Starting phenix.real_space_refine
on Wed Jun  4 15:38:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wog_32651/06_2025/7wog_32651.cif"
  }
  resolution = 4.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2122      2.51       5
     N     569      2.21       5
     O     655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3362
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1580
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 937
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 845
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
  Time building chain proxies: 2.70, per 1000 atoms: 0.80
  Number of scatterers: 3362
  At special positions: 0
  Unit cell: (69.16, 91.504, 87.248, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     655      8.00
     N     569      7.00
     C    2122      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 422.1 milliseconds
  

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  794

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.5% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 342
      removed outlier: 3.591A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.831A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 390
      removed outlier: 3.841A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.962A  pdb=" N   THR A  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 86
      removed outlier: 3.909A  pdb=" N   GLU B  86 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'C' and resid 356 through 358
      removed outlier: 4.174A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 21
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.756A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   THR A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   MET A  34 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.520A  pdb=" N   TYR B  90 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23

    82 hydrogen bonds defined for protein.
    189 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: 0.90

  Time building geometry restraints manager: 0.95 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: 1085
        1.34 -     1.46: 897
        1.46 -     1.58: 1446
        1.58 -     1.70: 0
        1.70 -     1.81: 20
  Bond restraints: 3448
  Sorted by residual:
  bond pdb=" N   GLY C 504 "
       pdb=" CA  GLY C 504 "
    ideal  model  delta    sigma   weight residual
    1.454  1.444  0.010 1.79e-02 3.12e+03 3.09e-01
  bond pdb=" C   LYS C 462 "
       pdb=" N   PRO C 463 "
    ideal  model  delta    sigma   weight residual
    1.334  1.346 -0.012 2.34e-02 1.83e+03 2.72e-01
  bond pdb=" C   LYS A  76 "
       pdb=" N   ASN A  77 "
    ideal  model  delta    sigma   weight residual
    1.331  1.337 -0.006 1.29e-02 6.01e+03 2.23e-01
  bond pdb=" N   ASN A  77 "
       pdb=" CA  ASN A  77 "
    ideal  model  delta    sigma   weight residual
    1.457  1.462 -0.005 1.31e-02 5.83e+03 1.73e-01
  bond pdb=" CZ  ARG B 112 "
       pdb=" NH2 ARG B 112 "
    ideal  model  delta    sigma   weight residual
    1.330  1.325  0.005 1.30e-02 5.92e+03 1.69e-01
  ... (remaining 3443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.65: 4288
        0.65 -     1.29: 302
        1.29 -     1.94: 64
        1.94 -     2.59: 21
        2.59 -     3.24: 14
  Bond angle restraints: 4689
  Sorted by residual:
  angle pdb=" C   LYS A  76 "
        pdb=" N   ASN A  77 "
        pdb=" CA  ASN A  77 "
      ideal   model   delta    sigma   weight residual
     121.56  124.80   -3.24 1.56e+00 4.11e-01 4.30e+00
  angle pdb=" N   ASN A  77 "
        pdb=" CA  ASN A  77 "
        pdb=" C   ASN A  77 "
      ideal   model   delta    sigma   weight residual
     110.42  112.79   -2.37 1.46e+00 4.69e-01 2.64e+00
  angle pdb=" NE  ARG C 357 "
        pdb=" CZ  ARG C 357 "
        pdb=" NH1 ARG C 357 "
      ideal   model   delta    sigma   weight residual
     121.50  120.03    1.47 1.00e+00 1.00e+00 2.16e+00
  angle pdb=" NE  ARG B  40 "
        pdb=" CZ  ARG B  40 "
        pdb=" NH1 ARG B  40 "
      ideal   model   delta    sigma   weight residual
     121.50  120.05    1.45 1.00e+00 1.00e+00 2.09e+00
  angle pdb=" NE  ARG C 457 "
        pdb=" CZ  ARG C 457 "
        pdb=" NH1 ARG C 457 "
      ideal   model   delta    sigma   weight residual
     121.50  120.06    1.44 1.00e+00 1.00e+00 2.08e+00
  ... (remaining 4684 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.09: 1876
       11.09 -    22.19: 114
       22.19 -    33.28: 30
       33.28 -    44.37: 10
       44.37 -    55.46: 3
  Dihedral angle restraints: 2033
    sinusoidal: 779
      harmonic: 1254
  Sorted by residual:
  dihedral pdb=" CA  LYS A  76 "
           pdb=" C   LYS A  76 "
           pdb=" N   ASN A  77 "
           pdb=" CA  ASN A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" N   ARG C 457 "
           pdb=" CA  ARG C 457 "
           pdb=" CB  ARG C 457 "
           pdb=" CG  ARG C 457 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.54  -55.46     3      1.50e+01 4.44e-03 9.35e+00
  dihedral pdb=" CA  CYS A  22 "
           pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -124.56   51.56     1      2.00e+01 2.50e-03 9.08e+00
  ... (remaining 2030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 293
       0.026 -    0.052: 130
       0.052 -    0.079: 35
       0.079 -    0.105: 28
       0.105 -    0.131: 16
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  ILE B  67 "
            pdb=" N   ILE B  67 "
            pdb=" C   ILE B  67 "
            pdb=" CB  ILE B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE B  49 "
            pdb=" N   ILE B  49 "
            pdb=" C   ILE B  49 "
            pdb=" CB  ILE B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CB  VAL C 433 "
            pdb=" CA  VAL C 433 "
            pdb=" CG1 VAL C 433 "
            pdb=" CG2 VAL C 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 499 not shown)

  Planarity restraints: 609
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 372 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO C 373 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 373 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 373 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B   6 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO B   7 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.016 5.00e-02 4.00e+02   2.35e-02 8.82e-01
        pdb=" N   PRO C 337 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.013 5.00e-02 4.00e+02
  ... (remaining 606 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1012
        2.81 -     3.34: 2783
        3.34 -     3.86: 5344
        3.86 -     4.38: 5893
        4.38 -     4.90: 10189
  Nonbonded interactions: 25221
  Sorted by model distance:
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TRP C 353 "
            pdb=" OH  TYR A 106 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   SER A  31 "
            pdb=" OG  SER A 102 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OG  SER C 349 "
            pdb=" O   LEU C 452 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" NH1 ARG A  67 "
            pdb=" O   SER A  85 "
     model   vdw
     2.360 3.120
  ... (remaining 25216 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5154
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   0.013   3454  Z= 0.077
  Angle     :  0.415   3.236   4701  Z= 0.239
  Chirality :  0.041   0.131    502
  Planarity :  0.003   0.032    609
  Dihedral  :  8.085  55.464   1221
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  :  6.76 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.98 (0.34), residues: 427
  helix:  None (None), residues: 0
  sheet: -1.23 (0.39), residues: 126
  loop : -3.58 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 103 
 HIS   0.001   0.000   HIS B  99 
 PHE   0.004   0.000   PHE C 490 
 TYR   0.008   0.001   TYR A  59 
 ARG   0.001   0.000   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14833 (   71)
  hydrogen bonds       : angle       7.11920 (  189)
  SS BOND              : bond        0.00101 (    6)
  SS BOND              : angle       0.40952 (   12)
  covalent geometry    : bond        0.00139 ( 3448)
  covalent geometry    : angle       0.41487 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 PHE cc_start: 0.6498 (m-10) cc_final: 0.5856 (m-10)
REVERT: C  358 ILE cc_start: 0.6075 (mm) cc_final: 0.5858 (mm)
REVERT: C  380 TYR cc_start: 0.7645 (m-80) cc_final: 0.7217 (m-80)
REVERT: C  408 ARG cc_start: 0.6717 (ptm-80) cc_final: 0.5396 (mmm-85)
REVERT: C  452 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7789 (pt)
REVERT: A    4 LEU cc_start: 0.0399 (OUTLIER) cc_final: 0.0053 (tm)
REVERT: A   11 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6667 (pp)
REVERT: A   34 MET cc_start: 0.6625 (mmm) cc_final: 0.6264 (mmm)
REVERT: A   83 MET cc_start: 0.5214 (mtp) cc_final: 0.3636 (mtp)
REVERT: B  102 PHE cc_start: 0.6892 (m-80) cc_final: 0.6553 (m-10)
REVERT: B  106 THR cc_start: 0.7464 (m) cc_final: 0.7132 (p)
  outliers start: 14
  outliers final: 3
  residues processed: 98
  average time/residue: 0.2335
  time to fit residues: 26.1603
Evaluate side-chains
  86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0270
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
C 334 ASN
C 354 ASN
C 409 GLN
C 437 ASN
C 448 ASN
** B  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 GLN
B  98 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.199813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.175412 restraints weight = 7793.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.180182 restraints weight = 5139.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.183626 restraints weight = 3703.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5353
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3454  Z= 0.163
  Angle     :  0.602   5.659   4701  Z= 0.327
  Chirality :  0.045   0.171    502
  Planarity :  0.005   0.041    609
  Dihedral  :  4.300  20.666    481
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.05 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.37), residues: 427
  helix: -5.23 (0.46), residues: 7
  sheet: -0.65 (0.43), residues: 129
  loop : -3.03 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 103 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.014   0.002   PHE C 377 
 TYR   0.027   0.002   TYR A 106 
 ARG   0.005   0.001   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (   71)
  hydrogen bonds       : angle       6.09667 (  189)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       0.70445 (   12)
  covalent geometry    : bond        0.00373 ( 3448)
  covalent geometry    : angle       0.60171 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.6887 (tpp80) cc_final: 0.6426 (tpp80)
REVERT: C  471 GLU cc_start: 0.7590 (pm20) cc_final: 0.7070 (pm20)
REVERT: A   34 MET cc_start: 0.6757 (mmm) cc_final: 0.5527 (mmp)
REVERT: A   51 ILE cc_start: 0.7714 (tt) cc_final: 0.7441 (tt)
REVERT: A   67 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7159 (mtp180)
REVERT: A   74 ASN cc_start: 0.7002 (m-40) cc_final: 0.6755 (m-40)
REVERT: A   77 ASN cc_start: 0.6189 (p0) cc_final: 0.5986 (p0)
REVERT: A  103 TRP cc_start: 0.6123 (OUTLIER) cc_final: 0.5879 (p-90)
REVERT: A  112 TRP cc_start: 0.7505 (m-10) cc_final: 0.7296 (m100)
REVERT: B   73 SER cc_start: 0.8026 (p) cc_final: 0.7726 (t)
REVERT: B  102 PHE cc_start: 0.7049 (m-80) cc_final: 0.6722 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2092
  time to fit residues: 19.6957
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
A  77 ASN
** B  92 GLN ** 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 = 0.4561 r_free = 0.4561 target = 0.197549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.172786 restraints weight = 7646.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.177653 restraints weight = 5068.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.181021 restraints weight = 3633.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5389
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3454  Z= 0.132
  Angle     :  0.557   4.657   4701  Z= 0.301
  Chirality :  0.045   0.138    502
  Planarity :  0.005   0.038    609
  Dihedral  :  4.143  17.859    481
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.97 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.38), residues: 427
  helix: -4.95 (0.75), residues: 7
  sheet: -0.49 (0.43), residues: 138
  loop : -2.95 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 103 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.011   0.001   PHE C 464 
 TYR   0.025   0.002   TYR A 106 
 ARG   0.004   0.001   ARG C 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02934 (   71)
  hydrogen bonds       : angle       5.93493 (  189)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       0.68662 (   12)
  covalent geometry    : bond        0.00294 ( 3448)
  covalent geometry    : angle       0.55702 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  471 GLU cc_start: 0.7572 (pm20) cc_final: 0.6950 (pm20)
REVERT: A   34 MET cc_start: 0.6462 (mmm) cc_final: 0.5551 (mmp)
REVERT: A   67 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7104 (mtm110)
REVERT: B   37 TYR cc_start: 0.5421 (m-80) cc_final: 0.4939 (m-10)
REVERT: B   73 SER cc_start: 0.7963 (p) cc_final: 0.7637 (t)
REVERT: B  102 PHE cc_start: 0.7055 (m-80) cc_final: 0.6638 (m-10)
REVERT: B  106 THR cc_start: 0.7755 (m) cc_final: 0.7319 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 74
  average time/residue: 0.2083
  time to fit residues: 17.9660
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.192596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.168427 restraints weight = 7527.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.173105 restraints weight = 4987.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.176576 restraints weight = 3601.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5493
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3454  Z= 0.160
  Angle     :  0.605   6.012   4701  Z= 0.325
  Chirality :  0.045   0.134    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.698  18.637    481
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.05 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.39), residues: 427
  helix: -4.93 (0.78), residues: 7
  sheet: -0.40 (0.46), residues: 123
  loop : -2.80 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 103 
 HIS   0.003   0.001   HIS C 505 
 PHE   0.013   0.002   PHE B 102 
 TYR   0.024   0.002   TYR A 106 
 ARG   0.004   0.001   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03326 (   71)
  hydrogen bonds       : angle       6.39844 (  189)
  SS BOND              : bond        0.00231 (    6)
  SS BOND              : angle       0.66668 (   12)
  covalent geometry    : bond        0.00345 ( 3448)
  covalent geometry    : angle       0.60481 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.5824 (ttp80)
REVERT: C  471 GLU cc_start: 0.7686 (pm20) cc_final: 0.7076 (pm20)
REVERT: A   34 MET cc_start: 0.6478 (mmm) cc_final: 0.6023 (mmm)
REVERT: A   36 TRP cc_start: 0.6662 (m100) cc_final: 0.6447 (m100)
REVERT: A   39 GLN cc_start: 0.7473 (tt0) cc_final: 0.7185 (tt0)
REVERT: A   67 ARG cc_start: 0.7310 (mtm110) cc_final: 0.6904 (mtp180)
REVERT: A   96 CYS cc_start: 0.4017 (p) cc_final: 0.3611 (p)
REVERT: B  102 PHE cc_start: 0.6951 (m-80) cc_final: 0.6546 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.2083
  time to fit residues: 18.7618
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.192950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.168232 restraints weight = 7584.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.173009 restraints weight = 5092.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.176519 restraints weight = 3690.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3454  Z= 0.147
  Angle     :  0.601   4.778   4701  Z= 0.324
  Chirality :  0.046   0.136    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.730  20.005    481
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.38), residues: 427
  helix: -4.31 (0.85), residues: 13
  sheet: -0.48 (0.45), residues: 127
  loop : -3.00 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 103 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.011   0.001   PHE B 102 
 TYR   0.022   0.002   TYR A 106 
 ARG   0.003   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (   71)
  hydrogen bonds       : angle       6.30129 (  189)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       0.52290 (   12)
  covalent geometry    : bond        0.00320 ( 3448)
  covalent geometry    : angle       0.60156 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  457 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.5984 (ttp80)
REVERT: C  471 GLU cc_start: 0.7636 (pm20) cc_final: 0.7003 (pm20)
REVERT: C  494 SER cc_start: 0.7909 (p) cc_final: 0.7668 (p)
REVERT: A   39 GLN cc_start: 0.7567 (tt0) cc_final: 0.7237 (tt0)
REVERT: A   67 ARG cc_start: 0.7316 (mtm110) cc_final: 0.6993 (mtm110)
REVERT: B  102 PHE cc_start: 0.6827 (m-80) cc_final: 0.6536 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.2264
  time to fit residues: 19.8103
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0570
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0040
   overall best weight:    0.2122

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.196785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.173342 restraints weight = 7678.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.177983 restraints weight = 5071.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.181279 restraints weight = 3645.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5374
moved from start:          0.5107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3454  Z= 0.105
  Angle     :  0.570   5.346   4701  Z= 0.302
  Chirality :  0.045   0.141    502
  Planarity :  0.004   0.037    609
  Dihedral  :  4.449  21.101    481
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.82 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.39), residues: 427
  helix: -3.83 (1.76), residues: 6
  sheet: -0.33 (0.46), residues: 127
  loop : -2.78 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A  36 
 HIS   0.001   0.000   HIS B  99 
 PHE   0.010   0.001   PHE A  29 
 TYR   0.015   0.001   TYR A 106 
 ARG   0.005   0.001   ARG C 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02840 (   71)
  hydrogen bonds       : angle       5.92993 (  189)
  SS BOND              : bond        0.00662 (    6)
  SS BOND              : angle       0.53492 (   12)
  covalent geometry    : bond        0.00229 ( 3448)
  covalent geometry    : angle       0.56976 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7118 (ptp90) cc_final: 0.6439 (ptp90)
REVERT: C  457 ARG cc_start: 0.7285 (tpp-160) cc_final: 0.5912 (ttp80)
REVERT: C  471 GLU cc_start: 0.7426 (pm20) cc_final: 0.6861 (pm20)
REVERT: A   19 ARG cc_start: 0.7075 (tpp80) cc_final: 0.6765 (tpp80)
REVERT: A   36 TRP cc_start: 0.6374 (m100) cc_final: 0.6170 (m100)
REVERT: A   39 GLN cc_start: 0.7353 (tt0) cc_final: 0.7121 (tt0)
REVERT: B   40 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.6923 (mmm-85)
REVERT: B   73 SER cc_start: 0.7913 (p) cc_final: 0.7680 (t)
REVERT: B   81 LEU cc_start: 0.8095 (tp) cc_final: 0.7684 (tp)
REVERT: B  102 PHE cc_start: 0.6687 (m-80) cc_final: 0.6432 (m-10)
REVERT: B  106 THR cc_start: 0.7633 (m) cc_final: 0.7113 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2341
  time to fit residues: 20.2274
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** C 448 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 = 0.4489 r_free = 0.4489 target = 0.191789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.168302 restraints weight = 7590.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.173116 restraints weight = 5025.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.176425 restraints weight = 3598.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5537
moved from start:          0.5687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3454  Z= 0.202
  Angle     :  0.680   8.755   4701  Z= 0.361
  Chirality :  0.048   0.142    502
  Planarity :  0.006   0.060    609
  Dihedral  :  5.246  20.530    481
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.16 %
    Favored  : 83.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.39), residues: 427
  helix: -4.31 (0.82), residues: 15
  sheet: -0.49 (0.46), residues: 126
  loop : -2.93 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP A  47 
 HIS   0.004   0.001   HIS B  99 
 PHE   0.014   0.002   PHE C 490 
 TYR   0.017   0.002   TYR A 106 
 ARG   0.008   0.001   ARG C 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (   71)
  hydrogen bonds       : angle       6.35966 (  189)
  SS BOND              : bond        0.00346 (    6)
  SS BOND              : angle       0.96866 (   12)
  covalent geometry    : bond        0.00441 ( 3448)
  covalent geometry    : angle       0.67908 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.6893 (ptp90) cc_final: 0.6679 (ptp90)
REVERT: C  457 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.5918 (ttp80)
REVERT: C  471 GLU cc_start: 0.7647 (pm20) cc_final: 0.6981 (pm20)
REVERT: A   36 TRP cc_start: 0.6543 (m100) cc_final: 0.6108 (m100)
REVERT: A   38 ARG cc_start: 0.6756 (ptt180) cc_final: 0.5573 (ptt180)
REVERT: B   40 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.7081 (mmm-85)
REVERT: B   62 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7750 (mmm160)
REVERT: B   81 LEU cc_start: 0.8000 (tp) cc_final: 0.7651 (tp)
REVERT: B  107 LYS cc_start: 0.7237 (ttpp) cc_final: 0.6891 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2158
  time to fit residues: 18.6706
Evaluate side-chains
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0170
   overall best weight:    0.5426

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
** B  32 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 = 0.4515 r_free = 0.4515 target = 0.194232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.171496 restraints weight = 7613.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.176353 restraints weight = 5008.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.179755 restraints weight = 3526.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5450
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3454  Z= 0.128
  Angle     :  0.589   6.818   4701  Z= 0.314
  Chirality :  0.045   0.134    502
  Planarity :  0.005   0.037    609
  Dihedral  :  4.928  21.258    481
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.39), residues: 427
  helix: -3.81 (1.13), residues: 14
  sheet: -0.50 (0.46), residues: 126
  loop : -2.93 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A  47 
 HIS   0.003   0.001   HIS B  99 
 PHE   0.008   0.001   PHE C 342 
 TYR   0.027   0.002   TYR A 106 
 ARG   0.008   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (   71)
  hydrogen bonds       : angle       6.27408 (  189)
  SS BOND              : bond        0.00305 (    6)
  SS BOND              : angle       0.53091 (   12)
  covalent geometry    : bond        0.00284 ( 3448)
  covalent geometry    : angle       0.58947 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7138 (ptp90) cc_final: 0.6755 (ptp90)
REVERT: C  457 ARG cc_start: 0.7232 (tpp-160) cc_final: 0.5970 (ttp80)
REVERT: C  471 GLU cc_start: 0.7555 (pm20) cc_final: 0.7023 (pm20)
REVERT: C  494 SER cc_start: 0.7863 (p) cc_final: 0.7640 (p)
REVERT: A   36 TRP cc_start: 0.6478 (m100) cc_final: 0.6063 (m100)
REVERT: A   38 ARG cc_start: 0.6539 (ptt180) cc_final: 0.5680 (ptt180)
REVERT: A   45 LEU cc_start: 0.8284 (mt) cc_final: 0.7796 (mt)
REVERT: B   40 ARG cc_start: 0.7320 (tpp-160) cc_final: 0.6962 (mmm-85)
REVERT: B  106 THR cc_start: 0.7738 (m) cc_final: 0.7206 (p)
REVERT: B  107 LYS cc_start: 0.7273 (ttpp) cc_final: 0.6902 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2118
  time to fit residues: 17.3902
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.192977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.167911 restraints weight = 7642.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.172747 restraints weight = 5080.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.176212 restraints weight = 3678.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5516
moved from start:          0.6098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3454  Z= 0.160
  Angle     :  0.668   7.435   4701  Z= 0.350
  Chirality :  0.046   0.133    502
  Planarity :  0.005   0.038    609
  Dihedral  :  5.216  20.166    481
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.46 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.39), residues: 427
  helix: -3.86 (1.15), residues: 14
  sheet: -0.58 (0.46), residues: 126
  loop : -2.90 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP A 112 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.020   0.002   PHE C 347 
 TYR   0.036   0.002   TYR A 106 
 ARG   0.012   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03365 (   71)
  hydrogen bonds       : angle       6.56459 (  189)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       0.67067 (   12)
  covalent geometry    : bond        0.00358 ( 3448)
  covalent geometry    : angle       0.66764 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7078 (ptp90) cc_final: 0.6701 (ptp90)
REVERT: C  471 GLU cc_start: 0.7630 (pm20) cc_final: 0.7024 (pm20)
REVERT: A   36 TRP cc_start: 0.6541 (m100) cc_final: 0.6007 (m100)
REVERT: A   38 ARG cc_start: 0.6694 (ptt180) cc_final: 0.5734 (ptt180)
REVERT: B   40 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.7018 (mmm-85)
REVERT: B   81 LEU cc_start: 0.7964 (tp) cc_final: 0.7579 (tp)
REVERT: B  107 LYS cc_start: 0.7455 (ttpp) cc_final: 0.7092 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2061
  time to fit residues: 16.8991
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0030
   chunk 33 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.194653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.170136 restraints weight = 7687.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.174879 restraints weight = 5094.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178317 restraints weight = 3671.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5464
moved from start:          0.6177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3454  Z= 0.125
  Angle     :  0.606   6.350   4701  Z= 0.321
  Chirality :  0.044   0.137    502
  Planarity :  0.005   0.048    609
  Dihedral  :  4.957  21.260    481
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.39), residues: 427
  helix: -3.79 (1.12), residues: 14
  sheet: -0.46 (0.46), residues: 127
  loop : -2.83 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 103 
 HIS   0.002   0.000   HIS B  99 
 PHE   0.011   0.001   PHE C 347 
 TYR   0.029   0.002   TYR A 106 
 ARG   0.008   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (   71)
  hydrogen bonds       : angle       6.35366 (  189)
  SS BOND              : bond        0.00308 (    6)
  SS BOND              : angle       0.44778 (   12)
  covalent geometry    : bond        0.00279 ( 3448)
  covalent geometry    : angle       0.60597 ( 4689)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7132 (ptp90) cc_final: 0.6813 (ptp90)
REVERT: C  471 GLU cc_start: 0.7568 (pm20) cc_final: 0.6935 (pm20)
REVERT: A   36 TRP cc_start: 0.6426 (m100) cc_final: 0.6115 (m100)
REVERT: A   38 ARG cc_start: 0.6647 (ptt180) cc_final: 0.5543 (ptt180)
REVERT: B   36 TRP cc_start: 0.6465 (m100) cc_final: 0.6253 (m-10)
REVERT: B   40 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.7057 (mmm-85)
REVERT: B   81 LEU cc_start: 0.7996 (tp) cc_final: 0.7598 (tp)
REVERT: B  106 THR cc_start: 0.7692 (m) cc_final: 0.7116 (p)
REVERT: B  107 LYS cc_start: 0.7347 (ttpp) cc_final: 0.6911 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1776
  time to fit residues: 14.6290
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0010
   chunk 2 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0050
   overall best weight:    0.2400

-------------------------------------------------------------------------------
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 = 0.197498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.172777 restraints weight = 7899.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.177673 restraints weight = 5191.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.181141 restraints weight = 3723.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5399
moved from start:          0.6170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3454  Z= 0.099
  Angle     :  0.572   5.513   4701  Z= 0.302
  Chirality :  0.044   0.139    502
  Planarity :  0.005   0.047    609
  Dihedral  :  4.636  19.822    481
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.39), residues: 427
  helix: -3.45 (1.32), residues: 12
  sheet: -0.43 (0.46), residues: 128
  loop : -2.73 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 103 
 HIS   0.002   0.001   HIS B  99 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.026   0.001   TYR A 106 
 ARG   0.006   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02729 (   71)
  hydrogen bonds       : angle       6.01038 (  189)
  SS BOND              : bond        0.00318 (    6)
  SS BOND              : angle       0.38720 (   12)
  covalent geometry    : bond        0.00216 ( 3448)
  covalent geometry    : angle       0.57254 ( 4689)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.58 seconds
wall clock time: 30 minutes 35.52 seconds (1835.52 seconds total)