Starting phenix.real_space_refine
on Tue Mar  3 12:14:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2026/7fij_31599.map"
  }
  resolution = 3.8
  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=   0.001 sd=   0.021
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 1212 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       4      5.16       5
     C    1865      2.51       5
     N     594      2.21       5
     O     598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3061
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "R"
      Number of atoms: 3061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 561, 3061
          Classifications: {'peptide': 561}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 412}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 534}
          Chain breaks: 1
          Unresolved chain link angles: 19
          Unresolved non-hydrogen bonds: 1442
          Unresolved non-hydrogen angles: 1848
          Unresolved non-hydrogen dihedrals: 1194
          Unresolved non-hydrogen chiralities: 167
          Planarities with less than four sites: {'ASP:plan': 15, 'ARG:plan': 17, 'TYR:plan': 15, 'GLN:plan1': 8, 'PHE:plan': 34, 'ASN:plan1': 22, 'GLU:plan': 23, 'HIS:plan': 6, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 673
  Time building chain proxies: 0.83, per 1000 atoms: 0.27
  Number of scatterers: 3061
  At special positions: 0
  Unit cell: (61.655, 81.51, 124.355, 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       4     16.00
     O     598      8.00
     N     594      7.00
     C    1865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 439 " - pdb=" SG  CYS R 514 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 186.5 milliseconds
  

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1068

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 4 sheets defined
      43.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'R' and resid 241 through 245
      removed outlier: 4.068A  pdb=" N   SER R 244 " --> pdb=" O   GLY R 241 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 283
    Processing helix  chain 'R' and resid 362 through 387
      removed outlier: 3.961A  pdb=" N   ILE R 366 " --> pdb=" O   LEU R 362 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   TRP R 367 " --> pdb=" O   ARG R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 392 through 420
    Processing helix  chain 'R' and resid 429 through 435
      removed outlier: 3.531A  pdb=" N   THR R 435 " --> pdb=" O   ILE R 431 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 437 through 468
      removed outlier: 3.717A  pdb=" N   ARG R 464 " --> pdb=" O   ILE R 460 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TRP R 465 " --> pdb=" O   THR R 461 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   HIS R 466 " --> pdb=" O   LEU R 462 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE R 468 " --> pdb=" O   ARG R 464 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 470 through 477
      removed outlier: 5.409A  pdb=" N   ASP R 475 " --> pdb=" O   ILE R 472 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 479 through 504
      Proline residue:  R 501  - end of helix
      removed outlier: 3.772A  pdb=" N   GLY R 504 " --> pdb=" O   LEU R 500 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 521 through 552
    Processing helix  chain 'R' and resid 560 through 595
      removed outlier: 3.555A  pdb=" N   CYS R 581 " --> pdb=" O   THR R 577 " (cutoff:3.500A)
      Proline residue:  R 584  - end of helix
    Processing helix  chain 'R' and resid 603 through 610
      removed outlier: 3.679A  pdb=" N   LEU R 607 " --> pdb=" O   ASN R 603 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LEU R 608 " --> pdb=" O   SER R 604 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 613 through 624
      removed outlier: 4.118A  pdb=" N   CYS R 617 " --> pdb=" O   PRO R 613 " (cutoff:3.500A)
      Proline residue:  R 620  - end of helix
    Processing helix  chain 'R' and resid 627 through 641
    Processing sheet with id=AA1, first strand: chain 'R' and resid 40 through 41
    Processing sheet with id=AA2, first strand: chain 'R' and resid 102 through 105
      removed outlier: 6.336A  pdb=" N   ILE R 103 " --> pdb=" O   SER R 129 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   CYS R 131 " --> pdb=" O   ILE R 103 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE R 105 " --> pdb=" O   CYS R 131 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL R 177 " --> pdb=" O   LEU R 199 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   SER R 201 " --> pdb=" O   VAL R 177 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'R' and resid 163 through 164
      removed outlier: 4.163A  pdb=" N   ILE R 164 " --> pdb=" O   GLU R 188 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'R' and resid 226 through 228

    185 hydrogen bonds defined for protein.
    537 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: 0.56

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1173
        1.34 -     1.46: 569
        1.46 -     1.58: 1335
        1.58 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3083
  Sorted by residual:
  bond pdb=" CB  PRO R 345 "
       pdb=" CG  PRO R 345 "
    ideal  model  delta    sigma   weight residual
    1.506  1.484  0.022 3.90e-02 6.57e+02 3.09e-01
  bond pdb=" C   SER R 512 "
       pdb=" N   ILE R 513 "
    ideal  model  delta    sigma   weight residual
    1.338  1.332  0.006 1.01e-02 9.80e+03 3.08e-01
  bond pdb=" C   VAL R 393 "
       pdb=" N   PRO R 394 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.007 1.36e-02 5.41e+03 2.57e-01
  bond pdb=" CA  TYR R 612 "
       pdb=" C   TYR R 612 "
    ideal  model  delta    sigma   weight residual
    1.520  1.526 -0.006 1.23e-02 6.61e+03 2.44e-01
  bond pdb=" CA  TYR R 275 "
       pdb=" CB  TYR R 275 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 1.71e-02 3.42e+03 2.24e-01
  ... (remaining 3078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 4246
        1.64 -     3.28: 23
        3.28 -     4.91: 8
        4.91 -     6.55: 1
        6.55 -     8.19: 1
  Bond angle restraints: 4279
  Sorted by residual:
  angle pdb=" N   ILE R 513 "
        pdb=" CA  ILE R 513 "
        pdb=" C   ILE R 513 "
      ideal   model   delta    sigma   weight residual
     112.98  109.68    3.30 1.25e+00 6.40e-01 6.95e+00
  angle pdb=" CA  LEU R 122 "
        pdb=" CB  LEU R 122 "
        pdb=" CG  LEU R 122 "
      ideal   model   delta    sigma   weight residual
     116.30  124.49   -8.19 3.50e+00 8.16e-02 5.47e+00
  angle pdb=" N   ASN R 132 "
        pdb=" CA  ASN R 132 "
        pdb=" CB  ASN R 132 "
      ideal   model   delta    sigma   weight residual
     113.65  110.34    3.31 1.47e+00 4.63e-01 5.06e+00
  angle pdb=" C   SER R 253 "
        pdb=" N   TYR R 254 "
        pdb=" CA  TYR R 254 "
      ideal   model   delta    sigma   weight residual
     121.54  125.21   -3.67 1.91e+00 2.74e-01 3.70e+00
  angle pdb=" N   ILE R 625 "
        pdb=" CA  ILE R 625 "
        pdb=" C   ILE R 625 "
      ideal   model   delta    sigma   weight residual
     109.34  112.81   -3.47 2.08e+00 2.31e-01 2.78e+00
  ... (remaining 4274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.22: 1752
       14.22 -    28.44: 40
       28.44 -    42.66: 12
       42.66 -    56.88: 0
       56.88 -    71.10: 3
  Dihedral angle restraints: 1807
    sinusoidal: 175
      harmonic: 1632
  Sorted by residual:
  dihedral pdb=" CB  CYS R 439 "
           pdb=" SG  CYS R 439 "
           pdb=" SG  CYS R 514 "
           pdb=" CB  CYS R 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.48   61.52     1      1.00e+01 1.00e-02 5.02e+01
  dihedral pdb=" N   ASN R 207 "
           pdb=" CA  ASN R 207 "
           pdb=" CB  ASN R 207 "
           pdb=" CG  ASN R 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.07  -38.93     3      1.50e+01 4.44e-03 6.88e+00
  dihedral pdb=" CA  ALA R 560 "
           pdb=" C   ALA R 560 "
           pdb=" N   THR R 561 "
           pdb=" CA  THR R 561 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -167.09  -12.91     0      5.00e+00 4.00e-02 6.67e+00
  ... (remaining 1804 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 307
       0.026 -    0.053: 146
       0.053 -    0.079: 67
       0.079 -    0.106: 30
       0.106 -    0.132: 12
  Chirality restraints: 562
  Sorted by residual:
  chirality pdb=" CA  ILE R  64 "
            pdb=" N   ILE R  64 "
            pdb=" C   ILE R  64 "
            pdb=" CB  ILE R  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE R  78 "
            pdb=" N   ILE R  78 "
            pdb=" C   ILE R  78 "
            pdb=" CB  ILE R  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE R 155 "
            pdb=" N   ILE R 155 "
            pdb=" C   ILE R 155 "
            pdb=" CB  ILE R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 559 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 612 "   -0.012 5.00e-02 4.00e+02   1.87e-02 5.62e-01
        pdb=" N   PRO R 613 "    0.032 5.00e-02 4.00e+02
        pdb=" CA  PRO R 613 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO R 613 "   -0.010 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 561 "    0.003 2.00e-02 2.50e+03   5.22e-03 2.72e-01
        pdb=" C   THR R 561 "   -0.009 2.00e-02 2.50e+03
        pdb=" O   THR R 561 "    0.003 2.00e-02 2.50e+03
        pdb=" N   ASN R 562 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 579 "    0.002 2.00e-02 2.50e+03   4.55e-03 2.07e-01
        pdb=" C   PHE R 579 "   -0.008 2.00e-02 2.50e+03
        pdb=" O   PHE R 579 "    0.003 2.00e-02 2.50e+03
        pdb=" N   THR R 580 "    0.003 2.00e-02 2.50e+03
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 1194
        2.86 -     3.37: 2958
        3.37 -     3.88: 4765
        3.88 -     4.39: 4448
        4.39 -     4.90: 8351
  Nonbonded interactions: 21716
  Sorted by model distance:
  nonbonded pdb=" O   THR R 133 "
            pdb=" ND2 ASN R 158 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" O   ILE R  76 "
            pdb=" N   SER R 101 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" O   LEU R 638 "
            pdb=" N   CYS R 644 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" O   ASP R 419 "
            pdb=" OG1 THR R 422 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" N   ILE R 229 "
            pdb=" O   ILE R 249 "
     model   vdw
     2.411 3.120
  ... (remaining 21711 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 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:             0.600
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.320
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5027
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      :  0.001   0.022   3084  Z= 0.076
  Angle     :  0.412   8.189   4281  Z= 0.237
  Chirality :  0.042   0.132    562
  Planarity :  0.001   0.019    603
  Dihedral  :  8.017  71.101    736
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.39), residues: 557
  helix:  3.63 (0.34), residues: 214
  sheet: -1.28 (0.74), residues: 49
  loop : -1.24 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R  43 
 TYR   0.006   0.001   TYR R 427 
 PHE   0.003   0.000   PHE R 265 
 TRP   0.001   0.000   TRP R 367 
 HIS   0.001   0.000   HIS R 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00127 ( 3083)
  covalent geometry    : angle       0.41174 ( 4279)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.27020 (    2)
  hydrogen bonds       : bond        0.11449 (  185)
  hydrogen bonds       : angle       4.65538 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0277
  time to fit residues: 1.5407
Evaluate side-chains
  35 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.2980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4600 r_free = 0.4600 target = 0.214626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.208287 restraints weight = 6185.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.207806 restraints weight = 8307.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.208225 restraints weight = 7160.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.208006 restraints weight = 6827.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.208356 restraints weight = 5382.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5245
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3084  Z= 0.188
  Angle     :  0.527   7.315   4281  Z= 0.307
  Chirality :  0.045   0.188    562
  Planarity :  0.003   0.034    603
  Dihedral  :  4.378  19.421    567
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  :  7.50 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.39), residues: 557
  helix:  3.19 (0.35), residues: 208
  sheet: -1.43 (0.77), residues: 47
  loop : -1.45 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.003   ARG R  43 
 TYR   0.010   0.001   TYR R 359 
 PHE   0.014   0.001   PHE R 265 
 TRP   0.002   0.000   TRP R 367 
 HIS   0.003   0.001   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3083)
  covalent geometry    : angle       0.52660 ( 4279)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.82639 (    2)
  hydrogen bonds       : bond        0.03758 (  185)
  hydrogen bonds       : angle       3.88285 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.107 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 39
  average time/residue: 0.0263
  time to fit residues: 1.6350
Evaluate side-chains
  38 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.4569 r_free = 0.4569 target = 0.211875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.205789 restraints weight = 6284.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.205075 restraints weight = 8277.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.205533 restraints weight = 7311.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.205825 restraints weight = 5705.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.205878 restraints weight = 4910.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4500 r_free = 0.4500    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4499 r_free = 0.4499    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5378
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3084  Z= 0.210
  Angle     :  0.566   6.622   4281  Z= 0.334
  Chirality :  0.046   0.150    562
  Planarity :  0.003   0.032    603
  Dihedral  :  5.385  21.099    567
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 17.50 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.38), residues: 557
  helix:  2.61 (0.35), residues: 209
  sheet: -1.53 (0.82), residues: 46
  loop : -1.91 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.003   ARG R  43 
 TYR   0.008   0.001   TYR R 427 
 PHE   0.024   0.002   PHE R 265 
 TRP   0.003   0.000   TRP R 367 
 HIS   0.007   0.003   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3083)
  covalent geometry    : angle       0.56476 ( 4279)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       2.04981 (    2)
  hydrogen bonds       : bond        0.04140 (  185)
  hydrogen bonds       : angle       4.56870 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.111 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0245
  time to fit residues: 1.5225
Evaluate side-chains
  41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  586 SER
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.211283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.204414 restraints weight = 6107.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.203481 restraints weight = 9915.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.204053 restraints weight = 8574.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.204037 restraints weight = 6936.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.204290 restraints weight = 5873.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.4479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4479 r_free = 0.4479    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4479 r_free = 0.4479    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5425
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3084  Z= 0.195
  Angle     :  0.551   6.911   4281  Z= 0.323
  Chirality :  0.046   0.163    562
  Planarity :  0.003   0.032    603
  Dihedral  :  5.525  19.736    567
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 23.75 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.38), residues: 557
  helix:  2.66 (0.35), residues: 203
  sheet: -1.81 (0.84), residues: 47
  loop : -1.99 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG R  43 
 TYR   0.014   0.002   TYR R 427 
 PHE   0.022   0.001   PHE R 265 
 TRP   0.001   0.000   TRP R 491 
 HIS   0.006   0.003   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3083)
  covalent geometry    : angle       0.54948 ( 4279)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       1.66495 (    2)
  hydrogen bonds       : bond        0.03912 (  185)
  hydrogen bonds       : angle       4.48664 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.111 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0246
  time to fit residues: 1.5474
Evaluate side-chains
  39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0470
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.5082

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

Flipped N/Q/H residues before XYZ refinement:
R 207 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.209640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.202204 restraints weight = 6106.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.201473 restraints weight = 7914.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.201877 restraints weight = 7532.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.201947 restraints weight = 6135.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.202071 restraints weight = 5820.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4454 r_free = 0.4454    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4454 r_free = 0.4454    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5485
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3084  Z= 0.215
  Angle     :  0.585   7.299   4281  Z= 0.345
  Chirality :  0.046   0.152    562
  Planarity :  0.003   0.032    603
  Dihedral  :  5.963  20.268    567
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 28.75 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.38), residues: 557
  helix:  2.32 (0.35), residues: 208
  sheet: -2.12 (0.83), residues: 45
  loop : -2.30 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG R  43 
 TYR   0.012   0.002   TYR R 240 
 PHE   0.022   0.001   PHE R 265 
 TRP   0.001   0.000   TRP R 491 
 HIS   0.005   0.002   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3083)
  covalent geometry    : angle       0.58408 ( 4279)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       1.88137 (    2)
  hydrogen bonds       : bond        0.04208 (  185)
  hydrogen bonds       : angle       4.75638 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.102 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0275
  time to fit residues: 1.7601
Evaluate side-chains
  40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0030
   chunk 52 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
R 207 ASN
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.211445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.204724 restraints weight = 6128.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.204082 restraints weight = 9717.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.204604 restraints weight = 8439.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.204540 restraints weight = 6647.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.204720 restraints weight = 6031.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4487 r_free = 0.4487    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4487 r_free = 0.4487    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5402
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3084  Z= 0.139
  Angle     :  0.508   6.560   4281  Z= 0.296
  Chirality :  0.045   0.146    562
  Planarity :  0.002   0.029    603
  Dihedral  :  5.230  18.094    567
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 27.50 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.38), residues: 557
  helix:  2.62 (0.35), residues: 209
  sheet: -2.52 (0.84), residues: 43
  loop : -2.19 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R  43 
 TYR   0.010   0.001   TYR R 427 
 PHE   0.011   0.001   PHE R 265 
 TRP   0.004   0.000   TRP R 491 
 HIS   0.004   0.002   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3083)
  covalent geometry    : angle       0.50603 ( 4279)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       2.14101 (    2)
  hydrogen bonds       : bond        0.03373 (  185)
  hydrogen bonds       : angle       4.31820 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.077 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0233
  time to fit residues: 1.4980
Evaluate side-chains
  42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  240 TYR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  586 SER
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0010
   chunk 49 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3390

-------------------------------------------------------------------------------
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 = 0.4543 r_free = 0.4543 target = 0.209744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.205016 restraints weight = 6158.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.204594 restraints weight = 9121.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.204694 restraints weight = 8124.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.204499 restraints weight = 7044.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.204639 restraints weight = 6015.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.4481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4481 r_free = 0.4481    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4481 r_free = 0.4481    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5431
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3084  Z= 0.193
  Angle     :  0.563   7.492   4281  Z= 0.329
  Chirality :  0.046   0.147    562
  Planarity :  0.003   0.029    603
  Dihedral  :  5.700  19.679    567
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 26.25 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.38), residues: 557
  helix:  2.42 (0.35), residues: 209
  sheet: -2.53 (0.83), residues: 43
  loop : -2.36 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG R  43 
 TYR   0.012   0.002   TYR R 427 
 PHE   0.018   0.001   PHE R 265 
 TRP   0.002   0.000   TRP R 491 
 HIS   0.006   0.003   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3083)
  covalent geometry    : angle       0.56149 ( 4279)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       2.23447 (    2)
  hydrogen bonds       : bond        0.03933 (  185)
  hydrogen bonds       : angle       4.58795 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.101 
Fit side-chains
  outliers start: 8
  outliers final: 8
  residues processed: 41
  average time/residue: 0.0240
  time to fit residues: 1.5854
Evaluate side-chains
  43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  240 TYR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  586 SER
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4554 r_free = 0.4554 target = 0.210661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.203919 restraints weight = 6312.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.203082 restraints weight = 9653.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.203714 restraints weight = 8638.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.204128 restraints weight = 6239.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.204208 restraints weight = 5667.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4464 r_free = 0.4464    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4464 r_free = 0.4464    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5421
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3084  Z= 0.153
  Angle     :  0.547   9.673   4281  Z= 0.311
  Chirality :  0.045   0.147    562
  Planarity :  0.002   0.029    603
  Dihedral  :  5.344  18.892    567
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 27.50 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.38), residues: 557
  helix:  2.58 (0.35), residues: 209
  sheet: -2.65 (0.83), residues: 43
  loop : -2.35 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  43 
 TYR   0.010   0.001   TYR R 427 
 PHE   0.012   0.001   PHE R 265 
 TRP   0.004   0.001   TRP R 491 
 HIS   0.004   0.002   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3083)
  covalent geometry    : angle       0.54442 ( 4279)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       2.40421 (    2)
  hydrogen bonds       : bond        0.03460 (  185)
  hydrogen bonds       : angle       4.38850 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 40
  average time/residue: 0.0246
  time to fit residues: 1.5552
Evaluate side-chains
  43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  240 TYR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    0.2980
   chunk 19 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4541 r_free = 0.4541 target = 0.209853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.204663 restraints weight = 6219.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.204167 restraints weight = 8923.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.204403 restraints weight = 8332.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.204393 restraints weight = 7012.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.204473 restraints weight = 6143.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4466 r_free = 0.4466    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4466 r_free = 0.4466    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5407
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3084  Z= 0.163
  Angle     :  0.560   9.255   4281  Z= 0.319
  Chirality :  0.045   0.147    562
  Planarity :  0.003   0.029    603
  Dihedral  :  5.422  20.470    567
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 27.50 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.38), residues: 557
  helix:  2.52 (0.35), residues: 209
  sheet: -2.70 (0.83), residues: 43
  loop : -2.42 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG R  43 
 TYR   0.013   0.002   TYR R 455 
 PHE   0.012   0.001   PHE R 265 
 TRP   0.005   0.001   TRP R 491 
 HIS   0.004   0.002   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3083)
  covalent geometry    : angle       0.55747 ( 4279)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       2.45661 (    2)
  hydrogen bonds       : bond        0.03636 (  185)
  hydrogen bonds       : angle       4.44603 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.063 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0195
  time to fit residues: 1.2831
Evaluate side-chains
  44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  240 TYR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
R 278 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.204860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.201282 restraints weight = 5970.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.200570 restraints weight = 8828.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.200351 restraints weight = 7843.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.199533 restraints weight = 9117.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.199859 restraints weight = 7822.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5564
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   3084  Z= 0.405
  Angle     :  0.814  10.847   4281  Z= 0.474
  Chirality :  0.051   0.171    562
  Planarity :  0.005   0.037    603
  Dihedral  :  7.385  29.936    567
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 26.25 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.36), residues: 557
  helix:  1.32 (0.34), residues: 214
  sheet: -2.95 (0.81), residues: 41
  loop : -3.04 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.004   ARG R  43 
 TYR   0.023   0.004   TYR R 240 
 PHE   0.039   0.002   PHE R 265 
 TRP   0.005   0.001   TRP R 367 
 HIS   0.015   0.005   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 ( 3083)
  covalent geometry    : angle       0.81175 ( 4279)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       2.66589 (    2)
  hydrogen bonds       : bond        0.06096 (  185)
  hydrogen bonds       : angle       5.76176 (  537)

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

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

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1114 Ramachandran restraints generated.
    557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.107 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 40
  average time/residue: 0.0277
  time to fit residues: 1.7646
Evaluate side-chains
  42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  162 THR
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  240 TYR
Chi-restraints excluded: chain R residue  422 THR
Chi-restraints excluded: chain R residue  429 HIS
Chi-restraints excluded: chain R residue  598 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0970
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
R 207 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.211220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.207217 restraints weight = 6297.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.207048 restraints weight = 8733.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.206891 restraints weight = 7238.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.206133 restraints weight = 9213.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.206363 restraints weight = 7856.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5372
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3084  Z= 0.121
  Angle     :  0.554   9.785   4281  Z= 0.314
  Chirality :  0.045   0.149    562
  Planarity :  0.002   0.026    603
  Dihedral  :  5.330  17.866    567
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 27.50 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.38), residues: 557
  helix:  2.47 (0.35), residues: 208
  sheet: -3.05 (0.80), residues: 43
  loop : -2.49 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R  43 
 TYR   0.013   0.001   TYR R 275 
 PHE   0.005   0.001   PHE R 194 
 TRP   0.009   0.001   TRP R 491 
 HIS   0.002   0.001   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3083)
  covalent geometry    : angle       0.55095 ( 4279)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       2.60023 (    2)
  hydrogen bonds       : bond        0.03278 (  185)
  hydrogen bonds       : angle       4.45153 (  537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 657.62 seconds
wall clock time: 11 minutes 47.25 seconds (707.25 seconds total)