Starting phenix.real_space_refine
on Sun Apr 27 08:45:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lkx_63187/04_2025/9lkx_63187.cif"
  }
  resolution = 3.76
  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=   0.000 sd=   0.012
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      30      5.16       5
     C    3204      2.51       5
     N     913      2.21       5
     O     958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5105
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "J"
      Number of atoms: 4932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4932
          Classifications: {'peptide': 627}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611}
    Chain: "K"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 173
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 4, 'TRANS': 18}
  Time building chain proxies: 6.88, per 1000 atoms: 1.35
  Number of scatterers: 5105
  At special positions: 0
  Unit cell: (72.98, 96.76, 101.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     958      8.00
     N     913      7.00
     C    3204      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 653.3 milliseconds
  

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1232

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 1 sheets defined
      63.1% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'J' and resid 1 through 14
      removed outlier: 3.526A  pdb=" N   ALA J   5 " --> pdb=" O   MET J   1 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER J  13 " --> pdb=" O   TYR J   9 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU J  14 " --> pdb=" O   LYS J  10 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 20 through 25
      removed outlier: 3.753A  pdb=" N   LEU J  24 " --> pdb=" O   LEU J  20 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 31 through 36
    Processing helix  chain 'J' and resid 48 through 57
    Processing helix  chain 'J' and resid 58 through 66
    Processing helix  chain 'J' and resid 90 through 98
    Processing helix  chain 'J' and resid 100 through 111
    Processing helix  chain 'J' and resid 123 through 131
      removed outlier: 4.292A  pdb=" N   ASP J 131 " --> pdb=" O   ALA J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 133 through 143
      removed outlier: 4.369A  pdb=" N   TYR J 139 " --> pdb=" O   ASP J 135 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU J 140 " --> pdb=" O   ILE J 136 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 156 through 164
    Processing helix  chain 'J' and resid 166 through 175
    Processing helix  chain 'J' and resid 191 through 197
      removed outlier: 3.588A  pdb=" N   ALA J 197 " --> pdb=" O   PHE J 193 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 199 through 209
    Processing helix  chain 'J' and resid 221 through 229
    Processing helix  chain 'J' and resid 232 through 240
    Processing helix  chain 'J' and resid 246 through 262
      removed outlier: 3.674A  pdb=" N   ASN J 262 " --> pdb=" O   ALA J 258 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 269 through 284
    Processing helix  chain 'J' and resid 299 through 303
      removed outlier: 3.533A  pdb=" N   GLY J 303 " --> pdb=" O   HIS J 300 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 317
    Processing helix  chain 'J' and resid 320 through 337
    Processing helix  chain 'J' and resid 343 through 357
      removed outlier: 4.216A  pdb=" N   ILE J 347 " --> pdb=" O   VAL J 343 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 359 through 377
    Processing helix  chain 'J' and resid 381 through 398
    Processing helix  chain 'J' and resid 403 through 428
    Processing helix  chain 'J' and resid 432 through 456
      removed outlier: 3.523A  pdb=" N   LYS J 456 " --> pdb=" O   CYS J 452 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 460 through 476
    Processing helix  chain 'J' and resid 486 through 493
      removed outlier: 3.619A  pdb=" N   ALA J 491 " --> pdb=" O   LEU J 487 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 501 through 506
    Processing helix  chain 'J' and resid 511 through 521
    Processing helix  chain 'J' and resid 534 through 541
      removed outlier: 3.538A  pdb=" N   ILE J 538 " --> pdb=" O   SER J 534 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 548 through 562
    Processing helix  chain 'J' and resid 582 through 593
    Processing helix  chain 'J' and resid 596 through 609
    Processing helix  chain 'J' and resid 617 through 627
    Processing sheet with id=AA1, first strand: chain 'J' and resid 79 through 81

    266 hydrogen bonds defined for protein.
    780 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1736
        1.34 -     1.46: 783
        1.46 -     1.57: 2637
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 5198
  Sorted by residual:
  bond pdb=" N   ARG K 232 "
       pdb=" CA  ARG K 232 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 1.46e-02 4.69e+03 3.39e+00
  bond pdb=" CA  HIS J 476 "
       pdb=" C   HIS J 476 "
    ideal  model  delta    sigma   weight residual
    1.522  1.549 -0.027 1.72e-02 3.38e+03 2.55e+00
  bond pdb=" C   ARG K 232 "
       pdb=" O   ARG K 232 "
    ideal  model  delta    sigma   weight residual
    1.233  1.251 -0.018 1.29e-02 6.01e+03 1.93e+00
  bond pdb=" C   PHE K 216 "
       pdb=" N   PHE K 217 "
    ideal  model  delta    sigma   weight residual
    1.327  1.342 -0.016 1.53e-02 4.27e+03 1.04e+00
  bond pdb=" CA  THR J 581 "
       pdb=" CB  THR J 581 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.016 1.69e-02 3.50e+03 9.32e-01
  ... (remaining 5193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 6741
        1.39 -     2.78: 244
        2.78 -     4.16: 45
        4.16 -     5.55: 8
        5.55 -     6.94: 8
  Bond angle restraints: 7046
  Sorted by residual:
  angle pdb=" C   HIS J 241 "
        pdb=" N   ALA J 242 "
        pdb=" CA  ALA J 242 "
      ideal   model   delta    sigma   weight residual
     121.54  128.27   -6.73 1.91e+00 2.74e-01 1.24e+01
  angle pdb=" C   SER J 580 "
        pdb=" N   THR J 581 "
        pdb=" CA  THR J 581 "
      ideal   model   delta    sigma   weight residual
     121.54  127.41   -5.87 1.91e+00 2.74e-01 9.44e+00
  angle pdb=" C   ALA J 211 "
        pdb=" N   ALA J 212 "
        pdb=" CA  ALA J 212 "
      ideal   model   delta    sigma   weight residual
     121.54  126.61   -5.07 1.91e+00 2.74e-01 7.06e+00
  angle pdb=" C   GLY J 625 "
        pdb=" N   PHE J 626 "
        pdb=" CA  PHE J 626 "
      ideal   model   delta    sigma   weight residual
     122.09  117.37    4.72 1.79e+00 3.12e-01 6.95e+00
  angle pdb=" C   PHE K 216 "
        pdb=" N   PHE K 217 "
        pdb=" CA  PHE K 217 "
      ideal   model   delta    sigma   weight residual
     120.51  124.17   -3.66 1.45e+00 4.76e-01 6.38e+00
  ... (remaining 7041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2784
       17.16 -    34.33: 289
       34.33 -    51.49: 58
       51.49 -    68.66: 10
       68.66 -    85.82: 5
  Dihedral angle restraints: 3146
    sinusoidal: 1242
      harmonic: 1904
  Sorted by residual:
  dihedral pdb=" CA  PRO K 228 "
           pdb=" C   PRO K 228 "
           pdb=" N   PRO K 229 "
           pdb=" CA  PRO K 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.75   22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER K 222 "
           pdb=" C   SER K 222 "
           pdb=" N   HIS K 223 "
           pdb=" CA  HIS K 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.25  -20.75     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CD  ARG K 232 "
           pdb=" NE  ARG K 232 "
           pdb=" CZ  ARG K 232 "
           pdb=" NH1 ARG K 232 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   33.13  -33.13     1      1.00e+01 1.00e-02 1.56e+01
  ... (remaining 3143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 521
       0.036 -    0.072: 224
       0.072 -    0.108: 52
       0.108 -    0.143: 9
       0.143 -    0.179: 3
  Chirality restraints: 809
  Sorted by residual:
  chirality pdb=" CA  PHE J 626 "
            pdb=" N   PHE J 626 "
            pdb=" C   PHE J 626 "
            pdb=" CB  PHE J 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.02e-01
  chirality pdb=" CB  VAL J 137 "
            pdb=" CA  VAL J 137 "
            pdb=" CG1 VAL J 137 "
            pdb=" CG2 VAL J 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.45e-01
  chirality pdb=" CB  VAL J 141 "
            pdb=" CA  VAL J 141 "
            pdb=" CG1 VAL J 141 "
            pdb=" CG2 VAL J 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 806 not shown)

  Planarity restraints: 916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K 232 "   -0.598 9.50e-02 1.11e+02   2.68e-01 4.39e+01
        pdb=" NE  ARG K 232 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG K 232 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG K 232 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG K 232 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE J 616 "    0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO J 617 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO J 617 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO J 617 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR J  48 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO J  49 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO J  49 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO J  49 "    0.025 5.00e-02 4.00e+02
  ... (remaining 913 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1390
        2.81 -     3.33: 5120
        3.33 -     3.85: 8629
        3.85 -     4.38: 9703
        4.38 -     4.90: 16263
  Nonbonded interactions: 41105
  Sorted by model distance:
  nonbonded pdb=" O   CYS J 452 "
            pdb=" OG1 THR J 455 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OH  TYR J   9 "
            pdb=" OG  SER J  47 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" ND1 HIS J 241 "
            pdb=" OD1 ASP J 243 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" OH  TYR J 449 "
            pdb=" O   PRO J 497 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG1 THR J 569 "
            pdb=" O   PHE J 626 "
     model   vdw
     2.338 3.040
  ... (remaining 41100 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             268.860
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     20.180
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  292.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5198  Z= 0.161
  Angle     :  0.644   6.938   7046  Z= 0.346
  Chirality :  0.042   0.179    809
  Planarity :  0.010   0.268    916
  Dihedral  : 14.634  85.822   1914
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.75 (0.32), residues: 646
  helix:  0.12 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -1.44 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  93 
 HIS   0.012   0.001   HIS J 627 
 PHE   0.012   0.002   PHE J 623 
 TYR   0.021   0.001   TYR J  38 
 ARG   0.003   0.000   ARG J 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13879 (  266)
  hydrogen bonds       : angle       5.17842 (  780)
  covalent geometry    : bond        0.00337 ( 5198)
  covalent geometry    : angle       0.64360 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  236 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6629 (tt0)
REVERT: J  273 TYR cc_start: 0.8435 (t80) cc_final: 0.8183 (t80)
REVERT: J  475 ILE cc_start: 0.8655 (mm) cc_final: 0.8406 (tp)
REVERT: J  627 HIS cc_start: 0.5576 (m90) cc_final: 0.4365 (m90)
REVERT: K  232 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4767 (mmt180)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2367
  time to fit residues: 44.0327
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 48 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
J 176 GLN
J 289 ASN
J 382 HIS
J 473 ASN
J 511 ASN
J 541 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.172099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.135561 restraints weight = 8191.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139456 restraints weight = 4723.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142006 restraints weight = 3208.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5198  Z= 0.157
  Angle     :  0.599   5.017   7046  Z= 0.317
  Chirality :  0.040   0.146    809
  Planarity :  0.004   0.035    916
  Dihedral  :  5.226  58.185    712
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  :  9.01 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.29 (0.33), residues: 646
  helix:  0.47 (0.25), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.27 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J 209 
 HIS   0.008   0.001   HIS J 476 
 PHE   0.008   0.001   PHE J 447 
 TYR   0.014   0.001   TYR J  38 
 ARG   0.004   0.001   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  266)
  hydrogen bonds       : angle       4.23936 (  780)
  covalent geometry    : bond        0.00344 ( 5198)
  covalent geometry    : angle       0.59922 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  236 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6619 (tt0)
REVERT: J  340 ASN cc_start: 0.8555 (t0) cc_final: 0.8222 (t0)
REVERT: J  561 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: J  627 HIS cc_start: 0.5633 (m90) cc_final: 0.5337 (m-70)
REVERT: K  232 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.4830 (mmt180)
  outliers start: 20
  outliers final: 8
  residues processed: 107
  average time/residue: 0.2718
  time to fit residues: 39.5256
Evaluate side-chains
  94 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  206 LEU
Chi-restraints excluded: chain J residue  225 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  557 ILE
Chi-restraints excluded: chain J residue  620 LEU
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    0.0870
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0870
   chunk 49 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
J 369 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.172163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.135626 restraints weight = 8079.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.139453 restraints weight = 4593.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141944 restraints weight = 3109.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5198  Z= 0.130
  Angle     :  0.551   7.755   7046  Z= 0.289
  Chirality :  0.038   0.130    809
  Planarity :  0.004   0.034    916
  Dihedral  :  4.997  54.971    712
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.25 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.02 (0.33), residues: 646
  helix:  0.77 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.26 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 209 
 HIS   0.005   0.001   HIS J 476 
 PHE   0.009   0.001   PHE J 623 
 TYR   0.026   0.001   TYR J 472 
 ARG   0.004   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  266)
  hydrogen bonds       : angle       4.02541 (  780)
  covalent geometry    : bond        0.00285 ( 5198)
  covalent geometry    : angle       0.55144 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   74 GLN cc_start: 0.6869 (mp-120) cc_final: 0.6482 (mp10)
REVERT: J  102 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8125 (tp30)
REVERT: J  236 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6451 (tt0)
REVERT: J  340 ASN cc_start: 0.8459 (t0) cc_final: 0.8114 (t0)
REVERT: J  627 HIS cc_start: 0.5230 (m90) cc_final: 0.3405 (m90)
REVERT: K  232 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4833 (mmt180)
  outliers start: 17
  outliers final: 10
  residues processed: 97
  average time/residue: 0.1501
  time to fit residues: 19.5073
Evaluate side-chains
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  122 SER
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  225 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  620 LEU
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    0.0060
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.171072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.134408 restraints weight = 8385.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.138251 restraints weight = 4805.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.140845 restraints weight = 3273.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5198  Z= 0.163
  Angle     :  0.577   7.891   7046  Z= 0.300
  Chirality :  0.039   0.129    809
  Planarity :  0.004   0.033    916
  Dihedral  :  5.019  54.538    712
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 12.25 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.15 (0.33), residues: 646
  helix:  0.87 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.21 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J 209 
 HIS   0.009   0.001   HIS J 382 
 PHE   0.009   0.001   PHE J 623 
 TYR   0.040   0.002   TYR J 273 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  266)
  hydrogen bonds       : angle       4.09891 (  780)
  covalent geometry    : bond        0.00356 ( 5198)
  covalent geometry    : angle       0.57674 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  236 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6599 (tt0)
REVERT: J  273 TYR cc_start: 0.8131 (t80) cc_final: 0.7903 (t80)
REVERT: J  326 MET cc_start: 0.7803 (mmm) cc_final: 0.7076 (mmt)
REVERT: J  382 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6723 (p90)
REVERT: J  627 HIS cc_start: 0.5929 (m90) cc_final: 0.3704 (m90)
REVERT: K  232 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.4858 (mmt180)
  outliers start: 21
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1489
  time to fit residues: 19.2311
Evaluate side-chains
  88 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  122 SER
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  200 ILE
Chi-restraints excluded: chain J residue  206 LEU
Chi-restraints excluded: chain J residue  225 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  382 HIS
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  620 LEU
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0050
   chunk 4 optimal weight:    0.0000
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
J  74 GLN
J 218 HIS
J 382 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.173020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136297 restraints weight = 8330.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.140221 restraints weight = 4835.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142850 restraints weight = 3296.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5198  Z= 0.128
  Angle     :  0.563   8.451   7046  Z= 0.292
  Chirality :  0.038   0.136    809
  Planarity :  0.004   0.036    916
  Dihedral  :  4.916  53.191    712
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.50 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.20 (0.33), residues: 646
  helix:  0.91 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.21 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J 209 
 HIS   0.007   0.001   HIS J 382 
 PHE   0.009   0.001   PHE J 623 
 TYR   0.031   0.002   TYR J 273 
 ARG   0.006   0.000   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  266)
  hydrogen bonds       : angle       4.00991 (  780)
  covalent geometry    : bond        0.00284 ( 5198)
  covalent geometry    : angle       0.56324 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8056 (tp30)
REVERT: J  236 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6517 (tt0)
REVERT: J  626 PHE cc_start: 0.7936 (p90) cc_final: 0.7720 (p90)
REVERT: J  627 HIS cc_start: 0.5706 (OUTLIER) cc_final: 0.3809 (m90)
REVERT: K  232 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.4900 (mmt180)
  outliers start: 19
  outliers final: 13
  residues processed: 95
  average time/residue: 0.2207
  time to fit residues: 28.4307
Evaluate side-chains
  85 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  235 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  341 ILE
Chi-restraints excluded: chain J residue  382 HIS
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0010
   chunk 4 optimal weight:    0.0060
   chunk 56 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.2202

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

Flipped N/Q/H residues before XYZ refinement:
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 382 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.173268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136834 restraints weight = 8377.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.140673 restraints weight = 4823.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.143181 restraints weight = 3266.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5198  Z= 0.117
  Angle     :  0.552   8.786   7046  Z= 0.287
  Chirality :  0.038   0.133    809
  Planarity :  0.003   0.033    916
  Dihedral  :  4.860  51.847    712
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.04 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.30 (0.33), residues: 646
  helix:  1.01 (0.26), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.18 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP J  93 
 HIS   0.009   0.001   HIS J 218 
 PHE   0.008   0.001   PHE J 626 
 TYR   0.020   0.001   TYR J 273 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  266)
  hydrogen bonds       : angle       3.85037 (  780)
  covalent geometry    : bond        0.00255 ( 5198)
  covalent geometry    : angle       0.55194 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8094 (tp30)
REVERT: J  236 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6421 (tt0)
REVERT: J  273 TYR cc_start: 0.7948 (t80) cc_final: 0.7506 (t80)
REVERT: J  278 LEU cc_start: 0.8484 (tp) cc_final: 0.7619 (mp)
REVERT: J  280 MET cc_start: 0.8113 (ttm) cc_final: 0.7889 (ttm)
REVERT: J  314 LEU cc_start: 0.7978 (tp) cc_final: 0.7499 (tp)
REVERT: J  326 MET cc_start: 0.7641 (mmm) cc_final: 0.7040 (mmt)
REVERT: J  627 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.4270 (m-70)
REVERT: K  232 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4987 (mmt180)
  outliers start: 19
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1968
  time to fit residues: 26.2402
Evaluate side-chains
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  201 ASP
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  382 HIS
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  577 LEU
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   chunk 61 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
J 116 HIS
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 382 HIS
J 443 ASN
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.171404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.134590 restraints weight = 8363.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.138295 restraints weight = 4898.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.140960 restraints weight = 3375.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5198  Z= 0.179
  Angle     :  0.604   8.027   7046  Z= 0.314
  Chirality :  0.040   0.153    809
  Planarity :  0.004   0.032    916
  Dihedral  :  4.890  48.902    712
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 16.58 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.29 (0.33), residues: 646
  helix:  0.96 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.10 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  93 
 HIS   0.008   0.001   HIS J 218 
 PHE   0.020   0.002   PHE J 626 
 TYR   0.022   0.002   TYR J 472 
 ARG   0.006   0.001   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  266)
  hydrogen bonds       : angle       4.01945 (  780)
  covalent geometry    : bond        0.00396 ( 5198)
  covalent geometry    : angle       0.60439 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8124 (tp30)
REVERT: J  236 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6566 (tt0)
REVERT: J  273 TYR cc_start: 0.8143 (t80) cc_final: 0.7879 (t80)
REVERT: J  280 MET cc_start: 0.8245 (ttm) cc_final: 0.8020 (ttm)
REVERT: J  282 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6551 (mt-10)
REVERT: J  326 MET cc_start: 0.7692 (mmm) cc_final: 0.7170 (mmt)
REVERT: J  627 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.4078 (m90)
REVERT: K  232 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.5119 (mmt180)
  outliers start: 24
  outliers final: 16
  residues processed: 94
  average time/residue: 0.1394
  time to fit residues: 17.8965
Evaluate side-chains
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  235 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  282 GLU
Chi-restraints excluded: chain J residue  290 ILE
Chi-restraints excluded: chain J residue  341 ILE
Chi-restraints excluded: chain J residue  382 HIS
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  443 ASN
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  577 LEU
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 241 HIS
J 382 HIS
J 443 ASN
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.169708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.132955 restraints weight = 8364.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.136649 restraints weight = 4917.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139330 restraints weight = 3351.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5198  Z= 0.185
  Angle     :  0.638   8.298   7046  Z= 0.335
  Chirality :  0.040   0.137    809
  Planarity :  0.004   0.031    916
  Dihedral  :  5.001  50.656    712
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.66 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.18 (0.33), residues: 646
  helix:  0.84 (0.25), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.09 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP J  93 
 HIS   0.015   0.002   HIS J 241 
 PHE   0.022   0.002   PHE J 626 
 TYR   0.014   0.001   TYR J 273 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  266)
  hydrogen bonds       : angle       4.05586 (  780)
  covalent geometry    : bond        0.00405 ( 5198)
  covalent geometry    : angle       0.63796 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8105 (tp30)
REVERT: J  236 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6738 (tt0)
REVERT: J  273 TYR cc_start: 0.8229 (t80) cc_final: 0.7927 (t80)
REVERT: J  282 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6597 (mt-10)
REVERT: J  326 MET cc_start: 0.7621 (mmm) cc_final: 0.7168 (mmt)
REVERT: J  327 GLU cc_start: 0.8167 (tp30) cc_final: 0.7618 (tm-30)
REVERT: J  542 TYR cc_start: 0.8097 (t80) cc_final: 0.7833 (t80)
REVERT: J  627 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.4060 (m90)
REVERT: K  232 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.4904 (mmt180)
  outliers start: 22
  outliers final: 17
  residues processed: 93
  average time/residue: 0.1501
  time to fit residues: 18.8165
Evaluate side-chains
  91 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  201 ASP
Chi-restraints excluded: chain J residue  248 SER
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  282 GLU
Chi-restraints excluded: chain J residue  290 ILE
Chi-restraints excluded: chain J residue  341 ILE
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  443 ASN
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  577 LEU
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  620 LEU
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 241 HIS
** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 443 ASN
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.171660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135517 restraints weight = 8266.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139254 restraints weight = 4866.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.141773 restraints weight = 3343.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5198  Z= 0.139
  Angle     :  0.612   9.974   7046  Z= 0.315
  Chirality :  0.039   0.155    809
  Planarity :  0.003   0.031    916
  Dihedral  :  4.946  51.413    712
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.38 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.33 (0.33), residues: 646
  helix:  0.99 (0.26), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.06 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP J  93 
 HIS   0.009   0.001   HIS J 218 
 PHE   0.021   0.001   PHE J 626 
 TYR   0.024   0.001   TYR J 472 
 ARG   0.005   0.000   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  266)
  hydrogen bonds       : angle       3.89723 (  780)
  covalent geometry    : bond        0.00302 ( 5198)
  covalent geometry    : angle       0.61166 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8013 (tp30)
REVERT: J  236 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6733 (tt0)
REVERT: J  273 TYR cc_start: 0.8199 (t80) cc_final: 0.7893 (t80)
REVERT: J  282 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6545 (mt-10)
REVERT: J  314 LEU cc_start: 0.8116 (tp) cc_final: 0.7869 (tp)
REVERT: J  326 MET cc_start: 0.7563 (mmm) cc_final: 0.7167 (mmt)
REVERT: J  627 HIS cc_start: 0.6056 (OUTLIER) cc_final: 0.3832 (m90)
REVERT: K  232 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.4862 (mpt90)
  outliers start: 20
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1513
  time to fit residues: 18.4294
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  248 SER
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  282 GLU
Chi-restraints excluded: chain J residue  290 ILE
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  443 ASN
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  565 HIS
Chi-restraints excluded: chain J residue  577 LEU
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 45 optimal weight:    0.2980
   chunk 58 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
J 218 HIS
** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 443 ASN
** J 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.170848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.134608 restraints weight = 8328.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.138372 restraints weight = 4879.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140569 restraints weight = 3359.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5198  Z= 0.157
  Angle     :  0.637   9.319   7046  Z= 0.328
  Chirality :  0.040   0.150    809
  Planarity :  0.004   0.031    916
  Dihedral  :  4.905  50.935    712
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.92 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.37 (0.33), residues: 646
  helix:  0.99 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.01 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  93 
 HIS   0.006   0.001   HIS J 241 
 PHE   0.022   0.001   PHE J 626 
 TYR   0.017   0.001   TYR K 214 
 ARG   0.005   0.000   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  266)
  hydrogen bonds       : angle       3.93633 (  780)
  covalent geometry    : bond        0.00347 ( 5198)
  covalent geometry    : angle       0.63687 ( 7046)

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7996 (tp30)
REVERT: J  236 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6750 (tt0)
REVERT: J  273 TYR cc_start: 0.8208 (t80) cc_final: 0.7861 (t80)
REVERT: J  278 LEU cc_start: 0.8510 (tp) cc_final: 0.7541 (mp)
REVERT: J  282 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6758 (mt-10)
REVERT: J  326 MET cc_start: 0.7585 (mmm) cc_final: 0.7160 (mmt)
REVERT: J  327 GLU cc_start: 0.8143 (tp30) cc_final: 0.7621 (tm-30)
REVERT: J  417 GLU cc_start: 0.8680 (tp30) cc_final: 0.8470 (tt0)
REVERT: J  542 TYR cc_start: 0.8073 (t80) cc_final: 0.7828 (t80)
REVERT: J  627 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.3896 (m90)
REVERT: K  232 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.4831 (mpt90)
  outliers start: 19
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1442
  time to fit residues: 17.1667
Evaluate side-chains
  85 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  123 THR
Chi-restraints excluded: chain J residue  191 LEU
Chi-restraints excluded: chain J residue  218 HIS
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  282 GLU
Chi-restraints excluded: chain J residue  290 ILE
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  443 ASN
Chi-restraints excluded: chain J residue  492 VAL
Chi-restraints excluded: chain J residue  515 THR
Chi-restraints excluded: chain J residue  539 ILE
Chi-restraints excluded: chain J residue  577 LEU
Chi-restraints excluded: chain J residue  596 SER
Chi-restraints excluded: chain J residue  627 HIS
Chi-restraints excluded: chain K residue  232 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0050
   chunk 24 optimal weight:    0.0040
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.3606

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

Flipped N/Q/H residues before XYZ refinement:
** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 443 ASN
** J 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.172038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136147 restraints weight = 8371.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.139913 restraints weight = 4876.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.142501 restraints weight = 3322.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5198  Z= 0.135
  Angle     :  0.624   9.617   7046  Z= 0.320
  Chirality :  0.039   0.150    809
  Planarity :  0.003   0.031    916
  Dihedral  :  4.884  51.065    712
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.10 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.43 (0.34), residues: 646
  helix:  1.06 (0.26), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.00 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP J  93 
 HIS   0.005   0.001   HIS J 218 
 PHE   0.023   0.001   PHE J 626 
 TYR   0.011   0.001   TYR J 273 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  266)
  hydrogen bonds       : angle       3.85360 (  780)
  covalent geometry    : bond        0.00298 ( 5198)
  covalent geometry    : angle       0.62371 ( 7046)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3238.60 seconds
wall clock time: 59 minutes 27.64 seconds (3567.64 seconds total)