Starting phenix.real_space_refine
on Wed Sep 17 05:27:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lkx_63187/09_2025/9lkx_63187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lkx_63187/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lkx_63187/09_2025/9lkx_63187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lkx_63187/09_2025/9lkx_63187.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lkx_63187/09_2025/9lkx_63187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lkx_63187/09_2025/9lkx_63187.map"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.38, per 1000 atoms: 0.27
  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: 0.41
  Conformation dependent library (CDL) restraints added in 199.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.10
  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: 0.57

  Time building geometry restraints manager: 0.56 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:             11.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.280
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.760
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG J 283 
 TYR   0.021   0.001   TYR J  38 
 PHE   0.012   0.002   PHE J 623 
 TRP   0.005   0.001   TRP J  93 
 HIS   0.012   0.001   HIS J 627 

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

*********************** 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  : 0.177 
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: 0.0951
  time to fit residues: 17.6924
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  : 0.215 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   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 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 = 0.4078 r_free = 0.4078 target = 0.170826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.134398 restraints weight = 8245.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.138139 restraints weight = 4720.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.140663 restraints weight = 3185.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.142082 restraints weight = 2428.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143315 restraints weight = 2044.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5198  Z= 0.156
  Angle     :  0.599   5.063   7046  Z= 0.317
  Chirality :  0.040   0.145    809
  Planarity :  0.004   0.035    916
  Dihedral  :  5.224  57.991    712
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  :  8.83 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.33), residues: 646
  helix:  0.47 (0.25), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.28 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 332 
 TYR   0.014   0.001   TYR J  38 
 PHE   0.008   0.001   PHE J 447 
 TRP   0.003   0.001   TRP J  93 
 HIS   0.008   0.001   HIS J 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5198)
  covalent geometry    : angle       0.59910 ( 7046)
  hydrogen bonds       : bond        0.04469 (  266)
  hydrogen bonds       : angle       4.24545 (  780)

*********************** 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
  112 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  236 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6665 (tt0)
REVERT: J  340 ASN cc_start: 0.8530 (t0) cc_final: 0.8209 (t0)
REVERT: J  472 TYR cc_start: 0.8725 (t80) cc_final: 0.8456 (t80)
REVERT: J  561 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7349 (mt-10)
REVERT: K  232 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4823 (mmt180)
  outliers start: 19
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0599
  time to fit residues: 8.6798
Evaluate side-chains
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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 11 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0270
   chunk 38 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.8642

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.169682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.132658 restraints weight = 8292.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.136496 restraints weight = 4836.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.139072 restraints weight = 3300.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140646 restraints weight = 2536.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.141854 restraints weight = 2118.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5198  Z= 0.196
  Angle     :  0.603   7.433   7046  Z= 0.317
  Chirality :  0.040   0.131    809
  Planarity :  0.004   0.033    916
  Dihedral  :  5.152  56.137    712
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.33), residues: 646
  helix:  0.57 (0.25), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.23 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 332 
 TYR   0.012   0.001   TYR J  38 
 PHE   0.016   0.001   PHE J 623 
 TRP   0.003   0.001   TRP J  93 
 HIS   0.003   0.001   HIS J 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 5198)
  covalent geometry    : angle       0.60309 ( 7046)
  hydrogen bonds       : bond        0.04277 (  266)
  hydrogen bonds       : angle       4.29809 (  780)

*********************** 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
  107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  102 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8072 (tp30)
REVERT: J  236 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6561 (tt0)
REVERT: J  327 GLU cc_start: 0.8127 (tp30) cc_final: 0.7540 (tm-30)
REVERT: J  340 ASN cc_start: 0.8591 (t0) cc_final: 0.8277 (t0)
REVERT: J  507 CYS cc_start: 0.8750 (m) cc_final: 0.8317 (m)
REVERT: J  542 TYR cc_start: 0.8090 (t80) cc_final: 0.7782 (t80)
REVERT: J  622 GLU cc_start: 0.7804 (tp30) cc_final: 0.7585 (tp30)
REVERT: K  232 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4910 (mmt180)
  outliers start: 21
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0652
  time to fit residues: 9.3821
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  : 0.194 
-------------------------------------------------------------------------------
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  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 37 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0970
   chunk 44 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
J  58 HIS
J  74 GLN
J 382 HIS
J 592 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.135073 restraints weight = 8229.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.138885 restraints weight = 4779.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141406 restraints weight = 3251.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.142801 restraints weight = 2495.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.144017 restraints weight = 2110.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5198  Z= 0.135
  Angle     :  0.553   8.397   7046  Z= 0.289
  Chirality :  0.038   0.129    809
  Planarity :  0.004   0.033    916
  Dihedral  :  4.959  53.904    712
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.95 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.33), residues: 646
  helix:  0.83 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.15 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.027   0.002   TYR J 472 
 PHE   0.015   0.001   PHE J 623 
 TRP   0.005   0.001   TRP J 209 
 HIS   0.009   0.001   HIS J 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5198)
  covalent geometry    : angle       0.55254 ( 7046)
  hydrogen bonds       : bond        0.03843 (  266)
  hydrogen bonds       : angle       4.02729 (  780)

*********************** 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
  97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.201 
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: 0.6825 (mp-120) cc_final: 0.6401 (mp10)
REVERT: J  102 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8021 (tp30)
REVERT: J  236 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6472 (tt0)
REVERT: J  273 TYR cc_start: 0.8107 (t80) cc_final: 0.7816 (t80)
REVERT: J  326 MET cc_start: 0.7657 (mmm) cc_final: 0.7216 (mmt)
REVERT: J  333 GLU cc_start: 0.8176 (tp30) cc_final: 0.7922 (tp30)
REVERT: J  340 ASN cc_start: 0.8539 (t0) cc_final: 0.8130 (t0)
REVERT: J  382 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6720 (p90)
REVERT: J  622 GLU cc_start: 0.7841 (tp30) cc_final: 0.7594 (tp30)
REVERT: K  232 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.4860 (mmt180)
  outliers start: 15
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0634
  time to fit residues: 7.9207
Evaluate side-chains
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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  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  577 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 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
J 382 HIS
** J 565 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 = 0.4077 r_free = 0.4077 target = 0.171266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.134476 restraints weight = 8430.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.138268 restraints weight = 4855.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.140876 restraints weight = 3301.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142357 restraints weight = 2527.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.143696 restraints weight = 2128.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3060

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= 0.141
  Angle     :  0.559   7.951   7046  Z= 0.288
  Chirality :  0.038   0.132    809
  Planarity :  0.003   0.032    916
  Dihedral  :  4.920  53.170    712
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 16.04 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.33), residues: 646
  helix:  0.91 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.18 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.016   0.001   TYR J 153 
 PHE   0.014   0.001   PHE J 623 
 TRP   0.004   0.001   TRP J 209 
 HIS   0.006   0.001   HIS J 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5198)
  covalent geometry    : angle       0.55894 ( 7046)
  hydrogen bonds       : bond        0.03867 (  266)
  hydrogen bonds       : angle       4.01876 (  780)

*********************** 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
  98 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   74 GLN cc_start: 0.6848 (mp-120) cc_final: 0.6484 (mp10)
REVERT: J  236 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6569 (tt0)
REVERT: J  273 TYR cc_start: 0.8241 (t80) cc_final: 0.8004 (t80)
REVERT: J  333 GLU cc_start: 0.8226 (tp30) cc_final: 0.7918 (tp30)
REVERT: J  340 ASN cc_start: 0.8612 (t0) cc_final: 0.8213 (t0)
REVERT: J  472 TYR cc_start: 0.8748 (t80) cc_final: 0.8409 (t80)
REVERT: J  593 MET cc_start: 0.6421 (mmm) cc_final: 0.6158 (tpp)
REVERT: J  622 GLU cc_start: 0.7873 (tp30) cc_final: 0.7619 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 94
  average time/residue: 0.0623
  time to fit residues: 8.0034
Evaluate side-chains
  88 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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  225 VAL
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  382 HIS
Chi-restraints excluded: chain J residue  416 LEU
Chi-restraints excluded: chain J residue  483 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  577 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 11 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
J 382 HIS
** J 565 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 = 0.4056 r_free = 0.4056 target = 0.169476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.132561 restraints weight = 8492.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.136266 restraints weight = 5045.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138837 restraints weight = 3425.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140568 restraints weight = 2608.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.141753 restraints weight = 2163.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5198  Z= 0.168
  Angle     :  0.578   9.696   7046  Z= 0.300
  Chirality :  0.039   0.131    809
  Planarity :  0.004   0.031    916
  Dihedral  :  4.930  52.973    712
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 15.86 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.33), residues: 646
  helix:  0.89 (0.25), residues: 408
  sheet:  None (None), residues: 0
  loop : -1.15 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.013   0.001   TYR J 153 
 PHE   0.014   0.001   PHE J 623 
 TRP   0.004   0.001   TRP J  93 
 HIS   0.006   0.001   HIS J 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5198)
  covalent geometry    : angle       0.57828 ( 7046)
  hydrogen bonds       : bond        0.03908 (  266)
  hydrogen bonds       : angle       4.09293 (  780)

*********************** 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
  107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.203 
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: 0.6922 (mp-120) cc_final: 0.6513 (mp10)
REVERT: J  236 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6590 (tt0)
REVERT: J  327 GLU cc_start: 0.8123 (tp30) cc_final: 0.7522 (tm-30)
REVERT: J  333 GLU cc_start: 0.8250 (tp30) cc_final: 0.7907 (tp30)
REVERT: J  340 ASN cc_start: 0.8673 (t0) cc_final: 0.8317 (t0)
REVERT: J  472 TYR cc_start: 0.8835 (t80) cc_final: 0.8627 (t80)
REVERT: J  542 TYR cc_start: 0.8078 (t80) cc_final: 0.7792 (t80)
REVERT: J  622 GLU cc_start: 0.7905 (tp30) cc_final: 0.7638 (tp30)
REVERT: K  232 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.4879 (mmt180)
  outliers start: 24
  outliers final: 18
  residues processed: 103
  average time/residue: 0.0574
  time to fit residues: 8.0294
Evaluate side-chains
  90 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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  235 VAL
Chi-restraints excluded: chain J residue  253 LEU
Chi-restraints excluded: chain J residue  265 GLU
Chi-restraints excluded: chain J residue  290 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0570
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
J 241 HIS
J 382 HIS
J 443 ASN
** J 565 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 = 0.4079 r_free = 0.4079 target = 0.171268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.135336 restraints weight = 8422.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.139108 restraints weight = 4865.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.141702 restraints weight = 3311.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143285 restraints weight = 2524.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.144437 restraints weight = 2108.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3306

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= 0.131
  Angle     :  0.584   9.421   7046  Z= 0.302
  Chirality :  0.038   0.135    809
  Planarity :  0.003   0.031    916
  Dihedral  :  5.007  51.992    712
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.33), residues: 646
  helix:  0.91 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.14 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.051   0.002   TYR J 273 
 PHE   0.020   0.001   PHE J 626 
 TRP   0.004   0.001   TRP J 209 
 HIS   0.011   0.001   HIS J 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5198)
  covalent geometry    : angle       0.58375 ( 7046)
  hydrogen bonds       : bond        0.03850 (  266)
  hydrogen bonds       : angle       3.96382 (  780)

*********************** 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
  96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.201 
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: 0.6868 (mp-120) cc_final: 0.6514 (mp10)
REVERT: J  102 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7985 (tp30)
REVERT: J  236 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6620 (tt0)
REVERT: J  273 TYR cc_start: 0.8007 (t80) cc_final: 0.7705 (t80)
REVERT: J  278 LEU cc_start: 0.8531 (tp) cc_final: 0.7682 (mp)
REVERT: J  282 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6975 (tm-30)
REVERT: J  333 GLU cc_start: 0.8282 (tp30) cc_final: 0.7901 (tp30)
REVERT: J  340 ASN cc_start: 0.8663 (t0) cc_final: 0.8287 (t0)
REVERT: J  622 GLU cc_start: 0.7853 (tp30) cc_final: 0.7570 (tp30)
REVERT: K  232 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5064 (mmt180)
  outliers start: 19
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0639
  time to fit residues: 8.0947
Evaluate side-chains
  89 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  225 VAL
Chi-restraints excluded: chain J residue  253 LEU
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 K residue  232 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0870
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
J 241 HIS
** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 443 ASN
** J 565 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 = 0.4072 r_free = 0.4072 target = 0.170682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.134497 restraints weight = 8391.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.138264 restraints weight = 4900.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.140808 restraints weight = 3352.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.142416 restraints weight = 2560.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.143340 restraints weight = 2133.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3381

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     :  0.588   9.223   7046  Z= 0.302
  Chirality :  0.039   0.158    809
  Planarity :  0.004   0.030    916
  Dihedral  :  5.016  51.499    712
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 18.02 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.33), residues: 646
  helix:  0.99 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.10 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.042   0.002   TYR J 273 
 PHE   0.020   0.001   PHE J 626 
 TRP   0.004   0.001   TRP J  93 
 HIS   0.007   0.001   HIS J 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5198)
  covalent geometry    : angle       0.58848 ( 7046)
  hydrogen bonds       : bond        0.03713 (  266)
  hydrogen bonds       : angle       3.95545 (  780)

*********************** 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
  96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.179 
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: 0.6861 (mp-120) cc_final: 0.6638 (mp10)
REVERT: J  102 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8017 (tp30)
REVERT: J  236 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6725 (tt0)
REVERT: J  273 TYR cc_start: 0.8114 (t80) cc_final: 0.7753 (t80)
REVERT: J  278 LEU cc_start: 0.8532 (tp) cc_final: 0.7743 (mp)
REVERT: J  333 GLU cc_start: 0.8298 (tp30) cc_final: 0.7898 (tp30)
REVERT: J  340 ASN cc_start: 0.8659 (t0) cc_final: 0.8313 (t0)
REVERT: J  437 MET cc_start: 0.8410 (tpp) cc_final: 0.8192 (tpp)
REVERT: J  622 GLU cc_start: 0.7885 (tp30) cc_final: 0.7602 (tp30)
REVERT: K  232 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5060 (mmt180)
  outliers start: 21
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0636
  time to fit residues: 7.8477
Evaluate side-chains
  90 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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  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  567 ASP
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 57 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0010
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   overall best weight:    0.2924

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

Flipped N/Q/H residues before XYZ refinement:
J 289 ASN
** J 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 443 ASN
** J 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 565 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 = 0.4092 r_free = 0.4092 target = 0.172553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.137149 restraints weight = 8288.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.140909 restraints weight = 4796.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143484 restraints weight = 3261.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145052 restraints weight = 2484.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.146240 restraints weight = 2062.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3460

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= 0.120
  Angle     :  0.586   9.730   7046  Z= 0.301
  Chirality :  0.039   0.153    809
  Planarity :  0.003   0.030    916
  Dihedral  :  4.910  50.412    712
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.34), residues: 646
  helix:  1.15 (0.26), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.14 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.038   0.002   TYR J 273 
 PHE   0.021   0.001   PHE J 626 
 TRP   0.003   0.001   TRP J  93 
 HIS   0.005   0.001   HIS J 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5198)
  covalent geometry    : angle       0.58622 ( 7046)
  hydrogen bonds       : bond        0.03633 (  266)
  hydrogen bonds       : angle       3.82292 (  780)

*********************** 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
  96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.193 
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: 0.6864 (mp-120) cc_final: 0.6647 (mp10)
REVERT: J  102 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7972 (tp30)
REVERT: J  236 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6685 (tt0)
REVERT: J  273 TYR cc_start: 0.8053 (t80) cc_final: 0.7651 (t80)
REVERT: J  278 LEU cc_start: 0.8522 (tp) cc_final: 0.7741 (mp)
REVERT: J  333 GLU cc_start: 0.8301 (tp30) cc_final: 0.7901 (tp30)
REVERT: J  340 ASN cc_start: 0.8601 (t0) cc_final: 0.8307 (t0)
REVERT: J  622 GLU cc_start: 0.7831 (tp30) cc_final: 0.7562 (tp30)
  outliers start: 16
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0550
  time to fit residues: 6.9846
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  : 0.193 
-------------------------------------------------------------------------------
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  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  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 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0270
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
J 443 ASN
** J 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 565 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 = 0.4066 r_free = 0.4066 target = 0.170519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.134327 restraints weight = 8438.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.137992 restraints weight = 4991.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140478 restraints weight = 3437.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142168 restraints weight = 2639.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143287 restraints weight = 2194.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5198  Z= 0.162
  Angle     :  0.637  10.554   7046  Z= 0.326
  Chirality :  0.040   0.156    809
  Planarity :  0.004   0.030    916
  Dihedral  :  4.979  52.320    712
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.34), residues: 646
  helix:  1.03 (0.26), residues: 407
  sheet:  None (None), residues: 0
  loop : -1.02 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.037   0.002   TYR J 273 
 PHE   0.021   0.001   PHE J 626 
 TRP   0.005   0.001   TRP J  93 
 HIS   0.012   0.001   HIS J 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5198)
  covalent geometry    : angle       0.63684 ( 7046)
  hydrogen bonds       : bond        0.03850 (  266)
  hydrogen bonds       : angle       3.94168 (  780)

********************** 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
  94 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   74 GLN cc_start: 0.6925 (mp-120) cc_final: 0.6721 (mp10)
REVERT: J  102 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7922 (tp30)
REVERT: J  236 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6719 (tt0)
REVERT: J  273 TYR cc_start: 0.8152 (t80) cc_final: 0.7767 (t80)
REVERT: J  278 LEU cc_start: 0.8494 (tp) cc_final: 0.7570 (mp)
REVERT: J  327 GLU cc_start: 0.8088 (tp30) cc_final: 0.7497 (tm-30)
REVERT: J  333 GLU cc_start: 0.8290 (tp30) cc_final: 0.8066 (tp30)
REVERT: J  340 ASN cc_start: 0.8657 (t0) cc_final: 0.8322 (t0)
REVERT: J  593 MET cc_start: 0.6309 (mmm) cc_final: 0.5941 (tpp)
REVERT: J  622 GLU cc_start: 0.7870 (tp30) cc_final: 0.7637 (tp30)
REVERT: K  232 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4831 (mpt90)
  outliers start: 16
  outliers final: 15
  residues processed: 91
  average time/residue: 0.0750
  time to fit residues: 9.0089
Evaluate side-chains
  89 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  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  575 THR
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 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 57 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   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 443 ASN
** J 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 565 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 = 0.4070 r_free = 0.4070 target = 0.170924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.134606 restraints weight = 8444.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.138376 restraints weight = 5030.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.140877 restraints weight = 3455.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.142571 restraints weight = 2651.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.143619 restraints weight = 2210.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5198  Z= 0.159
  Angle     :  0.645  10.857   7046  Z= 0.329
  Chirality :  0.040   0.169    809
  Planarity :  0.004   0.030    916
  Dihedral  :  5.002  52.698    712
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.18 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.33), residues: 646
  helix:  0.97 (0.26), residues: 406
  sheet:  None (None), residues: 0
  loop : -1.06 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 332 
 TYR   0.035   0.002   TYR J 273 
 PHE   0.023   0.002   PHE J 626 
 TRP   0.004   0.001   TRP J  93 
 HIS   0.005   0.001   HIS J 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5198)
  covalent geometry    : angle       0.64510 ( 7046)
  hydrogen bonds       : bond        0.03812 (  266)
  hydrogen bonds       : angle       3.95447 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1205.03 seconds
wall clock time: 21 minutes 31.82 seconds (1291.82 seconds total)