Starting phenix.real_space_refine
on Thu Mar  6 00:37:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikj_35514/03_2025/8ikj_35514.cif"
  }
  resolution = 3.2
  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=   0.013
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      28      5.16       5
     C    2712      2.51       5
     N     702      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4200
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 4158
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 532, 4147
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 20, 'TRANS': 511}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 532, 4147
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 20, 'TRANS': 511}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4226
    Chain: "R"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.13, per 1000 atoms: 1.22
  Number of scatterers: 4200
  At special positions: 0
  Unit cell: (79.98, 92.07, 119.97, 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      28     16.00
     O     758      8.00
     N     702      7.00
     C    2712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 495 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 513 " - pdb=" SG  CYS R 527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG R 901 " - " ASN R 413 "
      " NAG R 902 " - " ASN R 406 "
      " NAG R 903 " - " ASN R 520 "
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  988

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 3 sheets defined
      52.6% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'R' and resid 272 through 289
    Processing helix  chain 'R' and resid 293 through 311
    Processing helix  chain 'R' and resid 319 through 343
      removed outlier: 3.814A  pdb=" N   LYS R 343 " --> pdb=" O   ARG R 339 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 385 through 390
      removed outlier: 3.531A  pdb=" N   ALA R 389 " --> pdb=" O   TRP R 385 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLY R 390 " --> pdb=" O   ALA R 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 385 through 390'
    Processing helix  chain 'R' and resid 406 through 410
    Processing helix  chain 'R' and resid 419 through 431
    Processing helix  chain 'R' and resid 548 through 572
    Processing helix  chain 'R' and resid 577 through 601
    Processing helix  chain 'R' and resid 609 through 643
    Processing helix  chain 'R' and resid 651 through 674
      Proline residue:  R 663  - end of helix
    Processing helix  chain 'R' and resid 691 through 719
      removed outlier: 3.675A  pdb=" N   SER R 695 " --> pdb=" O   GLY R 691 " (cutoff:3.500A)
      Proline residue:  R 699  - end of helix
    Processing helix  chain 'R' and resid 735 through 756
    Processing helix  chain 'R' and resid 766 through 787
      removed outlier: 3.610A  pdb=" N   VAL R 770 " --> pdb=" O   VAL R 766 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 790 through 801
      removed outlier: 3.572A  pdb=" N   ARG R 794 " --> pdb=" O   ASN R 790 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 348 through 353
      removed outlier: 3.666A  pdb=" N   GLN R 365 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   VAL R 398 " --> pdb=" O   LEU R 450 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU R 450 " --> pdb=" O   VAL R 398 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   GLY R 400 " --> pdb=" O   ILE R 448 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE R 448 " --> pdb=" O   GLY R 400 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU R 402 " --> pdb=" O   ASN R 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 371 through 374
      removed outlier: 3.782A  pdb=" N   GLY R 517 " --> pdb=" O   THR R 524 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLN R 526 " --> pdb=" O   VAL R 515 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   VAL R 515 " --> pdb=" O   GLN R 526 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'R' and resid 436 through 438
      removed outlier: 4.520A  pdb=" N   SER R 532 " --> pdb=" O   TRP R 498 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA R 538 " --> pdb=" O   GLU R 492 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU R 492 " --> pdb=" O   ALA R 538 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    749 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: 1.27

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1088
        1.33 -     1.46: 869
        1.46 -     1.58: 2301
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 4296
  Sorted by residual:
  bond pdb=" C   ALA R 412 "
       pdb=" N   ASN R 413 "
    ideal  model  delta    sigma   weight residual
    1.332  1.576 -0.244 1.40e-02 5.10e+03 3.03e+02
  bond pdb=" C   LYS R 519 "
       pdb=" N   ASN R 520 "
    ideal  model  delta    sigma   weight residual
    1.333  1.444 -0.111 1.39e-02 5.18e+03 6.42e+01
  bond pdb=" C   GLN R 405 "
       pdb=" N   ASN R 406 "
    ideal  model  delta    sigma   weight residual
    1.330  1.269  0.061 1.52e-02 4.33e+03 1.60e+01
  bond pdb=" C   ASN R 406 "
       pdb=" N   MET R 407 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.029 1.33e-02 5.65e+03 4.74e+00
  bond pdb=" C   ASN R 520 "
       pdb=" N   GLY R 521 "
    ideal  model  delta    sigma   weight residual
    1.331  1.304  0.027 1.32e-02 5.74e+03 4.17e+00
  ... (remaining 4291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 5680
        1.88 -     3.76: 126
        3.76 -     5.63: 25
        5.63 -     7.51: 2
        7.51 -     9.39: 4
  Bond angle restraints: 5837
  Sorted by residual:
  angle pdb=" CA  GLN R 405 "
        pdb=" C   GLN R 405 "
        pdb=" N   ASN R 406 "
      ideal   model   delta    sigma   weight residual
     118.21  126.57   -8.36 1.36e+00 5.41e-01 3.78e+01
  angle pdb=" O   GLN R 405 "
        pdb=" C   GLN R 405 "
        pdb=" N   ASN R 406 "
      ideal   model   delta    sigma   weight residual
     122.46  114.48    7.98 1.37e+00 5.33e-01 3.40e+01
  angle pdb=" C   GLY R 647 "
        pdb=" N   GLN R 648 "
        pdb=" CA  GLN R 648 "
      ideal   model   delta    sigma   weight residual
     121.54  129.73   -8.19 1.91e+00 2.74e-01 1.84e+01
  angle pdb=" CA  LEU R 549 "
        pdb=" CB  LEU R 549 "
        pdb=" CG  LEU R 549 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  angle pdb=" CA  MET R 537 "
        pdb=" CB  MET R 537 "
        pdb=" CG  MET R 537 "
      ideal   model   delta    sigma   weight residual
     114.10  119.44   -5.34 2.00e+00 2.50e-01 7.13e+00
  ... (remaining 5832 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.04: 2306
       14.04 -    28.08: 193
       28.08 -    42.11: 61
       42.11 -    56.15: 14
       56.15 -    70.18: 6
  Dihedral angle restraints: 2580
    sinusoidal: 1048
      harmonic: 1532
  Sorted by residual:
  dihedral pdb=" CA  ASP R 761 "
           pdb=" C   ASP R 761 "
           pdb=" N   ASP R 762 "
           pdb=" CA  ASP R 762 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.47  -19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  MET R 537 "
           pdb=" C   MET R 537 "
           pdb=" N   ALA R 538 "
           pdb=" CA  ALA R 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.97  -19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CB  CYS R 612 "
           pdb=" SG  CYS R 612 "
           pdb=" SG  CYS R 684 "
           pdb=" CB  CYS R 684 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.85   30.85     1      1.00e+01 1.00e-02 1.36e+01
  ... (remaining 2577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.302: 684
       0.302 -    0.603: 0
       0.603 -    0.905: 0
       0.905 -    1.206: 1
       1.206 -    1.508: 1
  Chirality restraints: 686
  Sorted by residual:
  chirality pdb=" C1  NAG R 902 "
            pdb=" ND2 ASN R 406 "
            pdb=" C2  NAG R 902 "
            pdb=" O5  NAG R 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.89   -1.51 2.00e-01 2.50e+01 5.68e+01
  chirality pdb=" C1  NAG R 903 "
            pdb=" ND2 ASN R 520 "
            pdb=" C2  NAG R 903 "
            pdb=" O5  NAG R 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.35   -1.05 2.00e-01 2.50e+01 2.73e+01
  chirality pdb=" CA  MET R 537 "
            pdb=" N   MET R 537 "
            pdb=" C   MET R 537 "
            pdb=" CB  MET R 537 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.48e-01
  ... (remaining 683 not shown)

  Planarity restraints: 727
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 413 "   -0.128 2.00e-02 2.50e+03   1.43e-01 2.55e+02
        pdb=" CG  ASN R 413 "    0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 413 "    0.028 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 413 "    0.228 2.00e-02 2.50e+03
        pdb=" C1  NAG R 901 "   -0.175 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 348 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   GLY R 348 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY R 348 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO R 349 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 319 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO R 320 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO R 320 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO R 320 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 724 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 106
        2.71 -     3.26: 4103
        3.26 -     3.80: 6903
        3.80 -     4.35: 8293
        4.35 -     4.90: 14231
  Nonbonded interactions: 33636
  Sorted by model distance:
  nonbonded pdb=" O   ARG R 643 "
            pdb=" NE2 GLN R 646 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OG1 THR R 568 "
            pdb=" OH  TYR R 797 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER R 356 "
            pdb=" NE2 GLN R 405 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" NH1 ARG R 490 "
            pdb=" O   GLY R 605 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OE1 GLU R 295 "
            pdb=" NE2 GLN R 299 "
     model   vdw
     2.215 3.120
  ... (remaining 33631 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.800
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     19.450
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
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      :  0.005   0.244   4296  Z= 0.341
  Angle     :  0.697   9.389   5837  Z= 0.369
  Chirality :  0.083   1.508    686
  Planarity :  0.006   0.071    724
  Dihedral  : 12.439  70.184   1583
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.36), residues: 529
  helix:  2.40 (0.31), residues: 266
  sheet:  0.66 (0.58), residues: 78
  loop : -0.79 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 498 
 HIS   0.002   0.000   HIS R 585 
 PHE   0.015   0.001   PHE R 627 
 TYR   0.009   0.001   TYR R 769 
 ARG   0.014   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.7964 (mtm) cc_final: 0.7721 (mtm)
REVERT: R  338 MET cc_start: 0.8201 (mtm) cc_final: 0.7958 (mtm)
REVERT: R  491 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6241 (tm-30)
REVERT: R  537 MET cc_start: 0.5740 (tpt) cc_final: 0.5456 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.3028
  time to fit residues: 29.0296
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:   40.0000
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0470
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
R 271 HIS
R 299 GLN
R 646 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.175167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.124262 restraints weight = 10512.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.64
r_work: 0.3336 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4296  Z= 0.345
  Angle     :  0.687  11.799   5837  Z= 0.344
  Chirality :  0.046   0.280    686
  Planarity :  0.005   0.060    724
  Dihedral  :  5.072  37.068    632
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.36 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 529
  helix:  1.93 (0.30), residues: 269
  sheet:  0.36 (0.59), residues: 84
  loop : -0.37 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 498 
 HIS   0.002   0.001   HIS R 539 
 PHE   0.016   0.002   PHE R 627 
 TYR   0.014   0.002   TYR R 660 
 ARG   0.007   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8471 (mtm) cc_final: 0.8190 (mtm)
REVERT: R  338 MET cc_start: 0.8585 (mtm) cc_final: 0.8276 (mtm)
REVERT: R  407 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6993 (mmp)
REVERT: R  491 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: R  537 MET cc_start: 0.6415 (tpt) cc_final: 0.5852 (tpt)
REVERT: R  540 TYR cc_start: 0.7657 (m-10) cc_final: 0.7310 (m-10)
REVERT: R  576 GLN cc_start: 0.7362 (mm110) cc_final: 0.7037 (mm110)
REVERT: R  689 GLU cc_start: 0.6823 (tp30) cc_final: 0.6603 (tp30)
REVERT: R  693 LEU cc_start: 0.8140 (tp) cc_final: 0.7932 (tp)
REVERT: R  792 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8292 (mtpp)
  outliers start: 4
  outliers final: 2
  residues processed: 82
  average time/residue: 0.2833
  time to fit residues: 27.0120
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.175840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123061 restraints weight = 15966.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 4.79
r_work: 0.3279 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4296  Z= 0.293
  Angle     :  0.644  10.456   5837  Z= 0.325
  Chirality :  0.042   0.212    686
  Planarity :  0.005   0.056    724
  Dihedral  :  5.129  46.385    632
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  7.24 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.37), residues: 529
  helix:  1.98 (0.31), residues: 268
  sheet:  0.43 (0.60), residues: 79
  loop : -0.36 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 498 
 HIS   0.004   0.001   HIS R 539 
 PHE   0.014   0.002   PHE R 627 
 TYR   0.010   0.002   TYR R 674 
 ARG   0.005   0.000   ARG R 579 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8534 (mtm) cc_final: 0.8227 (mtm)
REVERT: R  338 MET cc_start: 0.8664 (mtm) cc_final: 0.8335 (mtm)
REVERT: R  407 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7211 (mmp)
REVERT: R  423 GLN cc_start: 0.8769 (mt0) cc_final: 0.8546 (mt0)
REVERT: R  491 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6876 (tm-30)
REVERT: R  537 MET cc_start: 0.6506 (tpt) cc_final: 0.6022 (tpt)
REVERT: R  540 TYR cc_start: 0.7827 (m-10) cc_final: 0.7498 (m-10)
REVERT: R  544 ASP cc_start: 0.6966 (p0) cc_final: 0.6294 (p0)
REVERT: R  546 LYS cc_start: 0.8567 (mttt) cc_final: 0.8279 (mtpp)
REVERT: R  576 GLN cc_start: 0.7498 (mm110) cc_final: 0.7133 (mm110)
REVERT: R  792 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8392 (mtpp)
  outliers start: 6
  outliers final: 3
  residues processed: 86
  average time/residue: 0.2787
  time to fit residues: 27.8490
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.175166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.122714 restraints weight = 10029.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.48
r_work: 0.3361 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4296  Z= 0.325
  Angle     :  0.667  10.365   5837  Z= 0.336
  Chirality :  0.042   0.186    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.900  40.017    632
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.77 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.36), residues: 529
  helix:  2.06 (0.30), residues: 261
  sheet:  0.37 (0.60), residues: 80
  loop : -0.50 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 585 
 PHE   0.023   0.002   PHE R 623 
 TYR   0.009   0.002   TYR R 660 
 ARG   0.009   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8391 (mtm) cc_final: 0.8102 (mtm)
REVERT: R  338 MET cc_start: 0.8531 (mtm) cc_final: 0.8204 (mtm)
REVERT: R  407 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6869 (mmp)
REVERT: R  423 GLN cc_start: 0.8675 (mt0) cc_final: 0.8434 (mt0)
REVERT: R  491 GLN cc_start: 0.7308 (tm-30) cc_final: 0.6662 (tm-30)
REVERT: R  537 MET cc_start: 0.6263 (tpt) cc_final: 0.5995 (tpt)
REVERT: R  540 TYR cc_start: 0.7816 (m-10) cc_final: 0.7479 (m-10)
REVERT: R  544 ASP cc_start: 0.6785 (p0) cc_final: 0.6140 (p0)
REVERT: R  546 LYS cc_start: 0.8568 (mttt) cc_final: 0.8267 (mtpp)
REVERT: R  576 GLN cc_start: 0.7381 (mm110) cc_final: 0.7007 (mm110)
REVERT: R  630 MET cc_start: 0.7564 (tpt) cc_final: 0.7040 (tpt)
REVERT: R  792 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8445 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 85
  average time/residue: 0.2707
  time to fit residues: 26.7123
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 51 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.5582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.176163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.123485 restraints weight = 10549.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 3.49
r_work: 0.3371 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4296  Z= 0.246
  Angle     :  0.641  10.731   5837  Z= 0.323
  Chirality :  0.040   0.167    686
  Planarity :  0.005   0.053    724
  Dihedral  :  4.800  38.319    632
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.77 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.37), residues: 529
  helix:  2.20 (0.31), residues: 262
  sheet:  0.17 (0.59), residues: 80
  loop : -0.45 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 498 
 HIS   0.004   0.001   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.006   0.001   TYR R 674 
 ARG   0.011   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8399 (mtm) cc_final: 0.8134 (mtm)
REVERT: R  338 MET cc_start: 0.8530 (mtm) cc_final: 0.8201 (mtm)
REVERT: R  407 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6806 (mmp)
REVERT: R  491 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6769 (tm-30)
REVERT: R  540 TYR cc_start: 0.7854 (m-10) cc_final: 0.7461 (m-10)
REVERT: R  544 ASP cc_start: 0.6772 (p0) cc_final: 0.6150 (p0)
REVERT: R  546 LYS cc_start: 0.8576 (mttt) cc_final: 0.8288 (mtpp)
REVERT: R  576 GLN cc_start: 0.7396 (mm110) cc_final: 0.7011 (mm110)
REVERT: R  792 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8485 (mttt)
  outliers start: 5
  outliers final: 4
  residues processed: 85
  average time/residue: 0.2906
  time to fit residues: 28.4140
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9980
   chunk 44 optimal weight:    0.3980
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
R 423 GLN
R 745 GLN
R 778 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.176270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.120801 restraints weight = 17293.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 4.88
r_work: 0.3293 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4296  Z= 0.253
  Angle     :  0.654  10.307   5837  Z= 0.330
  Chirality :  0.041   0.183    686
  Planarity :  0.005   0.053    724
  Dihedral  :  4.888  41.830    632
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.43 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.36), residues: 529
  helix:  2.19 (0.31), residues: 262
  sheet:  0.44 (0.61), residues: 74
  loop : -0.59 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.006   0.001   TYR R 769 
 ARG   0.011   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8479 (mtm) cc_final: 0.8188 (mtm)
REVERT: R  338 MET cc_start: 0.8631 (mtm) cc_final: 0.8283 (mtm)
REVERT: R  407 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6863 (mmp)
REVERT: R  540 TYR cc_start: 0.7908 (m-10) cc_final: 0.7562 (m-10)
REVERT: R  544 ASP cc_start: 0.6965 (p0) cc_final: 0.6354 (p0)
REVERT: R  546 LYS cc_start: 0.8610 (mttt) cc_final: 0.8310 (mtpp)
REVERT: R  576 GLN cc_start: 0.7532 (mm110) cc_final: 0.7120 (mm110)
REVERT: R  792 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8422 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 0.2613
  time to fit residues: 25.2625
Evaluate side-chains
  82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 491 GLN ** 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 = 0.4392 r_free = 0.4392 target = 0.175672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123853 restraints weight = 12070.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.96
r_work: 0.3333 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4296  Z= 0.302
  Angle     :  0.688  10.622   5837  Z= 0.348
  Chirality :  0.042   0.150    686
  Planarity :  0.005   0.076    724
  Dihedral  :  4.768  36.558    632
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.75 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.36), residues: 529
  helix:  2.09 (0.31), residues: 262
  sheet:  0.44 (0.60), residues: 74
  loop : -0.61 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.003   0.000   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.009   0.001   TYR R 674 
 ARG   0.009   0.001   ARG R 613 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8453 (mtm) cc_final: 0.8155 (mtm)
REVERT: R  338 MET cc_start: 0.8589 (mtm) cc_final: 0.8244 (mtm)
REVERT: R  407 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6739 (mmp)
REVERT: R  544 ASP cc_start: 0.6950 (p0) cc_final: 0.6220 (p0)
REVERT: R  546 LYS cc_start: 0.8615 (mttt) cc_final: 0.8311 (mtpp)
REVERT: R  576 GLN cc_start: 0.7457 (mm110) cc_final: 0.7064 (mm110)
REVERT: R  792 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8453 (mtpp)
  outliers start: 6
  outliers final: 5
  residues processed: 78
  average time/residue: 0.2538
  time to fit residues: 23.1406
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  646 GLN
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 19 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.175699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.121805 restraints weight = 15829.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 4.87
r_work: 0.3259 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4296  Z= 0.300
  Angle     :  0.695  11.287   5837  Z= 0.349
  Chirality :  0.042   0.155    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.460  22.819    632
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.75 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 529
  helix:  2.08 (0.31), residues: 262
  sheet:  0.51 (0.61), residues: 73
  loop : -0.55 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.001   0.000   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 674 
 ARG   0.009   0.001   ARG R 613 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8533 (mtm) cc_final: 0.8234 (mtm)
REVERT: R  338 MET cc_start: 0.8655 (mtm) cc_final: 0.8310 (mtm)
REVERT: R  407 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6733 (mmp)
REVERT: R  544 ASP cc_start: 0.7075 (p0) cc_final: 0.6465 (p0)
REVERT: R  546 LYS cc_start: 0.8619 (mttt) cc_final: 0.8264 (mtpp)
REVERT: R  576 GLN cc_start: 0.7561 (mm110) cc_final: 0.7149 (mm110)
REVERT: R  693 LEU cc_start: 0.8002 (tp) cc_final: 0.7796 (tp)
REVERT: R  792 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8471 (mtpp)
  outliers start: 7
  outliers final: 6
  residues processed: 80
  average time/residue: 0.3197
  time to fit residues: 29.4071
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.175507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122455 restraints weight = 10060.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 3.47
r_work: 0.3366 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4296  Z= 0.308
  Angle     :  0.727  11.190   5837  Z= 0.367
  Chirality :  0.042   0.156    686
  Planarity :  0.005   0.062    724
  Dihedral  :  4.479  23.076    632
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.96 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.37), residues: 529
  helix:  2.11 (0.31), residues: 261
  sheet:  0.45 (0.62), residues: 73
  loop : -0.53 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 629 
 HIS   0.001   0.000   HIS R 539 
 PHE   0.025   0.002   PHE R 623 
 TYR   0.010   0.001   TYR R 674 
 ARG   0.013   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8390 (mtm) cc_final: 0.8108 (mtm)
REVERT: R  338 MET cc_start: 0.8540 (mtm) cc_final: 0.8198 (mtm)
REVERT: R  407 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6588 (mmp)
REVERT: R  544 ASP cc_start: 0.6847 (p0) cc_final: 0.6160 (p0)
REVERT: R  546 LYS cc_start: 0.8579 (mttt) cc_final: 0.8226 (mtpp)
REVERT: R  576 GLN cc_start: 0.7413 (mm110) cc_final: 0.7028 (mm110)
REVERT: R  792 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8472 (mttm)
  outliers start: 7
  outliers final: 6
  residues processed: 78
  average time/residue: 0.3288
  time to fit residues: 30.3548
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.175904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122495 restraints weight = 10503.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 3.55
r_work: 0.3362 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4296  Z= 0.286
  Angle     :  0.752  17.452   5837  Z= 0.372
  Chirality :  0.042   0.173    686
  Planarity :  0.005   0.065    724
  Dihedral  :  4.446  22.778    632
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.96 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.37), residues: 529
  helix:  2.10 (0.31), residues: 261
  sheet:  0.32 (0.61), residues: 79
  loop : -0.47 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 629 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.027   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.014   0.001   ARG R 277 

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8422 (mtm) cc_final: 0.8131 (mtm)
REVERT: R  338 MET cc_start: 0.8579 (mtm) cc_final: 0.8232 (mtm)
REVERT: R  407 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6614 (mmp)
REVERT: R  544 ASP cc_start: 0.6846 (p0) cc_final: 0.6213 (p0)
REVERT: R  546 LYS cc_start: 0.8605 (mttt) cc_final: 0.8322 (mtpp)
REVERT: R  576 GLN cc_start: 0.7417 (mm110) cc_final: 0.7027 (mm110)
REVERT: R  792 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8477 (mttm)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2692
  time to fit residues: 23.6059
Evaluate side-chains
  77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 12 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.176397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.124891 restraints weight = 7355.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.87
r_work: 0.3423 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4296  Z= 0.264
  Angle     :  0.747  16.972   5837  Z= 0.367
  Chirality :  0.042   0.186    686
  Planarity :  0.005   0.064    724
  Dihedral  :  4.370  22.653    632
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.62 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.37), residues: 529
  helix:  2.10 (0.31), residues: 262
  sheet:  0.18 (0.59), residues: 81
  loop : -0.39 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 654 
 HIS   0.001   0.000   HIS R 539 
 PHE   0.027   0.002   PHE R 623 
 TYR   0.008   0.001   TYR R 674 
 ARG   0.014   0.001   ARG R 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3529.00 seconds
wall clock time: 62 minutes 40.76 seconds (3760.76 seconds total)