Starting phenix.real_space_refine
on Wed Jul 23 12:28:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yvj_34129/07_2025/7yvj_34129.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yvj_34129/07_2025/7yvj_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_34129/07_2025/7yvj_34129.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yvj_34129/07_2025/7yvj_34129.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yvj_34129/07_2025/7yvj_34129.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yvj_34129/07_2025/7yvj_34129.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
  Time building chain proxies: 5.30, per 1000 atoms: 1.62
  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: 0.86
  Conformation dependent library (CDL) restraints added in 422.2 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: 0.46
  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: 0.80

  Time building geometry restraints manager: 1.04 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:             273.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  292.510
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.021   0.002   TRP B 353 
 HIS   0.003   0.002   HIS A  41 
 PHE   0.008   0.001   PHE A 102 
 TYR   0.021   0.002   TYR C 104 
 ARG   0.004   0.001   ARG A  56 

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

*********************** 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  : 0.391 
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: 0.7221 (pttt)
  outliers start: 6
  outliers final: 1
  residues processed: 124
  average time/residue: 0.2105
  time to fit residues: 30.1213
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  : 0.383 
-------------------------------------------------------------------------------
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 35 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.091071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.081015 restraints weight = 8483.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.083368 restraints weight = 3918.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.084945 restraints weight = 2233.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2507

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= 0.175
  Angle     :  0.681   8.561   4572  Z= 0.352
  Chirality :  0.046   0.142    484
  Planarity :  0.005   0.041    594
  Dihedral  :  5.517  56.861    479
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  4.74 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.87 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.34), residues: 422
  helix: -5.19 (0.22), residues: 22
  sheet: -1.52 (0.37), residues: 154
  loop : -2.72 (0.33), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 353 
 HIS   0.003   0.001   HIS A  41 
 PHE   0.016   0.002   PHE C  68 
 TYR   0.022   0.002   TYR B 508 
 ARG   0.006   0.001   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (   93)
  hydrogen bonds       : angle       6.43307 (  216)
  SS BOND              : bond        0.00299 (    6)
  SS BOND              : angle       0.84552 (   12)
  covalent geometry    : bond        0.00374 ( 3352)
  covalent geometry    : angle       0.68076 ( 4560)

*********************** 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
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8019 (p90) cc_final: 0.7270 (p90)
REVERT: A   55 ASN cc_start: 0.7925 (t0) cc_final: 0.7360 (t0)
REVERT: C   13 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8505 (mmmt)
REVERT: C   98 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7175 (tmt170)
REVERT: B  386 LYS cc_start: 0.7719 (mttt) cc_final: 0.7294 (ttpt)
REVERT: B  403 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8345 (ttm-80)
REVERT: B  508 TYR cc_start: 0.8437 (m-80) cc_final: 0.8182 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1950
  time to fit residues: 25.4159
Evaluate side-chains
  104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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   91 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  104 TYR
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 5 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.4384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.088659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.078672 restraints weight = 8456.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.081008 restraints weight = 3960.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.082551 restraints weight = 2273.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3358  Z= 0.216
  Angle     :  0.685   7.276   4572  Z= 0.352
  Chirality :  0.046   0.144    484
  Planarity :  0.006   0.054    594
  Dihedral  :  5.521  56.511    479
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.40 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 20.46 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.36), residues: 422
  helix: -4.81 (0.35), residues: 23
  sheet: -1.03 (0.38), residues: 155
  loop : -2.34 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 115 
 HIS   0.002   0.001   HIS A  41 
 PHE   0.011   0.002   PHE C  68 
 TYR   0.030   0.002   TYR C  80 
 ARG   0.011   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (   93)
  hydrogen bonds       : angle       6.28886 (  216)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       0.80219 (   12)
  covalent geometry    : bond        0.00477 ( 3352)
  covalent geometry    : angle       0.68474 ( 4560)

*********************** 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
  122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8135 (p90) cc_final: 0.7574 (p90)
REVERT: A   55 ASN cc_start: 0.7876 (t0) cc_final: 0.7381 (t0)
REVERT: C  100 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7979 (tp-100)
REVERT: B  358 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9187 (tp)
REVERT: B  386 LYS cc_start: 0.7194 (mttt) cc_final: 0.6883 (ttpt)
REVERT: B  498 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7968 (mtt-85)
REVERT: B  508 TYR cc_start: 0.8425 (m-80) cc_final: 0.8096 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1819
  time to fit residues: 23.9955
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  : 0.382 
-------------------------------------------------------------------------------
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 A residue   75 LEU
Chi-restraints excluded: chain C residue   32 SER
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  358 ILE
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 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.089580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.079756 restraints weight = 8514.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.082142 restraints weight = 3871.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.083672 restraints weight = 2178.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3325

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= 0.146
  Angle     :  0.673   9.685   4572  Z= 0.334
  Chirality :  0.044   0.148    484
  Planarity :  0.005   0.039    594
  Dihedral  :  5.264  54.816    479
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.98 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 21.33 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.37), residues: 422
  helix: -4.63 (0.47), residues: 16
  sheet: -0.70 (0.40), residues: 158
  loop : -2.26 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 353 
 HIS   0.002   0.000   HIS A  41 
 PHE   0.014   0.001   PHE C  68 
 TYR   0.010   0.001   TYR C  80 
 ARG   0.009   0.001   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (   93)
  hydrogen bonds       : angle       5.90287 (  216)
  SS BOND              : bond        0.00380 (    6)
  SS BOND              : angle       0.72910 (   12)
  covalent geometry    : bond        0.00327 ( 3352)
  covalent geometry    : angle       0.67248 ( 4560)

*********************** 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
  120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8077 (p90) cc_final: 0.7476 (p90)
REVERT: A   55 ASN cc_start: 0.7922 (t0) cc_final: 0.7352 (t0)
REVERT: C   13 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8480 (mmmt)
REVERT: C   20 LEU cc_start: 0.8253 (mt) cc_final: 0.7970 (mp)
REVERT: C  100 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7943 (tp-100)
REVERT: B  386 LYS cc_start: 0.7077 (mttt) cc_final: 0.6752 (ttpt)
REVERT: B  498 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7949 (mtt-85)
REVERT: B  508 TYR cc_start: 0.8309 (m-80) cc_final: 0.8073 (m-80)
  outliers start: 20
  outliers final: 19
  residues processed: 109
  average time/residue: 0.1891
  time to fit residues: 24.1219
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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 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   32 SER
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  387 LEU
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  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 34 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9990
   overall best weight:    2.0026

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.085790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.076375 restraints weight = 8635.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.078655 restraints weight = 3979.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080142 restraints weight = 2234.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3358  Z= 0.280
  Angle     :  0.734   8.572   4572  Z= 0.379
  Chirality :  0.047   0.146    484
  Planarity :  0.007   0.099    594
  Dihedral  :  5.865  57.207    479
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.35 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 21.33 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.37), residues: 422
  helix: -4.52 (0.51), residues: 23
  sheet: -0.60 (0.41), residues: 153
  loop : -2.33 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 115 
 HIS   0.003   0.001   HIS A  41 
 PHE   0.012   0.002   PHE C  27 
 TYR   0.018   0.002   TYR C  80 
 ARG   0.014   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (   93)
  hydrogen bonds       : angle       6.07397 (  216)
  SS BOND              : bond        0.00422 (    6)
  SS BOND              : angle       0.89789 (   12)
  covalent geometry    : bond        0.00615 ( 3352)
  covalent geometry    : angle       0.73390 ( 4560)

*********************** 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
  119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8239 (p90) cc_final: 0.7344 (p90)
REVERT: A   55 ASN cc_start: 0.8253 (t0) cc_final: 0.7988 (t0)
REVERT: B  498 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7946 (mtt-85)
  outliers start: 22
  outliers final: 19
  residues processed: 107
  average time/residue: 0.1773
  time to fit residues: 22.3656
Evaluate side-chains
  110 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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 A residue   75 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   29 ILE
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   35 ASN
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  387 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  420 ASP
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 15 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.088159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.078306 restraints weight = 8781.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.080686 restraints weight = 3983.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.082262 restraints weight = 2238.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3358  Z= 0.146
  Angle     :  0.679   7.984   4572  Z= 0.341
  Chirality :  0.044   0.154    484
  Planarity :  0.004   0.044    594
  Dihedral  :  5.429  54.212    479
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.69 %
    Favored  : 94.08 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.38), residues: 422
  helix: -4.43 (0.57), residues: 23
  sheet: -0.35 (0.42), residues: 152
  loop : -2.20 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.015   0.001   PHE C  68 
 TYR   0.021   0.001   TYR B 508 
 ARG   0.007   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (   93)
  hydrogen bonds       : angle       5.72198 (  216)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       0.69943 (   12)
  covalent geometry    : bond        0.00334 ( 3352)
  covalent geometry    : angle       0.67925 ( 4560)

*********************** 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
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8166 (p90) cc_final: 0.7693 (p90)
REVERT: A   55 ASN cc_start: 0.8206 (t0) cc_final: 0.7716 (t0)
REVERT: C   13 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8686 (mmmt)
REVERT: B  498 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7949 (mtt-85)
  outliers start: 21
  outliers final: 20
  residues processed: 103
  average time/residue: 0.1667
  time to fit residues: 20.7525
Evaluate side-chains
  109 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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 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  119 ILE
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  387 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.087891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.078207 restraints weight = 8450.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.080499 restraints weight = 3946.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.082042 restraints weight = 2250.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3957

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= 0.186
  Angle     :  0.700   9.556   4572  Z= 0.347
  Chirality :  0.045   0.143    484
  Planarity :  0.004   0.043    594
  Dihedral  :  5.410  52.897    479
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.06 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 23.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.38), residues: 422
  helix: -4.48 (0.57), residues: 16
  sheet: -0.28 (0.42), residues: 152
  loop : -2.20 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 115 
 HIS   0.002   0.001   HIS A  41 
 PHE   0.011   0.001   PHE B 400 
 TYR   0.015   0.001   TYR C  80 
 ARG   0.006   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (   93)
  hydrogen bonds       : angle       5.69949 (  216)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       0.77034 (   12)
  covalent geometry    : bond        0.00420 ( 3352)
  covalent geometry    : angle       0.69967 ( 4560)

*********************** 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
  115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8167 (p90) cc_final: 0.7406 (p90)
REVERT: A   55 ASN cc_start: 0.8329 (t0) cc_final: 0.8118 (t0)
REVERT: C   34 MET cc_start: 0.9010 (mmp) cc_final: 0.8777 (mmp)
REVERT: B  498 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7935 (mtt-85)
  outliers start: 22
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1668
  time to fit residues: 21.0634
Evaluate side-chains
  109 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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 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  119 ILE
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  387 LEU
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 1 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.080068 restraints weight = 8532.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.082430 restraints weight = 3871.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.083987 restraints weight = 2164.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3358  Z= 0.135
  Angle     :  0.691   9.864   4572  Z= 0.340
  Chirality :  0.044   0.163    484
  Planarity :  0.004   0.038    594
  Dihedral  :  5.096  50.495    479
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.98 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 23.92 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.39), residues: 422
  helix: -3.97 (0.83), residues: 16
  sheet: -0.15 (0.42), residues: 152
  loop : -2.02 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.012   0.001   PHE B 400 
 TYR   0.014   0.001   TYR C  80 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (   93)
  hydrogen bonds       : angle       5.50872 (  216)
  SS BOND              : bond        0.00379 (    6)
  SS BOND              : angle       0.73568 (   12)
  covalent geometry    : bond        0.00311 ( 3352)
  covalent geometry    : angle       0.69117 ( 4560)

*********************** 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
  121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8078 (p90) cc_final: 0.7520 (p90)
REVERT: A   55 ASN cc_start: 0.8238 (t0) cc_final: 0.7680 (t0)
REVERT: B  498 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7936 (mtt-85)
  outliers start: 22
  outliers final: 21
  residues processed: 111
  average time/residue: 0.1723
  time to fit residues: 22.7269
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  119 ILE
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  387 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.089757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.080070 restraints weight = 8582.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.082384 restraints weight = 3894.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.083908 restraints weight = 2202.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3358  Z= 0.145
  Angle     :  0.719   9.508   4572  Z= 0.350
  Chirality :  0.044   0.153    484
  Planarity :  0.004   0.034    594
  Dihedral  :  5.005  49.210    479
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.16 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 25.07 %
    Favored  : 68.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.40), residues: 422
  helix: -3.73 (1.01), residues: 16
  sheet:  0.05 (0.43), residues: 152
  loop : -1.93 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.002   0.000   HIS A  41 
 PHE   0.012   0.001   PHE B 400 
 TYR   0.012   0.001   TYR B 508 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (   93)
  hydrogen bonds       : angle       5.46657 (  216)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       0.78346 (   12)
  covalent geometry    : bond        0.00340 ( 3352)
  covalent geometry    : angle       0.71844 ( 4560)

*********************** 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
  121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8062 (p90) cc_final: 0.7382 (p90)
REVERT: A   55 ASN cc_start: 0.8302 (t0) cc_final: 0.7858 (t0)
REVERT: C   34 MET cc_start: 0.8911 (mmp) cc_final: 0.8655 (mmp)
REVERT: C   98 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7380 (tmm-80)
REVERT: B  466 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.8222 (ptm-80)
REVERT: B  498 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7932 (mtt-85)
  outliers start: 23
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1620
  time to fit residues: 21.5499
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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   32 SER
Chi-restraints excluded: chain C residue   91 THR
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  350 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  387 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.0370
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0020
   overall best weight:    0.4066

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.091376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.081605 restraints weight = 8357.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083979 restraints weight = 3803.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.085548 restraints weight = 2138.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3358  Z= 0.127
  Angle     :  0.725   9.947   4572  Z= 0.350
  Chirality :  0.044   0.163    484
  Planarity :  0.004   0.035    594
  Dihedral  :  4.870  47.024    479
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.21 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 25.65 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.40), residues: 422
  helix: -3.95 (0.84), residues: 16
  sheet:  0.19 (0.43), residues: 152
  loop : -1.81 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 353 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.013   0.001   PHE C  68 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.007   0.001   ARG C  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (   93)
  hydrogen bonds       : angle       5.36807 (  216)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       0.79156 (   12)
  covalent geometry    : bond        0.00304 ( 3352)
  covalent geometry    : angle       0.72508 ( 4560)

********************** 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
  116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8008 (p90) cc_final: 0.7353 (p90)
REVERT: A   55 ASN cc_start: 0.8284 (t0) cc_final: 0.7761 (t0)
REVERT: C   34 MET cc_start: 0.8820 (mmp) cc_final: 0.8608 (mmp)
REVERT: B  378 LYS cc_start: 0.8884 (ptmm) cc_final: 0.8624 (ptmm)
REVERT: B  466 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8295 (ptm-80)
REVERT: B  498 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7891 (mtt-85)
  outliers start: 18
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1746
  time to fit residues: 23.0544
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  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
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  104 TYR
Chi-restraints excluded: chain C residue  119 ILE
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  483 VAL
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 13 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.087128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.077722 restraints weight = 8616.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.079971 restraints weight = 3995.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.081427 restraints weight = 2262.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3358  Z= 0.267
  Angle     :  0.785   9.845   4572  Z= 0.390
  Chirality :  0.047   0.159    484
  Planarity :  0.005   0.041    594
  Dihedral  :  5.563  50.073    479
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.58 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 25.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.40), residues: 422
  helix: -4.08 (0.66), residues: 22
  sheet:  0.03 (0.43), residues: 152
  loop : -1.86 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 353 
 HIS   0.003   0.001   HIS A  41 
 PHE   0.013   0.002   PHE C  68 
 TYR   0.013   0.002   TYR B 473 
 ARG   0.005   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (   93)
  hydrogen bonds       : angle       5.70050 (  216)
  SS BOND              : bond        0.00433 (    6)
  SS BOND              : angle       1.03049 (   12)
  covalent geometry    : bond        0.00596 ( 3352)
  covalent geometry    : angle       0.78406 ( 4560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3251.59 seconds
wall clock time: 58 minutes 34.90 seconds (3514.90 seconds total)