Starting phenix.real_space_refine
on Mon Feb 10 20:53:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c8p_16490/02_2025/8c8p_16490.cif"
  }
  resolution = 4.1
  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=   0.002 sd=   0.016
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      12      5.16       5
     C    1564      2.51       5
     N     409      2.21       5
     O     464      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2449
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "H"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 913
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
  Time building chain proxies: 2.48, per 1000 atoms: 1.01
  Number of scatterers: 2449
  At special positions: 0
  Unit cell: (60.1938, 67.9967, 85.8319, 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      12     16.00
     O     464      8.00
     N     409      7.00
     C    1564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " 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
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 321.3 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  566

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      13.4% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.775A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.901A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.677A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 4.008A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.733A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.682A  pdb=" N   ALA H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   THR H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER H  21 " --> pdb=" O   THR H   7 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR H  77 " --> pdb=" O   ASP H  72 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN H  81 " --> pdb=" O   THR H  68 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR H  68 " --> pdb=" O   GLN H  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.420A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA H  96 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR H 114 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.232A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474

    57 hydrogen bonds defined for protein.
    141 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: 0.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 785
        1.34 -     1.46: 673
        1.46 -     1.58: 1041
        1.58 -     1.70: 0
        1.70 -     1.82: 14
  Bond restraints: 2513
  Sorted by residual:
  bond pdb=" CA  ILE A 410 "
       pdb=" CB  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.016 1.31e-02 5.83e+03 1.56e+00
  bond pdb=" CA  ASN H  76 "
       pdb=" CB  ASN H  76 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.54e-02 4.22e+03 1.40e+00
  bond pdb=" CA  VAL H 118 "
       pdb=" CB  VAL H 118 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 7.01e-01
  bond pdb=" CA  VAL H  48 "
       pdb=" CB  VAL H  48 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.61e-01
  bond pdb=" N   GLY A 476 "
       pdb=" CA  GLY A 476 "
    ideal  model  delta    sigma   weight residual
    1.458  1.451  0.007 9.20e-03 1.18e+04 6.27e-01
  ... (remaining 2508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3330
        1.82 -     3.64: 71
        3.64 -     5.46: 9
        5.46 -     7.29: 4
        7.29 -     9.11: 1
  Bond angle restraints: 3415
  Sorted by residual:
  angle pdb=" C   LYS H  75 "
        pdb=" N   ASN H  76 "
        pdb=" CA  ASN H  76 "
      ideal   model   delta    sigma   weight residual
     122.08  128.13   -6.05 1.47e+00 4.63e-01 1.69e+01
  angle pdb=" CA  LEU H  31 "
        pdb=" CB  LEU H  31 "
        pdb=" CG  LEU H  31 "
      ideal   model   delta    sigma   weight residual
     116.30  125.41   -9.11 3.50e+00 8.16e-02 6.77e+00
  angle pdb=" C   PHE A 486 "
        pdb=" N   ASN A 487 "
        pdb=" CA  ASN A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  126.10   -4.56 1.91e+00 2.74e-01 5.71e+00
  angle pdb=" C   PHE A 497 "
        pdb=" N   GLN A 498 "
        pdb=" CA  GLN A 498 "
      ideal   model   delta    sigma   weight residual
     120.97  126.69   -5.72 2.84e+00 1.24e-01 4.06e+00
  angle pdb=" C   SER A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     122.40  125.31   -2.91 1.45e+00 4.76e-01 4.04e+00
  ... (remaining 3410 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 1317
       17.44 -    34.87: 124
       34.87 -    52.31: 19
       52.31 -    69.75: 2
       69.75 -    87.19: 2
  Dihedral angle restraints: 1464
    sinusoidal: 565
      harmonic: 899
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    1.19  -87.19     1      1.00e+01 1.00e-02 9.13e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.86   31.86     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CA  GLU H 103 "
           pdb=" C   GLU H 103 "
           pdb=" N   LEU H 104 "
           pdb=" CA  LEU H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 1461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 220
       0.034 -    0.068: 92
       0.068 -    0.102: 31
       0.102 -    0.135: 16
       0.135 -    0.169: 4
  Chirality restraints: 363
  Sorted by residual:
  chirality pdb=" CB  ILE A 472 "
            pdb=" CA  ILE A 472 "
            pdb=" CG1 ILE A 472 "
            pdb=" CG2 ILE A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  ASN H  76 "
            pdb=" N   ASN H  76 "
            pdb=" C   ASN H  76 "
            pdb=" CB  ASN H  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  VAL H  37 "
            pdb=" CA  VAL H  37 "
            pdb=" CG1 VAL H  37 "
            pdb=" CG2 VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 360 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO A 463 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 511 "    0.005 2.00e-02 2.50e+03   1.06e-02 1.11e+00
        pdb=" C   VAL A 511 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL A 511 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL A 512 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 383 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO A 384 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 654
        2.79 -     3.32: 2058
        3.32 -     3.85: 4163
        3.85 -     4.37: 4467
        4.37 -     4.90: 7751
  Nonbonded interactions: 19093
  Sorted by model distance:
  nonbonded pdb=" O   GLU H   1 "
            pdb=" OG  SER H  25 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   GLY H  10 "
            pdb=" OG1 THR H 117 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER H  17 "
            pdb=" O   MET H  82 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OG  SER H  17 "
            pdb=" OD1 ASN H  83 "
     model   vdw
     2.368 3.040
  ... (remaining 19088 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=0.00 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:             1.260
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.920
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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      :  0.002   0.018   2513  Z= 0.156
  Angle     :  0.670   9.107   3415  Z= 0.348
  Chirality :  0.048   0.169    363
  Planarity :  0.004   0.031    444
  Dihedral  : 13.499  77.692    883
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.45), residues: 310
  helix: -4.21 (0.52), residues: 34
  sheet: -0.20 (0.60), residues: 74
  loop : -1.37 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 347 
 TYR   0.010   0.001   TYR A 453 
 ARG   0.005   0.000   ARG H  66 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   20 LEU cc_start: 0.8907 (tp) cc_final: 0.8552 (tp)
REVERT: H   34 MET cc_start: 0.7425 (tmm) cc_final: 0.6735 (tmm)
REVERT: H   36 TRP cc_start: 0.7575 (m100) cc_final: 0.6672 (t-100)
REVERT: H   78 LEU cc_start: 0.7812 (tt) cc_final: 0.7470 (tt)
REVERT: A  340 GLU cc_start: 0.9163 (pt0) cc_final: 0.8881 (pm20)
REVERT: A  452 LEU cc_start: 0.9286 (mm) cc_final: 0.8854 (mm)
REVERT: A  454 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8809 (mtt-85)
REVERT: A  465 GLU cc_start: 0.9101 (tt0) cc_final: 0.8689 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2342
  time to fit residues: 22.0062
Evaluate side-chains
  42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
A 437 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 498 GLN
A 501 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.079144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.061657 restraints weight = 15507.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.063410 restraints weight = 10980.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.064588 restraints weight = 8561.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   2513  Z= 0.285
  Angle     :  0.673   6.617   3415  Z= 0.356
  Chirality :  0.045   0.145    363
  Planarity :  0.004   0.034    444
  Dihedral  :  5.049  19.919    348
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  7.17 %
    Favored  : 92.45 %
  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: -2.26 (0.45), residues: 310
  helix: -4.12 (0.46), residues: 39
  sheet: -1.14 (0.49), residues: 98
  loop : -0.97 (0.48), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  36 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.015   0.002   PHE A 347 
 TYR   0.015   0.001   TYR H  93 
 ARG   0.003   0.001   ARG A 509 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7907 (tmm) cc_final: 0.7083 (tmm)
REVERT: H   36 TRP cc_start: 0.7867 (m100) cc_final: 0.7327 (t-100)
REVERT: H   78 LEU cc_start: 0.8082 (tt) cc_final: 0.7475 (tt)
REVERT: H  107 PHE cc_start: 0.8068 (m-10) cc_final: 0.7426 (m-80)
REVERT: A  392 PHE cc_start: 0.8707 (m-80) cc_final: 0.8498 (m-10)
REVERT: A  454 ARG cc_start: 0.9355 (ttm-80) cc_final: 0.8793 (mmt180)
REVERT: A  461 LEU cc_start: 0.8531 (pt) cc_final: 0.7873 (pp)
REVERT: A  465 GLU cc_start: 0.8958 (tt0) cc_final: 0.8112 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2282
  time to fit residues: 11.4723
Evaluate side-chains
  33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.079569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.062978 restraints weight = 15713.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.064529 restraints weight = 11463.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.065607 restraints weight = 9147.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2513  Z= 0.163
  Angle     :  0.570   5.220   3415  Z= 0.290
  Chirality :  0.042   0.130    363
  Planarity :  0.003   0.035    444
  Dihedral  :  4.485  22.185    348
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.46), residues: 310
  helix: -3.91 (0.59), residues: 33
  sheet: -0.87 (0.50), residues: 101
  loop : -1.03 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.007   0.001   PHE A 338 
 TYR   0.008   0.001   TYR H  94 
 ARG   0.003   0.001   ARG H  38 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8105 (tmm) cc_final: 0.7427 (tmm)
REVERT: H   36 TRP cc_start: 0.8082 (m100) cc_final: 0.7251 (t-100)
REVERT: H   71 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7416 (ttp-170)
REVERT: H   76 ASN cc_start: 0.8838 (p0) cc_final: 0.8591 (t0)
REVERT: H   78 LEU cc_start: 0.8080 (tt) cc_final: 0.7531 (tt)
REVERT: H  110 TRP cc_start: 0.8301 (m-90) cc_final: 0.7832 (m-90)
REVERT: A  392 PHE cc_start: 0.8885 (m-80) cc_final: 0.8644 (m-80)
REVERT: A  402 ILE cc_start: 0.9322 (tp) cc_final: 0.8962 (tp)
REVERT: A  454 ARG cc_start: 0.9370 (ttm-80) cc_final: 0.9023 (mmt90)
REVERT: A  461 LEU cc_start: 0.8548 (pt) cc_final: 0.7936 (pp)
REVERT: A  465 GLU cc_start: 0.9004 (tt0) cc_final: 0.8280 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2225
  time to fit residues: 12.5789
Evaluate side-chains
  38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
H  76 ASN
** A 487 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.073714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.057348 restraints weight = 16269.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.058784 restraints weight = 11690.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.059555 restraints weight = 9340.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.5848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2513  Z= 0.263
  Angle     :  0.674   7.210   3415  Z= 0.347
  Chirality :  0.044   0.131    363
  Planarity :  0.004   0.036    444
  Dihedral  :  5.276  22.159    348
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.15 %
    Favored  : 95.47 %
  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: -1.85 (0.45), residues: 310
  helix: -3.75 (0.58), residues: 33
  sheet: -0.40 (0.51), residues: 90
  loop : -1.16 (0.45), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.020   0.002   PHE A 338 
 TYR   0.017   0.002   TYR H  33 
 ARG   0.003   0.001   ARG H  38 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8075 (tmm) cc_final: 0.7567 (tmm)
REVERT: H   36 TRP cc_start: 0.8412 (m100) cc_final: 0.7566 (t-100)
REVERT: H   72 ASP cc_start: 0.8649 (m-30) cc_final: 0.8158 (t0)
REVERT: H   76 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8832 (t0)
REVERT: H   78 LEU cc_start: 0.8118 (tt) cc_final: 0.7644 (tt)
REVERT: H  112 GLN cc_start: 0.7837 (mm-40) cc_final: 0.6780 (pm20)
REVERT: A  355 ARG cc_start: 0.9303 (ttt-90) cc_final: 0.9051 (tpp80)
REVERT: A  392 PHE cc_start: 0.9080 (m-80) cc_final: 0.8753 (m-80)
REVERT: A  454 ARG cc_start: 0.9417 (ttm-80) cc_final: 0.9021 (mmt90)
REVERT: A  461 LEU cc_start: 0.8572 (pt) cc_final: 0.7914 (pp)
REVERT: A  465 GLU cc_start: 0.8965 (tt0) cc_final: 0.8245 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1899
  time to fit residues: 10.4228
Evaluate side-chains
  37 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** 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 = 0.3718 r_free = 0.3718 target = 0.076920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.061891 restraints weight = 16959.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.063824 restraints weight = 15556.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.064807 restraints weight = 10844.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.5947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   2513  Z= 0.197
  Angle     :  0.644   8.266   3415  Z= 0.325
  Chirality :  0.047   0.340    363
  Planarity :  0.003   0.037    444
  Dihedral  :  4.655  20.461    348
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  3.77 %
    Favored  : 95.85 %
  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: -1.70 (0.46), residues: 310
  helix: -3.29 (0.72), residues: 33
  sheet: -0.35 (0.51), residues: 94
  loop : -1.11 (0.47), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 392 
 TYR   0.014   0.001   TYR H  33 
 ARG   0.002   0.000   ARG H  71 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.7938 (mpp-170) cc_final: 0.7428 (mpp-170)
REVERT: H   34 MET cc_start: 0.8089 (tmm) cc_final: 0.7467 (tmm)
REVERT: H   36 TRP cc_start: 0.8244 (m100) cc_final: 0.7436 (t-100)
REVERT: H   76 ASN cc_start: 0.8951 (p0) cc_final: 0.8508 (t0)
REVERT: H   78 LEU cc_start: 0.8338 (tt) cc_final: 0.7903 (tt)
REVERT: H  110 TRP cc_start: 0.8138 (m-90) cc_final: 0.7746 (m-90)
REVERT: H  112 GLN cc_start: 0.7791 (mm-40) cc_final: 0.6839 (pm20)
REVERT: A  392 PHE cc_start: 0.8889 (m-80) cc_final: 0.8636 (m-80)
REVERT: A  402 ILE cc_start: 0.9294 (tp) cc_final: 0.8916 (tp)
REVERT: A  454 ARG cc_start: 0.9403 (ttm-80) cc_final: 0.8993 (mmt90)
REVERT: A  461 LEU cc_start: 0.8627 (pt) cc_final: 0.8018 (pp)
REVERT: A  465 GLU cc_start: 0.9057 (tt0) cc_final: 0.8311 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1996
  time to fit residues: 10.9360
Evaluate side-chains
  40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0470
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.077781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.063101 restraints weight = 17012.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.065224 restraints weight = 14365.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.065894 restraints weight = 10725.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   2513  Z= 0.144
  Angle     :  0.576   7.161   3415  Z= 0.289
  Chirality :  0.043   0.149    363
  Planarity :  0.003   0.033    444
  Dihedral  :  4.457  18.786    348
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.46), residues: 310
  helix: -3.50 (0.66), residues: 33
  sheet: -0.03 (0.54), residues: 83
  loop : -1.33 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 392 
 TYR   0.014   0.001   TYR H  33 
 ARG   0.001   0.000   ARG H  71 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8036 (tmm) cc_final: 0.7326 (tmm)
REVERT: H   36 TRP cc_start: 0.8124 (m100) cc_final: 0.7020 (t-100)
REVERT: H   76 ASN cc_start: 0.9009 (p0) cc_final: 0.8501 (t0)
REVERT: H   78 LEU cc_start: 0.8329 (tt) cc_final: 0.7873 (tt)
REVERT: H   80 LEU cc_start: 0.9151 (tp) cc_final: 0.8901 (tp)
REVERT: H  107 PHE cc_start: 0.7583 (m-80) cc_final: 0.7225 (m-80)
REVERT: H  112 GLN cc_start: 0.7761 (mm-40) cc_final: 0.6733 (pm20)
REVERT: A  392 PHE cc_start: 0.8882 (m-80) cc_final: 0.8671 (m-80)
REVERT: A  402 ILE cc_start: 0.9329 (tp) cc_final: 0.9024 (tp)
REVERT: A  409 GLN cc_start: 0.9590 (mt0) cc_final: 0.9302 (tt0)
REVERT: A  454 ARG cc_start: 0.9376 (ttm-80) cc_final: 0.8961 (mmt90)
REVERT: A  461 LEU cc_start: 0.8605 (pt) cc_final: 0.8024 (pp)
REVERT: A  465 GLU cc_start: 0.9071 (tt0) cc_final: 0.8324 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1809
  time to fit residues: 10.5345
Evaluate side-chains
  40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.073987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.058334 restraints weight = 17664.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.059735 restraints weight = 12840.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.060771 restraints weight = 10233.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.6684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2513  Z= 0.221
  Angle     :  0.633   6.941   3415  Z= 0.320
  Chirality :  0.045   0.149    363
  Planarity :  0.003   0.031    444
  Dihedral  :  5.076  26.778    348
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  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: -1.66 (0.47), residues: 310
  helix: -3.22 (0.71), residues: 33
  sheet:  0.36 (0.61), residues: 73
  loop : -1.35 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.015   0.002   PHE A 338 
 TYR   0.016   0.002   TYR H  33 
 ARG   0.004   0.001   ARG A 355 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8090 (tmm) cc_final: 0.7432 (tmm)
REVERT: H   36 TRP cc_start: 0.8289 (m100) cc_final: 0.7275 (t-100)
REVERT: H   76 ASN cc_start: 0.9155 (p0) cc_final: 0.8577 (t0)
REVERT: H   78 LEU cc_start: 0.8393 (tt) cc_final: 0.7915 (tt)
REVERT: H   80 LEU cc_start: 0.9231 (tp) cc_final: 0.9007 (tp)
REVERT: A  347 PHE cc_start: 0.8308 (m-80) cc_final: 0.7602 (m-10)
REVERT: A  454 ARG cc_start: 0.9426 (ttm-80) cc_final: 0.8932 (mmt90)
REVERT: A  461 LEU cc_start: 0.8615 (pt) cc_final: 0.7870 (pp)
REVERT: A  465 GLU cc_start: 0.8964 (tt0) cc_final: 0.8219 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.2027
  time to fit residues: 9.3806
Evaluate side-chains
  29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0020
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.077293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.062726 restraints weight = 17070.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.064660 restraints weight = 14680.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.065575 restraints weight = 10667.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.6770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   2513  Z= 0.164
  Angle     :  0.682  13.626   3415  Z= 0.339
  Chirality :  0.046   0.207    363
  Planarity :  0.003   0.027    444
  Dihedral  :  4.850  28.009    348
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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: -1.67 (0.47), residues: 310
  helix: -3.18 (0.71), residues: 33
  sheet:  0.24 (0.57), residues: 83
  loop : -1.39 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H 110 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.031   0.002   PHE A 347 
 TYR   0.017   0.001   TYR H  33 
 ARG   0.002   0.000   ARG A 509 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8133 (tmm) cc_final: 0.7554 (tmm)
REVERT: H   36 TRP cc_start: 0.7828 (m100) cc_final: 0.7568 (t-100)
REVERT: H   76 ASN cc_start: 0.9060 (p0) cc_final: 0.8452 (t0)
REVERT: H   78 LEU cc_start: 0.8539 (tt) cc_final: 0.8055 (tt)
REVERT: A  409 GLN cc_start: 0.9605 (mt0) cc_final: 0.9333 (tt0)
REVERT: A  454 ARG cc_start: 0.9380 (ttm-80) cc_final: 0.8880 (mmt90)
REVERT: A  461 LEU cc_start: 0.8534 (pt) cc_final: 0.7779 (pp)
REVERT: A  465 GLU cc_start: 0.8982 (tt0) cc_final: 0.8170 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1762
  time to fit residues: 9.0296
Evaluate side-chains
  35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 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 = 0.3690 r_free = 0.3690 target = 0.074909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.058968 restraints weight = 17316.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.060525 restraints weight = 12430.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.061589 restraints weight = 9849.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.7239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2513  Z= 0.209
  Angle     :  0.677  10.554   3415  Z= 0.340
  Chirality :  0.046   0.163    363
  Planarity :  0.004   0.047    444
  Dihedral  :  5.124  29.256    348
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  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: -1.69 (0.46), residues: 310
  helix: -3.35 (0.67), residues: 33
  sheet:  0.50 (0.60), residues: 73
  loop : -1.42 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 110 
 HIS   0.002   0.002   HIS A 519 
 PHE   0.013   0.001   PHE A 338 
 TYR   0.006   0.001   TYR H  93 
 ARG   0.004   0.001   ARG A 355 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8070 (tmm) cc_final: 0.7457 (tmm)
REVERT: H   36 TRP cc_start: 0.8455 (m100) cc_final: 0.7580 (t-100)
REVERT: H   76 ASN cc_start: 0.9260 (p0) cc_final: 0.8584 (t0)
REVERT: H   78 LEU cc_start: 0.8307 (tt) cc_final: 0.7908 (tt)
REVERT: A  409 GLN cc_start: 0.9633 (mt0) cc_final: 0.9381 (tt0)
REVERT: A  454 ARG cc_start: 0.9358 (ttm-80) cc_final: 0.8902 (mmt90)
REVERT: A  461 LEU cc_start: 0.8571 (pt) cc_final: 0.7717 (pp)
REVERT: A  465 GLU cc_start: 0.8885 (tt0) cc_final: 0.8051 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1739
  time to fit residues: 7.3596
Evaluate side-chains
  29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0470
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0070
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0000
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4102

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

Flipped N/Q/H residues before XYZ refinement:
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.077875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.062723 restraints weight = 17011.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.064372 restraints weight = 12075.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.065516 restraints weight = 9425.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.7162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2513  Z= 0.135
  Angle     :  0.626   9.163   3415  Z= 0.308
  Chirality :  0.044   0.168    363
  Planarity :  0.003   0.027    444
  Dihedral  :  4.509  28.109    348
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.59 (0.46), residues: 310
  helix: -3.23 (0.71), residues: 33
  sheet:  0.37 (0.56), residues: 83
  loop : -1.35 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 110 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.014   0.001   PHE A 429 
 TYR   0.008   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 509 

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8138 (tmm) cc_final: 0.7549 (tmm)
REVERT: H   36 TRP cc_start: 0.8296 (m100) cc_final: 0.7641 (t-100)
REVERT: H   76 ASN cc_start: 0.9163 (p0) cc_final: 0.8596 (t0)
REVERT: H   78 LEU cc_start: 0.8335 (tt) cc_final: 0.7987 (tt)
REVERT: H  112 GLN cc_start: 0.8018 (mm110) cc_final: 0.7030 (pm20)
REVERT: A  402 ILE cc_start: 0.9277 (tp) cc_final: 0.8977 (tp)
REVERT: A  454 ARG cc_start: 0.9366 (ttm-80) cc_final: 0.8976 (tpp80)
REVERT: A  461 LEU cc_start: 0.8632 (pt) cc_final: 0.7828 (pp)
REVERT: A  465 GLU cc_start: 0.9028 (tt0) cc_final: 0.8164 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1843
  time to fit residues: 10.7063
Evaluate side-chains
  34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 17 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 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 = 0.3660 r_free = 0.3660 target = 0.073525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.058183 restraints weight = 17727.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.059696 restraints weight = 12770.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.060731 restraints weight = 10154.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.7670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2513  Z= 0.225
  Angle     :  0.666   8.436   3415  Z= 0.337
  Chirality :  0.045   0.156    363
  Planarity :  0.004   0.037    444
  Dihedral  :  5.032  24.281    348
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -1.52 (0.47), residues: 310
  helix: -3.28 (0.70), residues: 31
  sheet:  0.66 (0.61), residues: 72
  loop : -1.33 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 110 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.013   0.001   PHE A 338 
 TYR   0.009   0.001   TYR A 421 
 ARG   0.005   0.001   ARG A 509 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1435.56 seconds
wall clock time: 26 minutes 10.29 seconds (1570.29 seconds total)