Starting phenix.real_space_refine
on Sat May 10 05:03:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lkx_63187/05_2025/9lkx_63187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lkx_63187/05_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_63187/05_2025/9lkx_63187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lkx_63187/05_2025/9lkx_63187.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lkx_63187/05_2025/9lkx_63187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lkx_63187/05_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-5687/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: 6.10, per 1000 atoms: 1.19
  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: 1.27
  Conformation dependent library (CDL) restraints added in 642.8 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: 0.53
  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: 1.43

  Time building geometry restraints manager: 1.49 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:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.140
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.430
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.880
-------------------------------------------------------------------------------
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  : 0.568 
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: 0.2102
  time to fit residues: 38.8851
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  : 0.544 
-------------------------------------------------------------------------------
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 = 0.172098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.135576 restraints weight = 8191.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139464 restraints weight = 4721.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142043 restraints weight = 3205.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
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       4.23935 (  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  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  236 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6618 (tt0)
REVERT: J  340 ASN cc_start: 0.8557 (t0) cc_final: 0.8224 (t0)
REVERT: J  561 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7380 (mt-10)
REVERT: J  627 HIS cc_start: 0.5633 (m90) cc_final: 0.5338 (m-70)
REVERT: K  232 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4826 (mmt180)
  outliers start: 20
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1468
  time to fit residues: 20.9131
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  : 0.543 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0270
   chunk 2 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.4638

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.173157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136675 restraints weight = 8186.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.140590 restraints weight = 4690.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143226 restraints weight = 3187.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2542

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= 0.139
  Angle     :  0.559   7.617   7046  Z= 0.292
  Chirality :  0.038   0.130    809
  Planarity :  0.004   0.034    916
  Dihedral  :  5.013  55.251    712
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 11.71 %
    Favored  : 84.86 %
  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: -0.01 (0.33), residues: 646
  helix:  0.74 (0.25), 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   0.008   0.001   PHE J 623 
 TYR   0.025   0.001   TYR J 472 
 ARG   0.004   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  266)
  hydrogen bonds       : angle       4.05650 (  780)
  covalent geometry    : bond        0.00306 ( 5198)
  covalent geometry    : angle       0.55878 ( 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
  102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.541 
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: 0.6867 (mp-120) cc_final: 0.6481 (mp10)
REVERT: J  102 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8113 (tp30)
REVERT: J  236 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6464 (tt0)
REVERT: J  340 ASN cc_start: 0.8493 (t0) cc_final: 0.8157 (t0)
REVERT: J  627 HIS cc_start: 0.5409 (m90) cc_final: 0.4356 (m-70)
REVERT: K  232 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.4864 (mmt180)
  outliers start: 19
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1507
  time to fit residues: 19.7283
Evaluate side-chains
  88 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0470
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0570
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.4098 r_free = 0.4098 target = 0.172893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.136306 restraints weight = 8397.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140285 restraints weight = 4823.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.142904 restraints weight = 3250.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2783

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= 0.131
  Angle     :  0.557   8.544   7046  Z= 0.288
  Chirality :  0.038   0.129    809
  Planarity :  0.003   0.034    916
  Dihedral  :  4.965  54.079    712
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.15 %
    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:  0.23 (0.33), residues: 646
  helix:  0.93 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.19 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 209 
 HIS   0.009   0.001   HIS J 382 
 PHE   0.009   0.001   PHE J 447 
 TYR   0.019   0.001   TYR J 273 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  266)
  hydrogen bonds       : angle       3.98959 (  780)
  covalent geometry    : bond        0.00285 ( 5198)
  covalent geometry    : angle       0.55659 ( 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
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.600 
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: 0.7353 (mt-10) cc_final: 0.6512 (tt0)
REVERT: J  273 TYR cc_start: 0.8096 (t80) cc_final: 0.7779 (t80)
REVERT: J  382 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6666 (p90)
REVERT: J  627 HIS cc_start: 0.5462 (m90) cc_final: 0.3562 (m90)
REVERT: K  232 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.4851 (mmt180)
  outliers start: 16
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1575
  time to fit residues: 18.5917
Evaluate side-chains
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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  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  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:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0770
   chunk 4 optimal weight:    0.3980
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.172735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.136022 restraints weight = 8342.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.139877 restraints weight = 4851.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.142437 restraints weight = 3331.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2923

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= 0.138
  Angle     :  0.552   8.072   7046  Z= 0.288
  Chirality :  0.038   0.135    809
  Planarity :  0.004   0.037    916
  Dihedral  :  4.918  53.337    712
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.50 %
    Favored  : 80.72 %
  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:  0.24 (0.33), residues: 646
  helix:  0.96 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.21 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J 209 
 HIS   0.012   0.001   HIS J 382 
 PHE   0.009   0.001   PHE J 623 
 TYR   0.026   0.001   TYR J 472 
 ARG   0.006   0.000   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  266)
  hydrogen bonds       : angle       4.03221 (  780)
  covalent geometry    : bond        0.00306 ( 5198)
  covalent geometry    : angle       0.55196 ( 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
  100 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.544 
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: 0.6772 (mp-120) cc_final: 0.6361 (mp10)
REVERT: J  102 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8053 (tp30)
REVERT: J  236 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6384 (tt0)
REVERT: J  273 TYR cc_start: 0.8209 (t80) cc_final: 0.7975 (t80)
REVERT: J  340 ASN cc_start: 0.8467 (t0) cc_final: 0.8262 (t0)
REVERT: J  626 PHE cc_start: 0.7925 (p90) cc_final: 0.7705 (p90)
REVERT: J  627 HIS cc_start: 0.5869 (m90) cc_final: 0.3753 (m90)
REVERT: K  232 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.4876 (mmt180)
  outliers start: 21
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1443
  time to fit residues: 18.3135
Evaluate side-chains
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
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  248 SER
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  565 HIS
Chi-restraints excluded: chain J residue  620 LEU
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:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0670
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 4 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.2918

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.173913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.137476 restraints weight = 8448.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.141418 restraints weight = 4894.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.144070 restraints weight = 3326.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3149

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= 0.118
  Angle     :  0.546   8.610   7046  Z= 0.283
  Chirality :  0.037   0.133    809
  Planarity :  0.003   0.033    916
  Dihedral  :  4.812  52.113    712
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.50 %
    Favored  : 80.90 %
  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:  0.34 (0.33), residues: 646
  helix:  1.04 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.17 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J 209 
 HIS   0.008   0.001   HIS J 218 
 PHE   0.008   0.001   PHE J 447 
 TYR   0.014   0.001   TYR J 153 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  266)
  hydrogen bonds       : angle       3.87005 (  780)
  covalent geometry    : bond        0.00259 ( 5198)
  covalent geometry    : angle       0.54613 ( 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
  110 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.589 
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: 0.6808 (mp-120) cc_final: 0.6465 (mp10)
REVERT: J  102 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8049 (tp30)
REVERT: J  236 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6356 (tt0)
REVERT: J  273 TYR cc_start: 0.8227 (t80) cc_final: 0.7948 (t80)
REVERT: J  278 LEU cc_start: 0.8504 (tp) cc_final: 0.7605 (mp)
REVERT: J  340 ASN cc_start: 0.8451 (t0) cc_final: 0.8175 (t0)
REVERT: J  627 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.3853 (m90)
REVERT: K  232 ARG cc_start: 0.5579 (OUTLIER) cc_final: 0.4882 (mmt180)
  outliers start: 20
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1600
  time to fit residues: 22.0060
Evaluate side-chains
  89 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
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  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  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:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5276

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.172256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.135802 restraints weight = 8345.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.139592 restraints weight = 4854.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.142206 restraints weight = 3324.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3265

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= 0.145
  Angle     :  0.589   8.981   7046  Z= 0.303
  Chirality :  0.039   0.146    809
  Planarity :  0.003   0.031    916
  Dihedral  :  4.830  51.698    712
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.12 %
    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:  0.39 (0.34), residues: 646
  helix:  1.08 (0.26), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.14 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP J  93 
 HIS   0.008   0.001   HIS J 218 
 PHE   0.021   0.001   PHE J 626 
 TYR   0.022   0.001   TYR J 472 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  266)
  hydrogen bonds       : angle       3.91766 (  780)
  covalent geometry    : bond        0.00321 ( 5198)
  covalent geometry    : angle       0.58914 ( 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
  98 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.594 
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: 0.6782 (mp-120) cc_final: 0.6460 (mp10)
REVERT: J  102 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8105 (tp30)
REVERT: J  236 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6516 (tt0)
REVERT: J  273 TYR cc_start: 0.8289 (t80) cc_final: 0.8057 (t80)
REVERT: J  282 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6461 (mt-10)
REVERT: J  340 ASN cc_start: 0.8499 (t0) cc_final: 0.8185 (t0)
REVERT: J  627 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.4029 (m90)
REVERT: K  232 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5052 (mmt180)
  outliers start: 21
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1538
  time to fit residues: 19.0775
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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  201 ASP
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  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  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:    0.1980
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0170
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0570
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.2136

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.174762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.139046 restraints weight = 8374.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.142878 restraints weight = 4816.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.145507 restraints weight = 3281.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3454

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= 0.116
  Angle     :  0.586  10.486   7046  Z= 0.298
  Chirality :  0.038   0.157    809
  Planarity :  0.003   0.031    916
  Dihedral  :  4.798  50.745    712
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.02 %
    Favored  : 78.56 %
  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:  0.55 (0.34), residues: 646
  helix:  1.26 (0.26), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.17 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP J  93 
 HIS   0.010   0.001   HIS J 218 
 PHE   0.021   0.002   PHE J 626 
 TYR   0.011   0.001   TYR J 153 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  266)
  hydrogen bonds       : angle       3.76774 (  780)
  covalent geometry    : bond        0.00251 ( 5198)
  covalent geometry    : angle       0.58645 ( 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
  106 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.556 
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: 0.6728 (mp-120) cc_final: 0.6441 (mp10)
REVERT: J  102 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8072 (tp30)
REVERT: J  236 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6475 (tt0)
REVERT: J  273 TYR cc_start: 0.8218 (t80) cc_final: 0.7945 (t80)
REVERT: J  278 LEU cc_start: 0.8392 (tp) cc_final: 0.7125 (mt)
REVERT: J  282 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6451 (mt-10)
REVERT: J  340 ASN cc_start: 0.8384 (t0) cc_final: 0.8126 (t0)
REVERT: J  437 MET cc_start: 0.8368 (tpp) cc_final: 0.8148 (tpp)
REVERT: J  627 HIS cc_start: 0.5679 (OUTLIER) cc_final: 0.3661 (m90)
REVERT: K  232 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.4969 (mmt180)
  outliers start: 19
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1663
  time to fit residues: 22.0102
Evaluate side-chains
  91 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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  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  483 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0050
   chunk 34 optimal weight:    0.3980
   chunk 13 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 57 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 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 = 0.4108 r_free = 0.4108 target = 0.173806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138481 restraints weight = 8221.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.142250 restraints weight = 4801.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144839 restraints weight = 3274.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3522

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= 0.123
  Angle     :  0.594  10.343   7046  Z= 0.296
  Chirality :  0.039   0.163    809
  Planarity :  0.003   0.031    916
  Dihedral  :  4.735  52.446    712
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.74 %
    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:  0.64 (0.34), residues: 646
  helix:  1.32 (0.26), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.11 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  93 
 HIS   0.009   0.001   HIS J 218 
 PHE   0.022   0.001   PHE J 626 
 TYR   0.019   0.001   TYR J 472 
 ARG   0.005   0.000   ARG J 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  266)
  hydrogen bonds       : angle       3.76260 (  780)
  covalent geometry    : bond        0.00270 ( 5198)
  covalent geometry    : angle       0.59428 ( 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
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.619 
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: 0.6797 (mp-120) cc_final: 0.6506 (mp10)
REVERT: J  210 ARG cc_start: 0.8425 (mtt90) cc_final: 0.8224 (mtt-85)
REVERT: J  236 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6556 (tt0)
REVERT: J  273 TYR cc_start: 0.8203 (t80) cc_final: 0.7947 (t80)
REVERT: J  278 LEU cc_start: 0.8359 (tp) cc_final: 0.7238 (mp)
REVERT: J  282 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6577 (mt-10)
REVERT: J  340 ASN cc_start: 0.8371 (t0) cc_final: 0.8102 (t0)
REVERT: J  627 HIS cc_start: 0.5922 (OUTLIER) cc_final: 0.3823 (m90)
REVERT: K  232 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.4918 (mmt180)
  outliers start: 18
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1677
  time to fit residues: 19.3264
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
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  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  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 22 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 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 = 0.4096 r_free = 0.4096 target = 0.172677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.136677 restraints weight = 8308.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.140420 restraints weight = 4903.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.142921 restraints weight = 3363.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5198  Z= 0.151
  Angle     :  0.620  10.453   7046  Z= 0.311
  Chirality :  0.039   0.147    809
  Planarity :  0.003   0.030    916
  Dihedral  :  4.728  50.901    712
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.46 %
    Favored  : 77.30 %
  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:  0.60 (0.34), residues: 646
  helix:  1.27 (0.26), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.09 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J  93 
 HIS   0.012   0.001   HIS J 382 
 PHE   0.023   0.001   PHE J 626 
 TYR   0.017   0.001   TYR K 214 
 ARG   0.004   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  266)
  hydrogen bonds       : angle       3.84868 (  780)
  covalent geometry    : bond        0.00337 ( 5198)
  covalent geometry    : angle       0.62012 ( 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
  89 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.560 
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: 0.6827 (mp-120) cc_final: 0.6520 (mp10)
REVERT: J  102 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7871 (tp30)
REVERT: J  236 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6703 (tt0)
REVERT: J  273 TYR cc_start: 0.8247 (t80) cc_final: 0.7989 (t80)
REVERT: J  278 LEU cc_start: 0.8361 (tp) cc_final: 0.7218 (mp)
REVERT: J  282 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6658 (mt-10)
REVERT: J  340 ASN cc_start: 0.8460 (t0) cc_final: 0.8205 (t0)
REVERT: J  627 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.4008 (m90)
REVERT: K  232 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.4934 (mmt180)
  outliers start: 18
  outliers final: 13
  residues processed: 83
  average time/residue: 0.1649
  time to fit residues: 18.2797
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  : 0.597 
-------------------------------------------------------------------------------
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  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  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 34 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 443 ASN
** 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 = 0.172147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138818 restraints weight = 8384.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.140453 restraints weight = 5013.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141681 restraints weight = 3820.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5198  Z= 0.155
  Angle     :  0.638  11.073   7046  Z= 0.323
  Chirality :  0.039   0.145    809
  Planarity :  0.003   0.030    916
  Dihedral  :  4.748  50.503    712
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.64 %
    Favored  : 77.12 %
  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:  0.58 (0.34), residues: 646
  helix:  1.22 (0.26), residues: 405
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J  93 
 HIS   0.011   0.001   HIS J 382 
 PHE   0.024   0.002   PHE J 626 
 TYR   0.010   0.001   TYR J 153 
 ARG   0.005   0.000   ARG J 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  266)
  hydrogen bonds       : angle       3.86881 (  780)
  covalent geometry    : bond        0.00344 ( 5198)
  covalent geometry    : angle       0.63809 ( 7046)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2439.83 seconds
wall clock time: 44 minutes 56.40 seconds (2696.40 seconds total)