.057    594
  Dihedral  :  5.775  54.481    479
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.06 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 22.48 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.38), residues: 422
  helix: -4.06 (0.68), residues: 23
  sheet: -0.11 (0.42), residues: 152
  loop : -2.12 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  56 
 TYR   0.015   0.002   TYR A  93 
 PHE   0.015   0.002   PHE C  68 
 TRP   0.026   0.002   TRP C 115 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 ( 3352)
  covalent geometry    : angle       0.79154 ( 4560)
  SS BOND              : bond        0.00425 (    6)
  SS BOND              : angle       0.99108 (   12)
  hydrogen bonds       : bond        0.04355 (   93)
  hydrogen bonds       : angle       5.93820 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8262 (p90) cc_final: 0.7377 (p90)
REVERT: A   55 ASN cc_start: 0.8332 (t0) cc_final: 0.8079 (t0)
REVERT: C    6 GLU cc_start: 0.7347 (mp0) cc_final: 0.7002 (mp0)
REVERT: C   13 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8606 (mmmt)
REVERT: C   19 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.8150 (ttm-80)
REVERT: B  498 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7945 (mtt-85)
  outliers start: 21
  outliers final: 17
  residues processed: 110
  average time/residue: 0.0762
  time to fit residues: 9.8720
Evaluate side-chains
  108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0370
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.090014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.080179 restraints weight = 8641.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.082537 restraints weight = 4001.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.084077 restraints weight = 2270.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.085096 restraints weight = 1482.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.085808 restraints weight = 1068.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3358  Z= 0.125
  Angle     :  0.699   7.941   4572  Z= 0.346
  Chirality :  0.044   0.151    484
  Planarity :  0.004   0.027    594
  Dihedral  :  5.163  50.470    479
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.45 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 24.50 %
    Favored  : 70.61 %
  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: -1.85 (0.39), residues: 422
  helix: -3.97 (0.81), residues: 16
  sheet:  0.04 (0.42), residues: 152
  loop : -1.95 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 355 
 TYR   0.012   0.001   TYR B 508 
 PHE   0.014   0.001   PHE B 400 
 TRP   0.020   0.002   TRP B 353 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3352)
  covalent geometry    : angle       0.69901 ( 4560)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       0.81503 (   12)
  hydrogen bonds       : bond        0.03511 (   93)
  hydrogen bonds       : angle       5.42604 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8104 (p90) cc_final: 0.7550 (p90)
REVERT: A   55 ASN cc_start: 0.8131 (t0) cc_final: 0.7578 (t0)
REVERT: C   43 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8699 (mmtp)
REVERT: B  353 TRP cc_start: 0.8300 (p-90) cc_final: 0.8046 (p-90)
REVERT: B  498 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7930 (mtt-85)
  outliers start: 17
  outliers final: 17
  residues processed: 109
  average time/residue: 0.0689
  time to fit residues: 8.9901
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0050
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.3600

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.087920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.078053 restraints weight = 8698.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.080389 restraints weight = 4006.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.081890 restraints weight = 2277.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.082891 restraints weight = 1503.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.083643 restraints weight = 1083.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3358  Z= 0.207
  Angle     :  0.746   9.350   4572  Z= 0.371
  Chirality :  0.046   0.144    484
  Planarity :  0.004   0.032    594
  Dihedral  :  5.344  50.562    479
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.82 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 25.94 %
    Favored  : 69.45 %
  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: -1.87 (0.39), residues: 422
  helix: -4.26 (0.66), residues: 16
  sheet:  0.03 (0.42), residues: 152
  loop : -1.94 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  87 
 TYR   0.014   0.001   TYR C  56 
 PHE   0.011   0.001   PHE B 400 
 TRP   0.016   0.002   TRP C 115 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 3352)
  covalent geometry    : angle       0.74551 ( 4560)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.87361 (   12)
  hydrogen bonds       : bond        0.03822 (   93)
  hydrogen bonds       : angle       5.42102 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8173 (p90) cc_final: 0.7367 (p90)
REVERT: A   55 ASN cc_start: 0.8299 (t0) cc_final: 0.8056 (t0)
REVERT: C   13 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8499 (mmmt)
REVERT: C   98 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.7417 (tmm-80)
REVERT: B  498 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7935 (mtt-85)
  outliers start: 16
  outliers final: 16
  residues processed: 104
  average time/residue: 0.0807
  time to fit residues: 9.8690
Evaluate side-chains
  108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.089584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.079762 restraints weight = 8486.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.082163 restraints weight = 3891.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.083728 restraints weight = 2194.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.084730 restraints weight = 1417.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.085440 restraints weight = 1018.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3358  Z= 0.146
  Angle     :  0.744  10.040   4572  Z= 0.367
  Chirality :  0.045   0.158    484
  Planarity :  0.004   0.027    594
  Dihedral  :  5.169  48.275    479
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.92 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 26.22 %
    Favored  : 68.88 %
  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: -1.69 (0.40), residues: 422
  helix: -4.35 (0.64), residues: 16
  sheet:  0.14 (0.42), residues: 152
  loop : -1.78 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  19 
 TYR   0.010   0.001   TYR C  56 
 PHE   0.012   0.001   PHE B 400 
 TRP   0.034   0.002   TRP B 353 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3352)
  covalent geometry    : angle       0.74395 ( 4560)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       0.70881 (   12)
  hydrogen bonds       : bond        0.03563 (   93)
  hydrogen bonds       : angle       5.30313 (  216)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8108 (p90) cc_final: 0.7404 (p90)
REVERT: A   55 ASN cc_start: 0.8264 (t0) cc_final: 0.7812 (t0)
REVERT: C   13 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8491 (mmmt)
REVERT: C   98 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7427 (tmm-80)
REVERT: B  498 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7910 (mtt-85)
  outliers start: 17
  outliers final: 17
  residues processed: 105
  average time/residue: 0.0716
  time to fit residues: 9.0111
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   62 ASN
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  104 TYR
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0170
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.090082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.080201 restraints weight = 8635.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.082620 restraints weight = 3944.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.084209 restraints weight = 2222.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.085161 restraints weight = 1434.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.085871 restraints weight = 1045.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3358  Z= 0.139
  Angle     :  0.738  10.163   4572  Z= 0.360
  Chirality :  0.045   0.156    484
  Planarity :  0.004   0.028    594
  Dihedral  :  5.002  45.887    479
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.64 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 25.65 %
    Favored  : 69.45 %
  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: -1.58 (0.40), residues: 422
  helix: -4.35 (0.65), residues: 16
  sheet:  0.20 (0.42), residues: 152
  loop : -1.70 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  19 
 TYR   0.011   0.001   TYR B 508 
 PHE   0.013   0.001   PHE B 400 
 TRP   0.029   0.002   TRP B 353 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3352)
  covalent geometry    : angle       0.73796 ( 4560)
  SS BOND              : bond        0.00199 (    6)
  SS BOND              : angle       0.65020 (   12)
  hydrogen bonds       : bond        0.03532 (   93)
  hydrogen bonds       : angle       5.17933 (  216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 934.29 seconds
wall clock time: 16 minutes 42.70 seconds (1002.70 seconds total)