Starting phenix.real_space_refine
on Wed Sep 17 04:13:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z86_39839/09_2025/8z86_39839.cif"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 820 atoms to isotropic.
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      16      5.16       5
     C    2043      2.51       5
     N     552      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3219
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1540
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 12, 'TRANS': 180}
    Chain: "H"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 863
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100}
  Time building chain proxies: 1.17, per 1000 atoms: 0.36
  Number of scatterers: 3219
  At special positions: 0
  Unit cell: (67.6, 75.92, 86.32, 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      16     16.00
     O     608      8.00
     N     552      7.00
     C    2043      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 359 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 377 " - pdb=" SG  CYS A 430 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 523 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 478 " - pdb=" SG  CYS A 486 " distance=2.01
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04

  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: 0.30
  Conformation dependent library (CDL) restraints added in 163.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.7% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 4.118A  pdb=" N   TYR A 367 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.523A  pdb=" N   VAL A 405 " --> pdb=" O   GLY A 402 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   SER A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A 407 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE A 408 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA A 409 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.059A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 355
      removed outlier: 3.830A  pdb=" N   VAL A 510 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 508 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 511 " --> pdb=" O   CYS A 430 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 450 through 451
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.583A  pdb=" N   GLN H 110 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 22
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
      removed outlier: 4.062A  pdb=" N   SER L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.596A  pdb=" N   LEU L  11 " --> pdb=" O   ARG L 104 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 34 through 39

    60 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: 0.43

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 521
        1.32 -     1.44: 983
        1.44 -     1.57: 1775
        1.57 -     1.70: 2
        1.70 -     1.82: 20
  Bond restraints: 3301
  Sorted by residual:
  bond pdb=" C   PHE A 488 "
       pdb=" O   PHE A 488 "
    ideal  model  delta    sigma   weight residual
    1.238  1.191  0.046 1.28e-02 6.10e+03 1.31e+01
  bond pdb=" N   CYS A 486 "
       pdb=" CA  CYS A 486 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.18e-02 7.18e+03 9.23e+00
  bond pdb=" CA  ALA A 482 "
       pdb=" CB  ALA A 482 "
    ideal  model  delta    sigma   weight residual
    1.530  1.481  0.050 1.69e-02 3.50e+03 8.59e+00
  bond pdb=" N   VAL A 484 "
       pdb=" CA  VAL A 484 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.19e-02 7.06e+03 7.80e+00
  bond pdb=" CB  PRO H  87 "
       pdb=" CG  PRO H  87 "
    ideal  model  delta    sigma   weight residual
    1.492  1.624 -0.132 5.00e-02 4.00e+02 6.94e+00
  ... (remaining 3296 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.79: 4454
        4.79 -     9.59: 27
        9.59 -    14.38: 5
       14.38 -    19.18: 0
       19.18 -    23.97: 1
  Bond angle restraints: 4487
  Sorted by residual:
  angle pdb=" N   TYR A 487 "
        pdb=" CA  TYR A 487 "
        pdb=" CB  TYR A 487 "
      ideal   model   delta    sigma   weight residual
     111.53   87.56   23.97 1.86e+00 2.89e-01 1.66e+02
  angle pdb=" CA  PRO H  87 "
        pdb=" N   PRO H  87 "
        pdb=" CD  PRO H  87 "
      ideal   model   delta    sigma   weight residual
     112.00   98.92   13.08 1.40e+00 5.10e-01 8.73e+01
  angle pdb=" CA  PRO H  14 "
        pdb=" N   PRO H  14 "
        pdb=" CD  PRO H  14 "
      ideal   model   delta    sigma   weight residual
     112.00  101.96   10.04 1.40e+00 5.10e-01 5.14e+01
  angle pdb=" CA  TYR A 487 "
        pdb=" C   TYR A 487 "
        pdb=" O   TYR A 487 "
      ideal   model   delta    sigma   weight residual
     121.06  113.59    7.47 1.16e+00 7.43e-01 4.15e+01
  angle pdb=" C   ASN A 485 "
        pdb=" CA  ASN A 485 "
        pdb=" CB  ASN A 485 "
      ideal   model   delta    sigma   weight residual
     111.73  119.41   -7.68 1.42e+00 4.96e-01 2.93e+01
  ... (remaining 4482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 1589
       15.91 -    31.83: 253
       31.83 -    47.74: 74
       47.74 -    63.65: 24
       63.65 -    79.57: 2
  Dihedral angle restraints: 1942
    sinusoidal: 752
      harmonic: 1190
  Sorted by residual:
  dihedral pdb=" N   TYR A 487 "
           pdb=" C   TYR A 487 "
           pdb=" CA  TYR A 487 "
           pdb=" CB  TYR A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   96.12   26.68     0      2.50e+00 1.60e-01 1.14e+02
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  95 "
           pdb=" CB  CYS H  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.76   51.24     1      1.00e+01 1.00e-02 3.59e+01
  dihedral pdb=" CA  PHE A 398 "
           pdb=" C   PHE A 398 "
           pdb=" N   VAL A 399 "
           pdb=" CA  VAL A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.10   29.90     0      5.00e+00 4.00e-02 3.58e+01
  ... (remaining 1939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 364
       0.056 -    0.112: 91
       0.112 -    0.168: 17
       0.168 -    0.224: 3
       0.224 -    0.280: 3
  Chirality restraints: 478
  Sorted by residual:
  chirality pdb=" CA  TYR A 487 "
            pdb=" N   TYR A 487 "
            pdb=" C   TYR A 487 "
            pdb=" CB  TYR A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  PRO H  14 "
            pdb=" N   PRO H  14 "
            pdb=" C   PRO H  14 "
            pdb=" CB  PRO H  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  PRO H  87 "
            pdb=" N   PRO H  87 "
            pdb=" C   PRO H  87 "
            pdb=" CB  PRO H  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 475 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "    0.029 2.00e-02 2.50e+03   2.99e-02 2.24e+01
        pdb=" CG  TRP H  47 "   -0.076 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "   -0.079 5.00e-02 4.00e+02   1.13e-01 2.04e+01
        pdb=" N   PRO H  14 "    0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 481 "    0.023 2.00e-02 2.50e+03   4.48e-02 2.01e+01
        pdb=" C   VAL A 481 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   VAL A 481 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ALA A 482 "    0.026 2.00e-02 2.50e+03
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1001
        2.82 -     3.34: 2605
        3.34 -     3.86: 5032
        3.86 -     4.38: 5474
        4.38 -     4.90: 9748
  Nonbonded interactions: 23860
  Sorted by model distance:
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG  SER H  21 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" N   ASP H  61 "
            pdb=" OD1 ASP H  61 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" NH2 ARG A 401 "
            pdb=" OE2 GLU A 404 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OG  SER A 467 "
            pdb=" OE1 GLU A 469 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" NE  ARG A 452 "
            pdb=" OD2 ASP A 465 "
     model   vdw
     2.371 3.120
  ... (remaining 23855 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.730
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.132   3307  Z= 0.238
  Angle     :  1.064  23.974   4499  Z= 0.582
  Chirality :  0.055   0.280    478
  Planarity :  0.009   0.113    586
  Dihedral  : 17.269  79.565   1172
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.33 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 35.07 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.85 (0.39), residues: 409
  helix: -3.62 (0.89), residues: 15
  sheet: -1.33 (0.49), residues: 127
  loop : -2.18 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  24 
 TYR   0.019   0.002   TYR L  37 
 PHE   0.023   0.002   PHE L  72 
 TRP   0.076   0.005   TRP H  47 
 HIS   0.001   0.001   HIS A 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 3301)
  covalent geometry    : angle       1.05648 ( 4487)
  SS BOND              : bond        0.00807 (    6)
  SS BOND              : angle       2.62605 (   12)
  hydrogen bonds       : bond        0.28400 (   60)
  hydrogen bonds       : angle      11.62370 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.100 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 74
  average time/residue: 0.0620
  time to fit residues: 5.7183
Evaluate side-chains
  72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain H residue   39 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0010
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0010
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.2192

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

Flipped N/Q/H residues before XYZ refinement:
A 485 ASN
H   6 GLN
H  39 GLN
H  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.179660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.156484 restraints weight = 4401.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.158703 restraints weight = 3456.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159913 restraints weight = 2882.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.161284 restraints weight = 2573.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.161753 restraints weight = 2359.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   3307  Z= 0.100
  Angle     :  0.596   7.355   4499  Z= 0.304
  Chirality :  0.042   0.130    478
  Planarity :  0.005   0.055    586
  Dihedral  :  4.919  23.924    466
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 31.88 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.62 (0.40), residues: 409
  helix: -3.62 (1.09), residues: 15
  sheet: -1.23 (0.49), residues: 133
  loop : -1.97 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  19 
 TYR   0.012   0.001   TYR L  37 
 PHE   0.009   0.001   PHE A 398 
 TRP   0.030   0.002   TRP H  47 
 HIS   0.000   0.000   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3301)
  covalent geometry    : angle       0.59418 ( 4487)
  SS BOND              : bond        0.00482 (    6)
  SS BOND              : angle       1.16219 (   12)
  hydrogen bonds       : bond        0.03693 (   60)
  hydrogen bonds       : angle       7.24951 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7030 (pp)
REVERT: A  516 LEU cc_start: 0.7879 (mt) cc_final: 0.7643 (mt)
REVERT: H   92 MET cc_start: 0.7896 (ttm) cc_final: 0.7597 (ttm)
  outliers start: 13
  outliers final: 4
  residues processed: 84
  average time/residue: 0.0628
  time to fit residues: 6.4617
Evaluate side-chains
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 475 ASN
H   6 GLN
H  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.172476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147594 restraints weight = 4405.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149475 restraints weight = 3542.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151055 restraints weight = 3046.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151761 restraints weight = 2731.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152433 restraints weight = 2553.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3307  Z= 0.172
  Angle     :  0.643   9.456   4499  Z= 0.323
  Chirality :  0.043   0.148    478
  Planarity :  0.004   0.041    586
  Dihedral  :  5.051  29.009    463
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 30.43 %
    Favored  : 62.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.54 (0.41), residues: 409
  helix: -3.61 (1.08), residues: 15
  sheet: -1.09 (0.49), residues: 132
  loop : -1.97 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.012   0.001   TYR L  37 
 PHE   0.010   0.002   PHE A 340 
 TRP   0.032   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3301)
  covalent geometry    : angle       0.64107 ( 4487)
  SS BOND              : bond        0.00569 (    6)
  SS BOND              : angle       1.10184 (   12)
  hydrogen bonds       : bond        0.03911 (   60)
  hydrogen bonds       : angle       6.57353 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7315 (pp)
REVERT: H   47 TRP cc_start: 0.8160 (t60) cc_final: 0.7934 (t60)
REVERT: H   92 MET cc_start: 0.7871 (ttm) cc_final: 0.7602 (ttm)
REVERT: L   37 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6620 (p90)
REVERT: L   50 TYR cc_start: 0.8021 (p90) cc_final: 0.7712 (p90)
  outliers start: 23
  outliers final: 17
  residues processed: 84
  average time/residue: 0.0647
  time to fit residues: 6.6779
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0370
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9260

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.159022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128864 restraints weight = 4401.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.132132 restraints weight = 3069.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134261 restraints weight = 2422.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135915 restraints weight = 2071.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136625 restraints weight = 1859.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3307  Z= 0.169
  Angle     :  0.642   9.361   4499  Z= 0.325
  Chirality :  0.043   0.135    478
  Planarity :  0.004   0.036    586
  Dihedral  :  5.058  35.104    463
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 28.99 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.53 (0.40), residues: 409
  helix: -3.73 (0.98), residues: 15
  sheet: -1.02 (0.49), residues: 131
  loop : -1.99 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  38 
 TYR   0.011   0.001   TYR L  37 
 PHE   0.011   0.002   PHE A 390 
 TRP   0.022   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3301)
  covalent geometry    : angle       0.64067 ( 4487)
  SS BOND              : bond        0.00498 (    6)
  SS BOND              : angle       1.08493 (   12)
  hydrogen bonds       : bond        0.03498 (   60)
  hydrogen bonds       : angle       6.32536 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7837 (p0) cc_final: 0.7378 (p0)
REVERT: A  466 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7272 (pp)
REVERT: H   47 TRP cc_start: 0.8346 (t60) cc_final: 0.7978 (t60)
REVERT: H   92 MET cc_start: 0.7946 (ttm) cc_final: 0.7648 (ttm)
REVERT: L   37 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6603 (p90)
REVERT: L   50 TYR cc_start: 0.8087 (p90) cc_final: 0.7782 (p90)
  outliers start: 25
  outliers final: 19
  residues processed: 85
  average time/residue: 0.0537
  time to fit residues: 5.7950
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.150464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.118824 restraints weight = 4540.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.121936 restraints weight = 3218.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123848 restraints weight = 2587.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.125546 restraints weight = 2244.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126215 restraints weight = 2022.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   3307  Z= 0.194
  Angle     :  0.677   9.898   4499  Z= 0.340
  Chirality :  0.043   0.129    478
  Planarity :  0.004   0.034    586
  Dihedral  :  5.302  42.474    463
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  7.54 %
    Allowed  : 28.12 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.60 (0.40), residues: 409
  helix: -3.90 (0.86), residues: 15
  sheet: -1.36 (0.46), residues: 141
  loop : -1.84 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  19 
 TYR   0.012   0.001   TYR L  37 
 PHE   0.011   0.002   PHE A 390 
 TRP   0.018   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 3301)
  covalent geometry    : angle       0.67544 ( 4487)
  SS BOND              : bond        0.00504 (    6)
  SS BOND              : angle       1.21590 (   12)
  hydrogen bonds       : bond        0.03575 (   60)
  hydrogen bonds       : angle       6.31463 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  398 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8313 (m-80)
REVERT: A  426 ASP cc_start: 0.7885 (p0) cc_final: 0.7469 (p0)
REVERT: A  466 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7288 (pp)
REVERT: H   47 TRP cc_start: 0.8480 (t60) cc_final: 0.8095 (t60)
REVERT: H   92 MET cc_start: 0.7917 (ttm) cc_final: 0.7601 (ttm)
REVERT: L   37 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6549 (p90)
REVERT: L   50 TYR cc_start: 0.8224 (p90) cc_final: 0.7868 (p90)
REVERT: L   99 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 94
  average time/residue: 0.0535
  time to fit residues: 6.3989
Evaluate side-chains
  91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.151087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.124218 restraints weight = 4668.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.122531 restraints weight = 4276.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.123356 restraints weight = 4763.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.123856 restraints weight = 3933.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.124070 restraints weight = 3666.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3307  Z= 0.193
  Angle     :  0.687   9.596   4499  Z= 0.346
  Chirality :  0.043   0.128    478
  Planarity :  0.004   0.033    586
  Dihedral  :  5.389  44.742    463
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  7.83 %
    Allowed  : 28.12 %
    Favored  : 64.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.59 (0.40), residues: 409
  helix: -3.92 (0.83), residues: 15
  sheet: -1.22 (0.48), residues: 132
  loop : -1.92 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.015   0.001   TYR A 506 
 PHE   0.015   0.002   PHE A 369 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 3301)
  covalent geometry    : angle       0.68331 ( 4487)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       1.53834 (   12)
  hydrogen bonds       : bond        0.03587 (   60)
  hydrogen bonds       : angle       6.24006 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7744 (p0) cc_final: 0.7341 (p0)
REVERT: A  466 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7291 (pp)
REVERT: H    6 GLN cc_start: 0.8357 (pt0) cc_final: 0.8117 (pt0)
REVERT: H   22 CYS cc_start: 0.7005 (t) cc_final: 0.6778 (t)
REVERT: H   47 TRP cc_start: 0.8468 (t60) cc_final: 0.8119 (t60)
REVERT: H   92 MET cc_start: 0.7860 (ttm) cc_final: 0.7582 (ttm)
REVERT: L   50 TYR cc_start: 0.8165 (p90) cc_final: 0.7843 (p90)
REVERT: L   99 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8244 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 90
  average time/residue: 0.0509
  time to fit residues: 5.9839
Evaluate side-chains
  93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0070
   overall best weight:    0.6214

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.153912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.127179 restraints weight = 4701.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.125699 restraints weight = 4266.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126158 restraints weight = 4637.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.126691 restraints weight = 4013.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.126922 restraints weight = 3696.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3307  Z= 0.139
  Angle     :  0.663   9.431   4499  Z= 0.329
  Chirality :  0.043   0.123    478
  Planarity :  0.004   0.033    586
  Dihedral  :  5.104  40.505    463
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 29.86 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.44 (0.40), residues: 409
  helix: -3.90 (0.82), residues: 15
  sheet: -1.03 (0.50), residues: 125
  loop : -1.86 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.014   0.001   TYR A 506 
 PHE   0.008   0.001   PHE A 345 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3301)
  covalent geometry    : angle       0.65589 ( 4487)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       1.99832 (   12)
  hydrogen bonds       : bond        0.03126 (   60)
  hydrogen bonds       : angle       6.04200 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7554 (p0) cc_final: 0.7139 (p0)
REVERT: A  466 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7163 (pp)
REVERT: H   22 CYS cc_start: 0.6950 (t) cc_final: 0.6716 (t)
REVERT: H   47 TRP cc_start: 0.8394 (t60) cc_final: 0.8151 (t60)
REVERT: H   92 MET cc_start: 0.7807 (ttm) cc_final: 0.7547 (ttm)
REVERT: L   50 TYR cc_start: 0.8059 (p90) cc_final: 0.7799 (p90)
REVERT: L   99 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (t80)
  outliers start: 24
  outliers final: 22
  residues processed: 92
  average time/residue: 0.0531
  time to fit residues: 6.2801
Evaluate side-chains
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.153138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125589 restraints weight = 4719.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.124096 restraints weight = 4136.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.124952 restraints weight = 4529.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.125591 restraints weight = 3857.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.126161 restraints weight = 3454.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3307  Z= 0.148
  Angle     :  0.681  10.870   4499  Z= 0.336
  Chirality :  0.043   0.121    478
  Planarity :  0.004   0.033    586
  Dihedral  :  5.132  41.642    463
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 30.14 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.40 (0.40), residues: 409
  helix: -3.96 (0.77), residues: 15
  sheet: -1.01 (0.50), residues: 125
  loop : -1.82 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  19 
 TYR   0.013   0.001   TYR A 506 
 PHE   0.013   0.002   PHE A 369 
 TRP   0.012   0.002   TRP L  97 
 HIS   0.001   0.001   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3301)
  covalent geometry    : angle       0.67248 ( 4487)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       2.12723 (   12)
  hydrogen bonds       : bond        0.03202 (   60)
  hydrogen bonds       : angle       5.93999 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7600 (p0) cc_final: 0.7186 (p0)
REVERT: A  466 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7123 (pp)
REVERT: H   22 CYS cc_start: 0.7009 (t) cc_final: 0.6789 (t)
REVERT: H   47 TRP cc_start: 0.8421 (t60) cc_final: 0.8106 (t60)
REVERT: H   92 MET cc_start: 0.7848 (ttm) cc_final: 0.7584 (ttm)
REVERT: L   37 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6707 (p90)
REVERT: L   50 TYR cc_start: 0.8091 (p90) cc_final: 0.7805 (p90)
REVERT: L   99 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8227 (t80)
  outliers start: 23
  outliers final: 20
  residues processed: 85
  average time/residue: 0.0551
  time to fit residues: 5.9392
Evaluate side-chains
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.153273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.127027 restraints weight = 4658.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.125473 restraints weight = 4378.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.125923 restraints weight = 4856.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.126288 restraints weight = 4146.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.126755 restraints weight = 3861.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3307  Z= 0.133
  Angle     :  0.668  11.054   4499  Z= 0.330
  Chirality :  0.042   0.121    478
  Planarity :  0.003   0.032    586
  Dihedral  :  4.975  38.598    463
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 29.57 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.32 (0.40), residues: 409
  helix: -4.00 (0.73), residues: 15
  sheet: -0.92 (0.50), residues: 125
  loop : -1.78 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  19 
 TYR   0.013   0.001   TYR A 506 
 PHE   0.007   0.001   PHE L  72 
 TRP   0.010   0.001   TRP L  97 
 HIS   0.002   0.001   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3301)
  covalent geometry    : angle       0.66051 ( 4487)
  SS BOND              : bond        0.00412 (    6)
  SS BOND              : angle       2.06541 (   12)
  hydrogen bonds       : bond        0.03012 (   60)
  hydrogen bonds       : angle       5.83335 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7055 (pp)
REVERT: H   22 CYS cc_start: 0.6888 (t) cc_final: 0.6637 (t)
REVERT: H   47 TRP cc_start: 0.8389 (t60) cc_final: 0.8105 (t60)
REVERT: H   92 MET cc_start: 0.7869 (ttm) cc_final: 0.7586 (ttm)
REVERT: L   37 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6673 (p90)
REVERT: L   50 TYR cc_start: 0.8061 (p90) cc_final: 0.7796 (p90)
REVERT: L   99 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (t80)
  outliers start: 25
  outliers final: 21
  residues processed: 90
  average time/residue: 0.0522
  time to fit residues: 6.0053
Evaluate side-chains
  92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0770
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.153720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.127457 restraints weight = 4649.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125922 restraints weight = 4219.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.126122 restraints weight = 4585.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.127919 restraints weight = 4026.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.127911 restraints weight = 3517.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3307  Z= 0.141
  Angle     :  0.681  11.191   4499  Z= 0.337
  Chirality :  0.043   0.125    478
  Planarity :  0.004   0.031    586
  Dihedral  :  4.982  38.957    463
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 30.14 %
    Favored  : 62.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.29 (0.40), residues: 409
  helix: -4.11 (0.65), residues: 15
  sheet: -0.90 (0.50), residues: 125
  loop : -1.74 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 401 
 TYR   0.013   0.001   TYR A 506 
 PHE   0.013   0.002   PHE A 390 
 TRP   0.012   0.001   TRP L  97 
 HIS   0.001   0.000   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3301)
  covalent geometry    : angle       0.67350 ( 4487)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       2.04494 (   12)
  hydrogen bonds       : bond        0.03095 (   60)
  hydrogen bonds       : angle       5.83617 (  141)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7020 (pp)
REVERT: H   22 CYS cc_start: 0.6902 (t) cc_final: 0.6653 (t)
REVERT: H   47 TRP cc_start: 0.8391 (t60) cc_final: 0.8087 (t60)
REVERT: H   92 MET cc_start: 0.7854 (ttm) cc_final: 0.7569 (ttm)
REVERT: L   37 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6708 (p90)
REVERT: L   50 TYR cc_start: 0.8070 (p90) cc_final: 0.7792 (p90)
REVERT: L   99 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8198 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 87
  average time/residue: 0.0557
  time to fit residues: 6.2027
Evaluate side-chains
  91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   99 PHE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0020
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0570
   chunk 36 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.3304

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.158466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.132179 restraints weight = 4750.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130984 restraints weight = 3880.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.131515 restraints weight = 4253.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.132064 restraints weight = 3645.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.132351 restraints weight = 3383.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3307  Z= 0.112
  Angle     :  0.663  11.309   4499  Z= 0.326
  Chirality :  0.042   0.122    478
  Planarity :  0.004   0.029    586
  Dihedral  :  4.727  30.729    463
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 30.72 %
    Favored  : 62.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.14 (0.40), residues: 409
  helix: -4.07 (0.68), residues: 15
  sheet: -0.81 (0.49), residues: 125
  loop : -1.63 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  19 
 TYR   0.010   0.001   TYR A 506 
 PHE   0.007   0.001   PHE L  72 
 TRP   0.008   0.001   TRP L  97 
 HIS   0.001   0.000   HIS A 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3301)
  covalent geometry    : angle       0.65571 ( 4487)
  SS BOND              : bond        0.00363 (    6)
  SS BOND              : angle       2.06266 (   12)
  hydrogen bonds       : bond        0.02801 (   60)
  hydrogen bonds       : angle       5.61544 (  141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 835.97 seconds
wall clock time: 15 minutes 7.79 seconds (907.79 seconds total)