Starting phenix.real_space_refine
on Fri Aug 22 14:43:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j1t_35932/08_2025/8j1t_35932.map"
  }
  resolution = 3.3
  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=   0.016
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 1374 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      17      5.16       5
     C    2035      2.51       5
     N     543      2.21       5
     O     609      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3204
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 874
          Classifications: {'peptide': 115}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "K"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 825
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "F"
      Number of atoms: 1505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1505
          Classifications: {'peptide': 188}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 176}
          Chain breaks: 1
  Time building chain proxies: 0.97, per 1000 atoms: 0.30
  Number of scatterers: 3204
  At special positions: 0
  Unit cell: (63.05, 64.02, 92.15, 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      17     16.00
     O     609      8.00
     N     543      7.00
     C    2035      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 336 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 391 " - pdb=" SG  CYS F 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 480 " - pdb=" SG  CYS F 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.17
  Conformation dependent library (CDL) restraints added in 108.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 7 sheets defined
      10.2% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'H' and resid 29 through 33
      removed outlier: 3.895A  pdb=" N   ASN H  33 " --> pdb=" O   VAL H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 3.670A  pdb=" N   ARG H  65 " --> pdb=" O   ASP H  62 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 337 through 343
    Processing helix  chain 'F' and resid 366 through 372
      removed outlier: 3.851A  pdb=" N   ASN F 370 " --> pdb=" O   SER F 366 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE F 371 " --> pdb=" O   VAL F 367 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 384 through 388
      removed outlier: 4.094A  pdb=" N   ASN F 388 " --> pdb=" O   THR F 385 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 405 through 410
      removed outlier: 4.573A  pdb=" N   SER F 408 " --> pdb=" O   ASN F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 416 through 422
      removed outlier: 3.632A  pdb=" N   TYR F 421 " --> pdb=" O   ASN F 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 8
      removed outlier: 3.884A  pdb=" N   GLN H   4 " --> pdb=" O   SER H  26 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER H  22 " --> pdb=" O   SER H   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 13
      removed outlier: 6.178A  pdb=" N   GLY H  11 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL H 114 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   TYR H  34 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   MET H  35 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL H  51 " --> pdb=" O   MET H  35 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   TRP H  37 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 4 through 6
      removed outlier: 3.932A  pdb=" N   VAL K  19 " --> pdb=" O   ILE K  75 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE K  71 " --> pdb=" O   CYS K  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 45 through 48
      removed outlier: 5.799A  pdb=" N   LEU K  46 " --> pdb=" O   GLN K  37 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   GLN K  37 " --> pdb=" O   LEU K  46 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 354 through 355
      removed outlier: 3.585A  pdb=" N   ASN F 354 " --> pdb=" O   SER F 399 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER F 399 " --> pdb=" O   ASN F 354 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 391 through 392
    Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454

    76 hydrogen bonds defined for protein.
    183 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: 0.42

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1029
        1.34 -     1.46: 859
        1.46 -     1.58: 1377
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3287
  Sorted by residual:
  bond pdb=" CA  ILE K  29 "
       pdb=" CB  ILE K  29 "
    ideal  model  delta    sigma   weight residual
    1.553  1.538  0.015 7.40e-03 1.83e+04 4.28e+00
  bond pdb=" CB  ASN F 343 "
       pdb=" CG  ASN F 343 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.63e+00
  bond pdb=" CA  ILE H 107 "
       pdb=" CB  ILE H 107 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.03e+00
  bond pdb=" CA  VAL H  49 "
       pdb=" CB  VAL H  49 "
    ideal  model  delta    sigma   weight residual
    1.545  1.536  0.009 9.10e-03 1.21e+04 9.38e-01
  bond pdb=" CB  PHE F 400 "
       pdb=" CG  PHE F 400 "
    ideal  model  delta    sigma   weight residual
    1.502  1.480  0.022 2.30e-02 1.89e+03 8.92e-01
  ... (remaining 3282 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 4162
        1.03 -     2.07: 244
        2.07 -     3.10: 39
        3.10 -     4.14: 18
        4.14 -     5.17: 3
  Bond angle restraints: 4466
  Sorted by residual:
  angle pdb=" C   GLN K  89 "
        pdb=" CA  GLN K  89 "
        pdb=" CB  GLN K  89 "
      ideal   model   delta    sigma   weight residual
     111.17  106.80    4.37 1.96e+00 2.60e-01 4.98e+00
  angle pdb=" C   SER K  93 "
        pdb=" CA  SER K  93 "
        pdb=" CB  SER K  93 "
      ideal   model   delta    sigma   weight residual
     111.71  106.94    4.77 2.23e+00 2.01e-01 4.58e+00
  angle pdb=" CA  ALA F 411 "
        pdb=" C   ALA F 411 "
        pdb=" N   PRO F 412 "
      ideal   model   delta    sigma   weight residual
     117.62  119.65   -2.03 1.03e+00 9.43e-01 3.88e+00
  angle pdb=" N   GLN K  89 "
        pdb=" CA  GLN K  89 "
        pdb=" CB  GLN K  89 "
      ideal   model   delta    sigma   weight residual
     111.46  114.42   -2.96 1.54e+00 4.22e-01 3.70e+00
  angle pdb=" CA  GLY K  28 "
        pdb=" C   GLY K  28 "
        pdb=" O   GLY K  28 "
      ideal   model   delta    sigma   weight residual
     122.61  120.22    2.39 1.28e+00 6.10e-01 3.47e+00
  ... (remaining 4461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.68: 1761
       15.68 -    31.35: 129
       31.35 -    47.03: 31
       47.03 -    62.70: 6
       62.70 -    78.38: 3
  Dihedral angle restraints: 1930
    sinusoidal: 747
      harmonic: 1183
  Sorted by residual:
  dihedral pdb=" CB  CYS F 480 "
           pdb=" SG  CYS F 480 "
           pdb=" SG  CYS F 488 "
           pdb=" CB  CYS F 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.38  -78.38     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" CA  ASN H  84 "
           pdb=" C   ASN H  84 "
           pdb=" N   SER H  85 "
           pdb=" CA  SER H  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.42  -28.58     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CB  CYS F 391 "
           pdb=" SG  CYS F 391 "
           pdb=" SG  CYS F 525 "
           pdb=" CB  CYS F 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.38  -32.38     1      1.00e+01 1.00e-02 1.49e+01
  ... (remaining 1927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 288
       0.034 -    0.067: 133
       0.067 -    0.100: 32
       0.100 -    0.134: 16
       0.134 -    0.167: 5
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  SER K  93 "
            pdb=" N   SER K  93 "
            pdb=" C   SER K  93 "
            pdb=" CB  SER K  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CA  VAL H  51 "
            pdb=" N   VAL H  51 "
            pdb=" C   VAL H  51 "
            pdb=" CB  VAL H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  ILE F 402 "
            pdb=" N   ILE F 402 "
            pdb=" C   ILE F 402 "
            pdb=" CB  ILE F 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.24e-01
  ... (remaining 471 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 343 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   ASN F 343 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ASN F 343 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA F 344 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 396 "    0.011 2.00e-02 2.50e+03   7.76e-03 1.20e+00
        pdb=" CG  TYR F 396 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 396 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 396 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 396 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 396 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR F 396 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR H  53 "    0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO H  54 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO H  54 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO H  54 "    0.015 5.00e-02 4.00e+02
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 469
        2.76 -     3.29: 2996
        3.29 -     3.83: 4905
        3.83 -     4.36: 5946
        4.36 -     4.90: 10335
  Nonbonded interactions: 24651
  Sorted by model distance:
  nonbonded pdb=" OH  TYR K  36 "
            pdb=" OE1 GLN K  89 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   GLN K  38 "
            pdb=" OG1 THR K  85 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OE1 GLN K   6 "
            pdb=" OG1 THR K 104 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ASN F 439 "
            pdb=" OG  SER F 443 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OD1 ASN F 388 "
            pdb=" N   ASP F 389 "
     model   vdw
     2.343 3.120
  ... (remaining 24646 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.790
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
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      :  0.004   0.032   3293  Z= 0.193
  Angle     :  0.586   5.169   4478  Z= 0.321
  Chirality :  0.044   0.167    474
  Planarity :  0.004   0.027    582
  Dihedral  : 11.734  66.984   1164
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.39), residues: 403
  helix: -3.01 (0.65), residues: 33
  sheet: -0.44 (0.47), residues: 134
  loop : -1.47 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 355 
 TYR   0.018   0.002   TYR F 396 
 PHE   0.009   0.001   PHE F 338 
 TRP   0.011   0.002   TRP F 353 
 HIS   0.005   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3287)
  covalent geometry    : angle       0.58469 ( 4466)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       0.86616 (   12)
  hydrogen bonds       : bond        0.29604 (   76)
  hydrogen bonds       : angle      10.28924 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: K   63 SER cc_start: 0.6549 (t) cc_final: 0.6239 (t)
REVERT: F  453 TYR cc_start: 0.8207 (p90) cc_final: 0.7912 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0686
  time to fit residues: 4.9334
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
F 354 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.124242 restraints weight = 4461.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.19
r_work: 0.3490 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3293  Z= 0.155
  Angle     :  0.565   5.220   4478  Z= 0.305
  Chirality :  0.045   0.152    474
  Planarity :  0.004   0.031    582
  Dihedral  :  5.029  37.185    458
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.05 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.39), residues: 403
  helix: -3.07 (0.67), residues: 33
  sheet: -0.34 (0.47), residues: 133
  loop : -1.44 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  61 
 TYR   0.013   0.001   TYR K  49 
 PHE   0.008   0.001   PHE F 338 
 TRP   0.014   0.002   TRP F 436 
 HIS   0.005   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3287)
  covalent geometry    : angle       0.56347 ( 4466)
  SS BOND              : bond        0.00455 (    6)
  SS BOND              : angle       0.98265 (   12)
  hydrogen bonds       : bond        0.04344 (   76)
  hydrogen bonds       : angle       6.91078 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: H   35 MET cc_start: 0.8100 (mmm) cc_final: 0.7771 (mtt)
  outliers start: 3
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0612
  time to fit residues: 4.1148
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain F residue  393 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 343 ASN
F 354 ASN
F 417 ASN
F 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.138691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121957 restraints weight = 4473.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.21
r_work: 0.3457 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3293  Z= 0.221
  Angle     :  0.589   5.214   4478  Z= 0.319
  Chirality :  0.046   0.156    474
  Planarity :  0.004   0.033    582
  Dihedral  :  5.102  29.282    458
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.36 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.39), residues: 403
  helix: -3.05 (0.75), residues: 27
  sheet: -0.33 (0.46), residues: 133
  loop : -1.57 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  61 
 TYR   0.015   0.002   TYR F 423 
 PHE   0.012   0.002   PHE F 377 
 TRP   0.014   0.002   TRP F 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 3287)
  covalent geometry    : angle       0.58718 ( 4466)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       1.12832 (   12)
  hydrogen bonds       : bond        0.04273 (   76)
  hydrogen bonds       : angle       6.52007 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0535
  time to fit residues: 3.7683
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  343 ASN
Chi-restraints excluded: chain F residue  393 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    0.1980
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
H  40 GLN
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 354 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.123583 restraints weight = 4465.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.26
r_work: 0.3479 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3293  Z= 0.143
  Angle     :  0.550   5.126   4478  Z= 0.293
  Chirality :  0.044   0.151    474
  Planarity :  0.003   0.031    582
  Dihedral  :  4.867  25.315    458
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.95 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.39), residues: 403
  helix: -3.01 (0.76), residues: 27
  sheet: -0.31 (0.45), residues: 133
  loop : -1.56 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.012   0.001   TYR F 423 
 PHE   0.012   0.001   PHE F 377 
 TRP   0.013   0.002   TRP F 436 
 HIS   0.004   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3287)
  covalent geometry    : angle       0.54794 ( 4466)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       0.98883 (   12)
  hydrogen bonds       : bond        0.03510 (   76)
  hydrogen bonds       : angle       6.25647 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: F  343 ASN cc_start: 0.8107 (t0) cc_final: 0.7804 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0493
  time to fit residues: 3.3465
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  393 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0270
   chunk 5 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.3438

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 354 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.141084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.124197 restraints weight = 4425.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.23
r_work: 0.3489 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3293  Z= 0.133
  Angle     :  0.527   5.116   4478  Z= 0.282
  Chirality :  0.044   0.153    474
  Planarity :  0.003   0.032    582
  Dihedral  :  4.669  23.991    458
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.80 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.39), residues: 403
  helix: -3.07 (0.74), residues: 27
  sheet: -0.24 (0.46), residues: 133
  loop : -1.56 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 355 
 TYR   0.010   0.001   TYR K  49 
 PHE   0.011   0.001   PHE F 377 
 TRP   0.012   0.002   TRP F 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3287)
  covalent geometry    : angle       0.52558 ( 4466)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       0.97480 (   12)
  hydrogen bonds       : bond        0.03237 (   76)
  hydrogen bonds       : angle       6.14315 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: F  343 ASN cc_start: 0.8219 (t0) cc_final: 0.7852 (t0)
REVERT: F  406 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8008 (tt0)
  outliers start: 7
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0491
  time to fit residues: 3.5032
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0970
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0040
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
H 103 HIS
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 354 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.140248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.123469 restraints weight = 4416.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.21
r_work: 0.3479 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3293  Z= 0.167
  Angle     :  0.556   5.075   4478  Z= 0.297
  Chirality :  0.045   0.194    474
  Planarity :  0.004   0.033    582
  Dihedral  :  4.783  24.761    458
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.24 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.39), residues: 403
  helix: -3.14 (0.74), residues: 27
  sheet: -0.18 (0.46), residues: 133
  loop : -1.60 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.017   0.001   TYR F 423 
 PHE   0.009   0.001   PHE F 377 
 TRP   0.012   0.002   TRP F 436 
 HIS   0.003   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3287)
  covalent geometry    : angle       0.55370 ( 4466)
  SS BOND              : bond        0.00417 (    6)
  SS BOND              : angle       1.11793 (   12)
  hydrogen bonds       : bond        0.03501 (   76)
  hydrogen bonds       : angle       6.10527 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: H  113 MET cc_start: 0.7523 (mmm) cc_final: 0.7243 (mmm)
REVERT: F  343 ASN cc_start: 0.8232 (t0) cc_final: 0.7870 (t0)
REVERT: F  355 ARG cc_start: 0.8636 (ttt90) cc_final: 0.8393 (ttt180)
REVERT: F  406 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8009 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0629
  time to fit residues: 4.2974
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 354 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.138891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.121774 restraints weight = 4556.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.26
r_work: 0.3453 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3293  Z= 0.207
  Angle     :  0.581   5.339   4478  Z= 0.313
  Chirality :  0.046   0.158    474
  Planarity :  0.004   0.035    582
  Dihedral  :  4.997  27.392    458
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.95 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.39), residues: 403
  helix: -3.20 (0.73), residues: 27
  sheet: -0.17 (0.46), residues: 133
  loop : -1.65 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.014   0.002   TYR F 423 
 PHE   0.007   0.002   PHE F 338 
 TRP   0.013   0.002   TRP F 436 
 HIS   0.004   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 3287)
  covalent geometry    : angle       0.57782 ( 4466)
  SS BOND              : bond        0.00438 (    6)
  SS BOND              : angle       1.31456 (   12)
  hydrogen bonds       : bond        0.03655 (   76)
  hydrogen bonds       : angle       6.09671 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: H   77 ASN cc_start: 0.7980 (t0) cc_final: 0.7610 (t0)
REVERT: F  343 ASN cc_start: 0.8221 (t0) cc_final: 0.7868 (t0)
REVERT: F  355 ARG cc_start: 0.8698 (ttt90) cc_final: 0.8376 (ttt180)
REVERT: F  406 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (tt0)
  outliers start: 8
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0603
  time to fit residues: 4.1712
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain K residue    4 MET
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0870
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    0.2980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.1758

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

Flipped N/Q/H residues before XYZ refinement:
** H  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.141256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.124219 restraints weight = 4519.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.23
r_work: 0.3493 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3293  Z= 0.102
  Angle     :  0.525   5.077   4478  Z= 0.278
  Chirality :  0.044   0.153    474
  Planarity :  0.003   0.034    582
  Dihedral  :  4.568  21.242    458
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.24 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.39), residues: 403
  helix: -3.06 (0.76), residues: 27
  sheet:  0.10 (0.48), residues: 121
  loop : -1.63 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  20 
 TYR   0.008   0.001   TYR F 453 
 PHE   0.012   0.001   PHE F 377 
 TRP   0.012   0.001   TRP F 436 
 HIS   0.004   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3287)
  covalent geometry    : angle       0.52298 ( 4466)
  SS BOND              : bond        0.00394 (    6)
  SS BOND              : angle       1.00229 (   12)
  hydrogen bonds       : bond        0.03018 (   76)
  hydrogen bonds       : angle       6.03127 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: F  343 ASN cc_start: 0.8196 (t0) cc_final: 0.7805 (t0)
REVERT: F  406 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7961 (tt0)
REVERT: F  410 ILE cc_start: 0.8381 (mm) cc_final: 0.8115 (mt)
REVERT: F  451 TYR cc_start: 0.7883 (m-10) cc_final: 0.7677 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0584
  time to fit residues: 4.4796
Evaluate side-chains
  64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  422 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
K  89 GLN
F 354 ASN
F 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.139186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.122219 restraints weight = 4537.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.22
r_work: 0.3473 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3293  Z= 0.157
  Angle     :  0.554   5.319   4478  Z= 0.295
  Chirality :  0.045   0.160    474
  Planarity :  0.004   0.035    582
  Dihedral  :  4.672  23.324    458
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.97 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.39), residues: 403
  helix: -3.22 (0.72), residues: 27
  sheet:  0.06 (0.48), residues: 121
  loop : -1.61 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.017   0.001   TYR F 423 
 PHE   0.008   0.001   PHE F 377 
 TRP   0.011   0.002   TRP F 436 
 HIS   0.005   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3287)
  covalent geometry    : angle       0.55070 ( 4466)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       1.27267 (   12)
  hydrogen bonds       : bond        0.03354 (   76)
  hydrogen bonds       : angle       6.01763 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: H   77 ASN cc_start: 0.7890 (t0) cc_final: 0.7545 (t0)
REVERT: F  343 ASN cc_start: 0.8206 (t0) cc_final: 0.7825 (t0)
REVERT: F  406 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7878 (tt0)
  outliers start: 10
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0665
  time to fit residues: 4.7144
Evaluate side-chains
  62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain K residue    4 MET
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  422 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.139429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.122592 restraints weight = 4416.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.22
r_work: 0.3468 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3293  Z= 0.193
  Angle     :  0.577   5.627   4478  Z= 0.307
  Chirality :  0.046   0.160    474
  Planarity :  0.004   0.035    582
  Dihedral  :  4.824  25.230    458
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.68 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.39), residues: 403
  helix: -3.27 (0.71), residues: 27
  sheet: -0.08 (0.47), residues: 123
  loop : -1.64 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  61 
 TYR   0.015   0.002   TYR F 423 
 PHE   0.006   0.001   PHE F 375 
 TRP   0.012   0.002   TRP F 436 
 HIS   0.006   0.002   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 3287)
  covalent geometry    : angle       0.57370 ( 4466)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       1.31624 (   12)
  hydrogen bonds       : bond        0.03574 (   76)
  hydrogen bonds       : angle       6.08797 (  183)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: H   77 ASN cc_start: 0.7944 (t0) cc_final: 0.7572 (t0)
REVERT: F  343 ASN cc_start: 0.8226 (t0) cc_final: 0.7871 (t0)
REVERT: F  406 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8020 (tt0)
REVERT: F  453 TYR cc_start: 0.8455 (p90) cc_final: 0.8101 (p90)
  outliers start: 10
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0611
  time to fit residues: 4.4010
Evaluate side-chains
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain K residue    4 MET
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   96 SER
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain F residue  393 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  422 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 24 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.123154 restraints weight = 4500.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.26
r_work: 0.3474 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3293  Z= 0.143
  Angle     :  0.546   5.527   4478  Z= 0.292
  Chirality :  0.044   0.158    474
  Planarity :  0.004   0.036    582
  Dihedral  :  4.701  23.800    458
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.54 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.39), residues: 403
  helix: -3.15 (0.73), residues: 27
  sheet: -0.01 (0.48), residues: 121
  loop : -1.66 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  61 
 TYR   0.015   0.001   TYR F 423 
 PHE   0.009   0.001   PHE F 377 
 TRP   0.012   0.002   TRP F 436 
 HIS   0.005   0.001   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3287)
  covalent geometry    : angle       0.54406 ( 4466)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.09965 (   12)
  hydrogen bonds       : bond        0.03309 (   76)
  hydrogen bonds       : angle       5.95178 (  183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 961.98 seconds
wall clock time: 17 minutes 4.28 seconds (1024.28 seconds total)