Starting phenix.real_space_refine
on Fri Aug 22 12:56:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c8p_16490/08_2025/8c8p_16490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c8p_16490/08_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_16490/08_2025/8c8p_16490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c8p_16490/08_2025/8c8p_16490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c8p_16490/08_2025/8c8p_16490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c8p_16490/08_2025/8c8p_16490.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.94, per 1000 atoms: 0.38
  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: 0.18
  Conformation dependent library (CDL) restraints added in 91.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.09
  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: 0.34

  Time building geometry restraints manager: 0.25 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:             1.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.700
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.190
-------------------------------------------------------------------------------
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   2518  Z= 0.133
  Angle     :  0.673   9.107   3425  Z= 0.349
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.005   0.000   ARG H  66 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.008   0.001   PHE A 347 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2513)
  covalent geometry    : angle       0.66970 ( 3415)
  SS BOND              : bond        0.00334 (    5)
  SS BOND              : angle       1.37889 (   10)
  hydrogen bonds       : bond        0.27763 (   57)
  hydrogen bonds       : angle      12.54723 (  141)

*********************** 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  : 0.060 
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: 0.1059
  time to fit residues: 9.9092
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  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.079613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.062008 restraints weight = 15395.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.063709 restraints weight = 10925.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.064937 restraints weight = 8553.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.065781 restraints weight = 7177.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.066463 restraints weight = 6310.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   2518  Z= 0.195
  Angle     :  0.684   9.329   3425  Z= 0.358
  Chirality :  0.045   0.150    363
  Planarity :  0.004   0.034    444
  Dihedral  :  4.974  19.679    348
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.17 %
    Favored  : 92.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.45), residues: 310
  helix: -4.14 (0.45), residues: 39
  sheet: -1.11 (0.48), residues: 101
  loop : -0.99 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 509 
 TYR   0.012   0.001   TYR H  93 
 PHE   0.013   0.002   PHE A 338 
 TRP   0.011   0.002   TRP H  36 
 HIS   0.002   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 2513)
  covalent geometry    : angle       0.65782 ( 3415)
  SS BOND              : bond        0.01481 (    5)
  SS BOND              : angle       3.56162 (   10)
  hydrogen bonds       : bond        0.04674 (   57)
  hydrogen bonds       : angle       9.17687 (  141)

*********************** 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
  47 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7826 (tmm) cc_final: 0.6992 (tmm)
REVERT: H   36 TRP cc_start: 0.7775 (m100) cc_final: 0.7259 (t-100)
REVERT: H   76 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8377 (t0)
REVERT: H   78 LEU cc_start: 0.8036 (tt) cc_final: 0.7478 (tt)
REVERT: H  107 PHE cc_start: 0.7977 (m-10) cc_final: 0.6533 (m-80)
REVERT: A  392 PHE cc_start: 0.8703 (m-80) cc_final: 0.8464 (m-10)
REVERT: A  454 ARG cc_start: 0.9351 (ttm-80) cc_final: 0.8796 (mmt180)
REVERT: A  461 LEU cc_start: 0.8543 (pt) cc_final: 0.7873 (pp)
REVERT: A  465 GLU cc_start: 0.8966 (tt0) cc_final: 0.8084 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1170
  time to fit residues: 6.1425
Evaluate side-chains
  35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 10 optimal weight:    0.3980
   chunk 5 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.8788

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.076162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.060295 restraints weight = 16654.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.061823 restraints weight = 11808.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.062845 restraints weight = 9370.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.063612 restraints weight = 7899.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.063980 restraints weight = 7024.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2518  Z= 0.175
  Angle     :  0.643   5.020   3425  Z= 0.335
  Chirality :  0.043   0.137    363
  Planarity :  0.004   0.034    444
  Dihedral  :  4.995  23.577    348
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.45), residues: 310
  helix: -3.97 (0.57), residues: 33
  sheet: -0.78 (0.51), residues: 96
  loop : -1.06 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.014   0.001   TYR H  94 
 PHE   0.016   0.002   PHE A 338 
 TRP   0.004   0.001   TRP H 110 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 2513)
  covalent geometry    : angle       0.63037 ( 3415)
  SS BOND              : bond        0.00877 (    5)
  SS BOND              : angle       2.38917 (   10)
  hydrogen bonds       : bond        0.03685 (   57)
  hydrogen bonds       : angle       8.50852 (  141)

*********************** 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
  49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8067 (tmm) cc_final: 0.7514 (tmm)
REVERT: H   36 TRP cc_start: 0.8326 (m100) cc_final: 0.7213 (t-100)
REVERT: H   76 ASN cc_start: 0.8941 (p0) cc_final: 0.8534 (t0)
REVERT: H   78 LEU cc_start: 0.8121 (tt) cc_final: 0.7614 (tt)
REVERT: A  392 PHE cc_start: 0.8915 (m-80) cc_final: 0.8627 (m-80)
REVERT: A  454 ARG cc_start: 0.9396 (ttm-80) cc_final: 0.9001 (mmt90)
REVERT: A  461 LEU cc_start: 0.8632 (pt) cc_final: 0.8029 (pp)
REVERT: A  465 GLU cc_start: 0.9040 (tt0) cc_final: 0.8254 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0865
  time to fit residues: 4.8076
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  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.076892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.062303 restraints weight = 17311.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.064213 restraints weight = 12320.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.065533 restraints weight = 8901.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.065801 restraints weight = 7611.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.066022 restraints weight = 6953.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2518  Z= 0.109
  Angle     :  0.588   6.541   3425  Z= 0.296
  Chirality :  0.043   0.137    363
  Planarity :  0.003   0.033    444
  Dihedral  :  4.393  20.869    348
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.47), residues: 310
  helix: -3.69 (0.64), residues: 33
  sheet: -0.35 (0.53), residues: 94
  loop : -1.14 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 355 
 TYR   0.009   0.001   TYR H  94 
 PHE   0.010   0.001   PHE A 392 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2513)
  covalent geometry    : angle       0.58108 ( 3415)
  SS BOND              : bond        0.00144 (    5)
  SS BOND              : angle       1.71405 (   10)
  hydrogen bonds       : bond        0.03068 (   57)
  hydrogen bonds       : angle       7.68553 (  141)

*********************** 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
  48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.7919 (mpp-170) cc_final: 0.7269 (mpp-170)
REVERT: H   34 MET cc_start: 0.8122 (tmm) cc_final: 0.7535 (tmm)
REVERT: H   36 TRP cc_start: 0.8098 (m100) cc_final: 0.7230 (t-100)
REVERT: H   76 ASN cc_start: 0.8829 (p0) cc_final: 0.8511 (t0)
REVERT: H   78 LEU cc_start: 0.8079 (tt) cc_final: 0.7662 (tt)
REVERT: H  107 PHE cc_start: 0.6944 (m-80) cc_final: 0.6589 (m-10)
REVERT: A  392 PHE cc_start: 0.8866 (m-80) cc_final: 0.8581 (m-80)
REVERT: A  454 ARG cc_start: 0.9393 (ttm-80) cc_final: 0.9019 (mmt90)
REVERT: A  461 LEU cc_start: 0.8649 (pt) cc_final: 0.8073 (pp)
REVERT: A  465 GLU cc_start: 0.9078 (tt0) cc_final: 0.8244 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1076
  time to fit residues: 5.8267
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  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 26 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.075615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.060210 restraints weight = 16628.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.062586 restraints weight = 11755.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.063622 restraints weight = 8257.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.063926 restraints weight = 6932.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.064235 restraints weight = 6546.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.5918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2518  Z= 0.118
  Angle     :  0.598   6.528   3425  Z= 0.298
  Chirality :  0.043   0.137    363
  Planarity :  0.004   0.045    444
  Dihedral  :  4.472  19.614    348
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.47), residues: 310
  helix: -3.48 (0.68), residues: 33
  sheet: -0.28 (0.52), residues: 93
  loop : -1.02 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 355 
 TYR   0.016   0.001   TYR H  33 
 PHE   0.010   0.001   PHE A 338 
 TRP   0.005   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 2513)
  covalent geometry    : angle       0.58690 ( 3415)
  SS BOND              : bond        0.00193 (    5)
  SS BOND              : angle       2.16654 (   10)
  hydrogen bonds       : bond        0.02960 (   57)
  hydrogen bonds       : angle       7.58946 (  141)

*********************** 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
  49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7965 (tmm) cc_final: 0.7492 (tmm)
REVERT: H   36 TRP cc_start: 0.8105 (m100) cc_final: 0.6971 (t-100)
REVERT: H   76 ASN cc_start: 0.8960 (p0) cc_final: 0.8534 (t0)
REVERT: H   78 LEU cc_start: 0.8177 (tt) cc_final: 0.7823 (tt)
REVERT: H   80 LEU cc_start: 0.9203 (tp) cc_final: 0.8975 (tp)
REVERT: H  112 GLN cc_start: 0.7768 (mm-40) cc_final: 0.6666 (pm20)
REVERT: A  392 PHE cc_start: 0.8881 (m-80) cc_final: 0.8641 (m-80)
REVERT: A  402 ILE cc_start: 0.9354 (tp) cc_final: 0.8996 (tp)
REVERT: A  454 ARG cc_start: 0.9402 (ttm-80) cc_final: 0.9011 (mmt90)
REVERT: A  461 LEU cc_start: 0.8659 (pt) cc_final: 0.8045 (pp)
REVERT: A  465 GLU cc_start: 0.9069 (tt0) cc_final: 0.8298 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0824
  time to fit residues: 4.6842
Evaluate side-chains
  37 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.075553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.060680 restraints weight = 16599.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.062172 restraints weight = 15108.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.063727 restraints weight = 10906.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.064267 restraints weight = 8059.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.064659 restraints weight = 7364.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.6233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2518  Z= 0.118
  Angle     :  0.616   7.183   3425  Z= 0.306
  Chirality :  0.043   0.135    363
  Planarity :  0.003   0.031    444
  Dihedral  :  4.607  25.107    348
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.47), residues: 310
  helix: -3.34 (0.72), residues: 33
  sheet:  0.22 (0.55), residues: 82
  loop : -1.34 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 355 
 TYR   0.015   0.001   TYR H  33 
 PHE   0.010   0.001   PHE A 392 
 TRP   0.005   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2513)
  covalent geometry    : angle       0.60234 ( 3415)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       2.49186 (   10)
  hydrogen bonds       : bond        0.03342 (   57)
  hydrogen bonds       : angle       7.50887 (  141)

*********************** 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
  49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7943 (tmm) cc_final: 0.7314 (tmm)
REVERT: H   36 TRP cc_start: 0.7995 (m100) cc_final: 0.6946 (t-100)
REVERT: H   76 ASN cc_start: 0.8978 (p0) cc_final: 0.8567 (t0)
REVERT: H   78 LEU cc_start: 0.8231 (tt) cc_final: 0.7801 (tt)
REVERT: H   80 LEU cc_start: 0.9237 (tp) cc_final: 0.9013 (tp)
REVERT: H  112 GLN cc_start: 0.7929 (mm-40) cc_final: 0.6935 (pm20)
REVERT: A  392 PHE cc_start: 0.8911 (m-80) cc_final: 0.8631 (m-80)
REVERT: A  454 ARG cc_start: 0.9378 (ttm-80) cc_final: 0.9011 (mmt90)
REVERT: A  461 LEU cc_start: 0.8570 (pt) cc_final: 0.7961 (pp)
REVERT: A  465 GLU cc_start: 0.9055 (tt0) cc_final: 0.8296 (tm-30)
REVERT: A  513 LEU cc_start: 0.9476 (mp) cc_final: 0.9186 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0824
  time to fit residues: 4.6953
Evaluate side-chains
  37 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0980
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0470
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.5082

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.079073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.062501 restraints weight = 16173.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.064079 restraints weight = 11600.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.065186 restraints weight = 9258.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.065992 restraints weight = 7800.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.066419 restraints weight = 6864.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.6309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   2518  Z= 0.106
  Angle     :  0.672  13.468   3425  Z= 0.333
  Chirality :  0.046   0.272    363
  Planarity :  0.003   0.028    444
  Dihedral  :  4.448  24.754    348
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.47), residues: 310
  helix: -3.34 (0.70), residues: 33
  sheet:  0.11 (0.57), residues: 83
  loop : -1.30 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.017   0.001   TYR H  33 
 PHE   0.020   0.001   PHE A 429 
 TRP   0.017   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 2513)
  covalent geometry    : angle       0.65988 ( 3415)
  SS BOND              : bond        0.00949 (    5)
  SS BOND              : angle       2.41356 (   10)
  hydrogen bonds       : bond        0.03299 (   57)
  hydrogen bonds       : angle       7.27172 (  141)

*********************** 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
  45 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7923 (tmm) cc_final: 0.7189 (tmm)
REVERT: H   36 TRP cc_start: 0.7934 (m100) cc_final: 0.7302 (t-100)
REVERT: H   76 ASN cc_start: 0.8938 (p0) cc_final: 0.8469 (t0)
REVERT: H   78 LEU cc_start: 0.8317 (tt) cc_final: 0.7846 (tt)
REVERT: H  112 GLN cc_start: 0.7959 (mm-40) cc_final: 0.6846 (pm20)
REVERT: A  392 PHE cc_start: 0.8800 (m-80) cc_final: 0.8576 (m-80)
REVERT: A  402 ILE cc_start: 0.9381 (tp) cc_final: 0.9077 (tp)
REVERT: A  454 ARG cc_start: 0.9411 (ttm-80) cc_final: 0.9003 (mmt90)
REVERT: A  461 LEU cc_start: 0.8637 (pt) cc_final: 0.7978 (pp)
REVERT: A  465 GLU cc_start: 0.9089 (tt0) cc_final: 0.8253 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0871
  time to fit residues: 4.5159
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  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.076797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.061591 restraints weight = 17177.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.064004 restraints weight = 12568.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.065581 restraints weight = 8631.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.065794 restraints weight = 6684.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.065888 restraints weight = 6481.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.6655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   2518  Z= 0.113
  Angle     :  0.635  10.177   3425  Z= 0.319
  Chirality :  0.044   0.175    363
  Planarity :  0.003   0.028    444
  Dihedral  :  4.682  25.148    348
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.47), residues: 310
  helix: -3.29 (0.69), residues: 33
  sheet:  0.63 (0.62), residues: 72
  loop : -1.36 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.009   0.001   TYR H  94 
 PHE   0.018   0.001   PHE A 429 
 TRP   0.011   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2513)
  covalent geometry    : angle       0.62513 ( 3415)
  SS BOND              : bond        0.00814 (    5)
  SS BOND              : angle       2.17094 (   10)
  hydrogen bonds       : bond        0.02976 (   57)
  hydrogen bonds       : angle       7.08690 (  141)

*********************** 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
  45 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7941 (tmm) cc_final: 0.7226 (tmm)
REVERT: H   36 TRP cc_start: 0.7966 (m100) cc_final: 0.7049 (t-100)
REVERT: H   76 ASN cc_start: 0.9123 (p0) cc_final: 0.8617 (t0)
REVERT: H   78 LEU cc_start: 0.8300 (tt) cc_final: 0.7961 (tt)
REVERT: H  112 GLN cc_start: 0.8001 (mm-40) cc_final: 0.6872 (pm20)
REVERT: A  392 PHE cc_start: 0.8868 (m-80) cc_final: 0.8638 (m-80)
REVERT: A  454 ARG cc_start: 0.9388 (ttm-80) cc_final: 0.8994 (mmt90)
REVERT: A  461 LEU cc_start: 0.8673 (pt) cc_final: 0.8030 (pp)
REVERT: A  465 GLU cc_start: 0.9094 (tt0) cc_final: 0.8278 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0844
  time to fit residues: 4.4111
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  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.0870
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.077508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.062228 restraints weight = 17859.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.063856 restraints weight = 12584.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.064959 restraints weight = 9797.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.065524 restraints weight = 8187.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.066308 restraints weight = 7182.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.6855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   2518  Z= 0.097
  Angle     :  0.616   9.167   3425  Z= 0.304
  Chirality :  0.043   0.164    363
  Planarity :  0.003   0.028    444
  Dihedral  :  4.315  21.957    348
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.47), residues: 310
  helix: -3.20 (0.75), residues: 31
  sheet:  0.40 (0.58), residues: 82
  loop : -1.28 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.013   0.001   TYR H  33 
 PHE   0.015   0.001   PHE A 429 
 TRP   0.010   0.001   TRP H  36 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 2513)
  covalent geometry    : angle       0.60759 ( 3415)
  SS BOND              : bond        0.00787 (    5)
  SS BOND              : angle       2.01119 (   10)
  hydrogen bonds       : bond        0.02853 (   57)
  hydrogen bonds       : angle       6.83613 (  141)

*********************** 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
  44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7969 (tmm) cc_final: 0.7315 (tmm)
REVERT: H   36 TRP cc_start: 0.7943 (m100) cc_final: 0.7037 (t-100)
REVERT: H   76 ASN cc_start: 0.9147 (p0) cc_final: 0.8590 (t0)
REVERT: H   78 LEU cc_start: 0.8312 (tt) cc_final: 0.7996 (tt)
REVERT: H  112 GLN cc_start: 0.7775 (mm-40) cc_final: 0.6929 (pm20)
REVERT: A  454 ARG cc_start: 0.9382 (ttm-80) cc_final: 0.8978 (mmt90)
REVERT: A  461 LEU cc_start: 0.8791 (pt) cc_final: 0.8211 (pp)
REVERT: A  465 GLU cc_start: 0.9169 (tt0) cc_final: 0.8361 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0909
  time to fit residues: 4.6111
Evaluate side-chains
  32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 2 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.075986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.061558 restraints weight = 18243.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.063597 restraints weight = 16361.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.065068 restraints weight = 11082.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.065688 restraints weight = 8219.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.066059 restraints weight = 7389.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.7181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2518  Z= 0.111
  Angle     :  0.626   8.529   3425  Z= 0.312
  Chirality :  0.043   0.160    363
  Planarity :  0.003   0.028    444
  Dihedral  :  4.522  22.996    348
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.47), residues: 310
  helix: -3.38 (0.68), residues: 33
  sheet:  0.64 (0.65), residues: 72
  loop : -1.33 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 355 
 TYR   0.008   0.001   TYR H  94 
 PHE   0.014   0.001   PHE H 101 
 TRP   0.007   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2513)
  covalent geometry    : angle       0.61709 ( 3415)
  SS BOND              : bond        0.00761 (    5)
  SS BOND              : angle       2.09075 (   10)
  hydrogen bonds       : bond        0.02897 (   57)
  hydrogen bonds       : angle       6.79539 (  141)

********************** 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
  44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7991 (tmm) cc_final: 0.7380 (tmm)
REVERT: H   36 TRP cc_start: 0.7985 (m100) cc_final: 0.7135 (t-100)
REVERT: H   76 ASN cc_start: 0.9099 (p0) cc_final: 0.8494 (t0)
REVERT: H   78 LEU cc_start: 0.8404 (tt) cc_final: 0.8070 (tt)
REVERT: H  112 GLN cc_start: 0.7978 (mm-40) cc_final: 0.6952 (pm20)
REVERT: A  454 ARG cc_start: 0.9415 (ttm-80) cc_final: 0.9066 (tpp80)
REVERT: A  461 LEU cc_start: 0.8777 (pt) cc_final: 0.8135 (pp)
REVERT: A  465 GLU cc_start: 0.9095 (tt0) cc_final: 0.8357 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0871
  time to fit residues: 4.4260
Evaluate side-chains
  28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.074183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.059128 restraints weight = 17433.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.061860 restraints weight = 12243.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.062797 restraints weight = 8367.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.063246 restraints weight = 7417.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.063750 restraints weight = 6419.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.7540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2518  Z= 0.132
  Angle     :  0.640   7.985   3425  Z= 0.322
  Chirality :  0.043   0.152    363
  Planarity :  0.003   0.027    444
  Dihedral  :  4.845  23.976    348
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.48), residues: 310
  helix: -3.33 (0.74), residues: 31
  sheet:  0.73 (0.65), residues: 72
  loop : -1.27 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 355 
 TYR   0.009   0.001   TYR H  94 
 PHE   0.014   0.002   PHE A 347 
 TRP   0.009   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 2513)
  covalent geometry    : angle       0.62739 ( 3415)
  SS BOND              : bond        0.00761 (    5)
  SS BOND              : angle       2.43108 (   10)
  hydrogen bonds       : bond        0.02975 (   57)
  hydrogen bonds       : angle       7.00521 (  141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.72 seconds
wall clock time: 16 minutes 27.66 seconds (987.66 seconds total)