Starting phenix.real_space_refine
on Fri Aug 22 12:59:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xsn_38623/08_2025/8xsn_38623.cif"
  }
  resolution = 3.29
  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=   0.063
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      26      5.16       5
     C    1807      2.51       5
     N     417      2.21       5
     O     453      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 2703
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2676
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'RBF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.90, per 1000 atoms: 0.33
  Number of scatterers: 2703
  At special positions: 0
  Unit cell: (60.35, 71.4, 73.95, 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      26     16.00
     O     453      8.00
     N     417      7.00
     C    1807      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 69.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  662

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      85.2% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 15
      removed outlier: 4.032A  pdb=" N   MET A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A  15 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 31
      Proline residue:  A  28  - end of helix
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 39 through 51
      removed outlier: 3.618A  pdb=" N   TYR A  43 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A  46 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 65
      removed outlier: 3.807A  pdb=" N   LEU A  56 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 93
      removed outlier: 3.654A  pdb=" N   ILE A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE A  91 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TRP A  93 " --> pdb=" O   PHE A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 126
      removed outlier: 3.979A  pdb=" N   VAL A 124 " --> pdb=" O   CYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.885A  pdb=" N   MET A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 126 through 131'
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 137 through 147
      removed outlier: 4.057A  pdb=" N   PHE A 141 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 160
      removed outlier: 3.917A  pdb=" N   ALA A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 242
      removed outlier: 3.747A  pdb=" N   PHE A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   VAL A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLN A 242 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 316
      removed outlier: 4.132A  pdb=" N   ALA A 301 " --> pdb=" O   PRO A 297 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ILE A 303 " --> pdb=" O   HIS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 320
    Processing helix  chain 'A' and resid 321 through 327
    Processing helix  chain 'A' and resid 330 through 355
      removed outlier: 3.805A  pdb=" N   TYR A 334 " --> pdb=" O   GLY A 330 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ASN A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
    Processing helix  chain 'A' and resid 359 through 382
      removed outlier: 3.565A  pdb=" N   MET A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 425
      removed outlier: 3.694A  pdb=" N   GLU A 396 " --> pdb=" O   HIS A 392 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A 397 " --> pdb=" O   TRP A 393 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL A 413 " --> pdb=" O   CYS A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 452
      Proline residue:  A 449  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98
      removed outlier: 3.513A  pdb=" N   SER A  97 " --> pdb=" O   HIS A 104 " (cutoff:3.500A)

    195 hydrogen bonds defined for protein.
    582 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: 0.29

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 394
        1.30 -     1.43: 771
        1.43 -     1.56: 1573
        1.56 -     1.68: 0
        1.68 -     1.81: 40
  Bond restraints: 2778
  Sorted by residual:
  bond pdb=" C4  RBF A 501 "
       pdb=" C4A RBF A 501 "
    ideal  model  delta    sigma   weight residual
    1.481  1.346  0.135 2.00e-02 2.50e+03 4.56e+01
  bond pdb=" C10 RBF A 501 "
       pdb=" C4A RBF A 501 "
    ideal  model  delta    sigma   weight residual
    1.440  1.350  0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C9A RBF A 501 "
       pdb=" N10 RBF A 501 "
    ideal  model  delta    sigma   weight residual
    1.376  1.326  0.050 2.00e-02 2.50e+03 6.14e+00
  bond pdb=" C2  RBF A 501 "
       pdb=" N3  RBF A 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.348  0.049 2.00e-02 2.50e+03 5.92e+00
  bond pdb=" C4  RBF A 501 "
       pdb=" N3  RBF A 501 "
    ideal  model  delta    sigma   weight residual
    1.362  1.314  0.048 2.00e-02 2.50e+03 5.68e+00
  ... (remaining 2773 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.78: 3782
        3.78 -     7.56: 25
        7.56 -    11.33: 1
       11.33 -    15.11: 0
       15.11 -    18.89: 1
  Bond angle restraints: 3809
  Sorted by residual:
  angle pdb=" N   GLY A 160 "
        pdb=" CA  GLY A 160 "
        pdb=" C   GLY A 160 "
      ideal   model   delta    sigma   weight residual
     115.08  133.97  -18.89 1.54e+00 4.22e-01 1.50e+02
  angle pdb=" N   SER A 161 "
        pdb=" CA  SER A 161 "
        pdb=" C   SER A 161 "
      ideal   model   delta    sigma   weight residual
     111.00  120.43   -9.43 2.80e+00 1.28e-01 1.13e+01
  angle pdb=" C   SER A 384 "
        pdb=" N   PRO A 385 "
        pdb=" CA  PRO A 385 "
      ideal   model   delta    sigma   weight residual
     127.00  133.83   -6.83 2.40e+00 1.74e-01 8.10e+00
  angle pdb=" C   CYS A 409 "
        pdb=" N   LEU A 410 "
        pdb=" CA  LEU A 410 "
      ideal   model   delta    sigma   weight residual
     121.52  116.39    5.13 1.84e+00 2.95e-01 7.78e+00
  angle pdb=" N   SER A 161 "
        pdb=" CA  SER A 161 "
        pdb=" CB  SER A 161 "
      ideal   model   delta    sigma   weight residual
     110.50  115.18   -4.68 1.70e+00 3.46e-01 7.56e+00
  ... (remaining 3804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 1404
       16.45 -    32.90: 143
       32.90 -    49.35: 32
       49.35 -    65.80: 4
       65.80 -    82.25: 2
  Dihedral angle restraints: 1585
    sinusoidal: 561
      harmonic: 1024
  Sorted by residual:
  dihedral pdb=" N   SER A 161 "
           pdb=" C   SER A 161 "
           pdb=" CA  SER A 161 "
           pdb=" CB  SER A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.32  -14.52     0      2.50e+00 1.60e-01 3.37e+01
  dihedral pdb=" C   SER A 161 "
           pdb=" N   SER A 161 "
           pdb=" CA  SER A 161 "
           pdb=" CB  SER A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.17   12.57     0      2.50e+00 1.60e-01 2.53e+01
  dihedral pdb=" CA  VAL A 451 "
           pdb=" C   VAL A 451 "
           pdb=" N   ASN A 452 "
           pdb=" CA  ASN A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.77  -17.23     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 1582 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 467
       0.130 -    0.259: 4
       0.259 -    0.388: 0
       0.388 -    0.518: 0
       0.518 -    0.647: 1
  Chirality restraints: 472
  Sorted by residual:
  chirality pdb=" CA  SER A 161 "
            pdb=" N   SER A 161 "
            pdb=" C   SER A 161 "
            pdb=" CB  SER A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" CA  MET A  32 "
            pdb=" N   MET A  32 "
            pdb=" C   MET A  32 "
            pdb=" CB  MET A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" C4' RBF A 501 "
            pdb=" C3' RBF A 501 "
            pdb=" C5' RBF A 501 "
            pdb=" O4' RBF A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.49    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 469 not shown)

  Planarity restraints: 452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  27 "    0.040 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO A  28 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 318 "   -0.034 5.00e-02 4.00e+02   5.05e-02 4.09e+00
        pdb=" N   PRO A 319 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 319 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 319 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 355 "    0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO A 356 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "    0.017 5.00e-02 4.00e+02
  ... (remaining 449 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 626
        2.77 -     3.30: 2656
        3.30 -     3.84: 4252
        3.84 -     4.37: 4962
        4.37 -     4.90: 8690
  Nonbonded interactions: 21186
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 225 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH2 ARG A 422 "
            pdb=" OD1 ASP A 423 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   PRO A 346 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASN A 357 "
            pdb=" OG  SER A 359 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ARG A 422 "
            pdb=" NH2 ARG A 426 "
     model   vdw
     2.289 3.120
  ... (remaining 21181 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.830
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.100
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
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      :  0.007   0.135   2778  Z= 0.313
  Angle     :  0.845  18.888   3809  Z= 0.442
  Chirality :  0.054   0.647    472
  Planarity :  0.006   0.060    452
  Dihedral  : 14.246  82.253    923
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.27 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.43 (0.40), residues: 351
  helix: -0.62 (0.29), residues: 261
  sheet:  None (None), residues: 0
  loop : -1.48 (0.60), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 243 
 TYR   0.010   0.001   TYR A 412 
 PHE   0.015   0.002   PHE A 218 
 TRP   0.009   0.002   TRP A  93 
 HIS   0.005   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 2778)
  covalent geometry    : angle       0.84503 ( 3809)
  hydrogen bonds       : bond        0.13404 (  195)
  hydrogen bonds       : angle       5.54532 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.060 
Fit side-chains
REVERT: A   87 ILE cc_start: 0.6226 (mt) cc_final: 0.5874 (mt)
REVERT: A   98 TRP cc_start: 0.8193 (t-100) cc_final: 0.7796 (t-100)
REVERT: A  219 SER cc_start: 0.7860 (p) cc_final: 0.7625 (t)
  outliers start: 2
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0287
  time to fit residues: 1.9434
Evaluate side-chains
  39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0470
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
A 159 GLN
A 392 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.132361 restraints weight = 3773.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.00
r_work: 0.3367 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2778  Z= 0.138
  Angle     :  0.570   5.627   3809  Z= 0.284
  Chirality :  0.038   0.111    472
  Planarity :  0.005   0.047    452
  Dihedral  :  6.345  37.773    384
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.41 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.42 (0.42), residues: 351
  helix:  0.75 (0.30), residues: 265
  sheet:  None (None), residues: 0
  loop : -0.97 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 422 
 TYR   0.006   0.001   TYR A 324 
 PHE   0.011   0.001   PHE A 406 
 TRP   0.006   0.001   TRP A  24 
 HIS   0.002   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2778)
  covalent geometry    : angle       0.57039 ( 3809)
  hydrogen bonds       : bond        0.04300 (  195)
  hydrogen bonds       : angle       3.97108 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8529 (mt) cc_final: 0.8313 (mp)
REVERT: A  219 SER cc_start: 0.7909 (p) cc_final: 0.7609 (t)
REVERT: A  358 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7247 (mpt180)
  outliers start: 5
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0439
  time to fit residues: 2.7985
Evaluate side-chains
  44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0770
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 392 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.157181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135479 restraints weight = 3800.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.00
r_work: 0.3397 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2778  Z= 0.120
  Angle     :  0.526   5.492   3809  Z= 0.260
  Chirality :  0.036   0.106    472
  Planarity :  0.005   0.059    452
  Dihedral  :  6.074  39.741    384
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.12 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.37 (0.43), residues: 351
  helix:  1.45 (0.31), residues: 269
  sheet:  None (None), residues: 0
  loop : -0.81 (0.63), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.008   0.001   TYR A 412 
 PHE   0.011   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2778)
  covalent geometry    : angle       0.52566 ( 3809)
  hydrogen bonds       : bond        0.03868 (  195)
  hydrogen bonds       : angle       3.62321 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8490 (mt) cc_final: 0.8151 (mp)
REVERT: A   95 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7022 (mtp)
REVERT: A  358 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7202 (mpt180)
REVERT: A  412 TYR cc_start: 0.7982 (t80) cc_final: 0.7653 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0413
  time to fit residues: 2.7716
Evaluate side-chains
  47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0020
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 315 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 = 0.3771 r_free = 0.3771 target = 0.157610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.136107 restraints weight = 3741.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.96
r_work: 0.3399 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2778  Z= 0.122
  Angle     :  0.519   5.546   3809  Z= 0.255
  Chirality :  0.036   0.106    472
  Planarity :  0.005   0.042    452
  Dihedral  :  6.020  40.623    384
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.15 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.88 (0.44), residues: 351
  helix:  1.71 (0.31), residues: 274
  sheet:  None (None), residues: 0
  loop : -0.32 (0.67), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 426 
 TYR   0.007   0.001   TYR A 412 
 PHE   0.013   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2778)
  covalent geometry    : angle       0.51910 ( 3809)
  hydrogen bonds       : bond        0.03809 (  195)
  hydrogen bonds       : angle       3.55944 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7190 (mpt180)
REVERT: A  412 TYR cc_start: 0.7966 (t80) cc_final: 0.7653 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0369
  time to fit residues: 2.3054
Evaluate side-chains
  45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
A 315 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.134016 restraints weight = 3708.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.00
r_work: 0.3388 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2778  Z= 0.130
  Angle     :  0.536   5.768   3809  Z= 0.262
  Chirality :  0.037   0.107    472
  Planarity :  0.005   0.040    452
  Dihedral  :  6.021  40.085    384
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.81 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.97 (0.43), residues: 351
  helix:  1.76 (0.30), residues: 274
  sheet:  None (None), residues: 0
  loop : -0.22 (0.68), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 426 
 TYR   0.008   0.001   TYR A 412 
 PHE   0.013   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2778)
  covalent geometry    : angle       0.53577 ( 3809)
  hydrogen bonds       : bond        0.03913 (  195)
  hydrogen bonds       : angle       3.59389 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7218 (mtt90)
REVERT: A  412 TYR cc_start: 0.8002 (t80) cc_final: 0.7715 (t80)
REVERT: A  424 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5361 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0484
  time to fit residues: 2.9645
Evaluate side-chains
  47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.155978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.134305 restraints weight = 3804.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.00
r_work: 0.3389 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2778  Z= 0.133
  Angle     :  0.548   6.305   3809  Z= 0.265
  Chirality :  0.037   0.109    472
  Planarity :  0.005   0.040    452
  Dihedral  :  6.023  40.224    384
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 17.12 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.43), residues: 351
  helix:  1.84 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop : -0.04 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.007   0.001   TYR A 412 
 PHE   0.014   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 2778)
  covalent geometry    : angle       0.54836 ( 3809)
  hydrogen bonds       : bond        0.03933 (  195)
  hydrogen bonds       : angle       3.62035 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7202 (mtt90)
REVERT: A  412 TYR cc_start: 0.8004 (t80) cc_final: 0.7709 (t80)
REVERT: A  424 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5397 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 48
  average time/residue: 0.0425
  time to fit residues: 2.6837
Evaluate side-chains
  48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0470
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.135506 restraints weight = 3718.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.94
r_work: 0.3406 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2778  Z= 0.122
  Angle     :  0.536   6.647   3809  Z= 0.258
  Chirality :  0.037   0.106    472
  Planarity :  0.005   0.039    452
  Dihedral  :  5.985  40.508    384
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.84 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.43), residues: 351
  helix:  1.95 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop :  0.03 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.007   0.001   TYR A 412 
 PHE   0.013   0.001   PHE A 406 
 TRP   0.013   0.001   TRP A  98 
 HIS   0.002   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2778)
  covalent geometry    : angle       0.53610 ( 3809)
  hydrogen bonds       : bond        0.03784 (  195)
  hydrogen bonds       : angle       3.56492 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7184 (mtt90)
REVERT: A  412 TYR cc_start: 0.7972 (t80) cc_final: 0.7667 (t80)
REVERT: A  424 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5378 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0415
  time to fit residues: 2.5874
Evaluate side-chains
  48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  450 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0670
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.135096 restraints weight = 3826.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.97
r_work: 0.3401 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2778  Z= 0.127
  Angle     :  0.545   7.289   3809  Z= 0.261
  Chirality :  0.037   0.107    472
  Planarity :  0.005   0.040    452
  Dihedral  :  5.970  40.301    384
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.15 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.43), residues: 351
  helix:  1.96 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop :  0.03 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.007   0.001   TYR A 412 
 PHE   0.014   0.001   PHE A 406 
 TRP   0.014   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2778)
  covalent geometry    : angle       0.54454 ( 3809)
  hydrogen bonds       : bond        0.03820 (  195)
  hydrogen bonds       : angle       3.58247 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7169 (mtt90)
REVERT: A  412 TYR cc_start: 0.7977 (t80) cc_final: 0.7699 (t80)
REVERT: A  424 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5398 (mt)
  outliers start: 10
  outliers final: 9
  residues processed: 46
  average time/residue: 0.0431
  time to fit residues: 2.5649
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  450 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.134462 restraints weight = 3774.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.94
r_work: 0.3397 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2778  Z= 0.132
  Angle     :  0.554   7.832   3809  Z= 0.266
  Chirality :  0.037   0.108    472
  Planarity :  0.005   0.041    452
  Dihedral  :  5.981  40.405    384
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.81 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.43), residues: 351
  helix:  1.94 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop :  0.01 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.007   0.001   TYR A 412 
 PHE   0.013   0.001   PHE A 406 
 TRP   0.014   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2778)
  covalent geometry    : angle       0.55414 ( 3809)
  hydrogen bonds       : bond        0.03893 (  195)
  hydrogen bonds       : angle       3.60699 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7150 (mtt90)
REVERT: A  412 TYR cc_start: 0.7969 (t80) cc_final: 0.7684 (t80)
REVERT: A  424 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5431 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 48
  average time/residue: 0.0344
  time to fit residues: 2.1858
Evaluate side-chains
  49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0370
   chunk 13 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0070
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3276

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.159053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137787 restraints weight = 3794.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.96
r_work: 0.3433 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2778  Z= 0.110
  Angle     :  0.524   6.774   3809  Z= 0.251
  Chirality :  0.036   0.108    472
  Planarity :  0.005   0.041    452
  Dihedral  :  5.907  42.030    384
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.49 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.44), residues: 351
  helix:  2.14 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop :  0.12 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 358 
 TYR   0.006   0.001   TYR A 412 
 PHE   0.011   0.001   PHE A 406 
 TRP   0.014   0.001   TRP A  98 
 HIS   0.002   0.000   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2778)
  covalent geometry    : angle       0.52384 ( 3809)
  hydrogen bonds       : bond        0.03591 (  195)
  hydrogen bonds       : angle       3.48409 (  582)

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

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

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  702 Ramachandran restraints generated.
    351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7125 (mtt90)
REVERT: A  412 TYR cc_start: 0.7921 (t80) cc_final: 0.7602 (t80)
REVERT: A  424 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5379 (mt)
REVERT: A  447 MET cc_start: 0.8452 (mmm) cc_final: 0.8174 (tpt)
  outliers start: 9
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0399
  time to fit residues: 2.5352
Evaluate side-chains
  50 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  424 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0020
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.156590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135282 restraints weight = 3779.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.96
r_work: 0.3406 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2778  Z= 0.132
  Angle     :  0.563   7.943   3809  Z= 0.270
  Chirality :  0.038   0.155    472
  Planarity :  0.005   0.040    452
  Dihedral  :  5.950  40.588    384
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.86 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.43), residues: 351
  helix:  2.04 (0.30), residues: 273
  sheet:  None (None), residues: 0
  loop :  0.15 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 358 
 TYR   0.008   0.001   TYR A 412 
 PHE   0.014   0.001   PHE A 406 
 TRP   0.014   0.001   TRP A  98 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2778)
  covalent geometry    : angle       0.56335 ( 3809)
  hydrogen bonds       : bond        0.03922 (  195)
  hydrogen bonds       : angle       3.65953 (  582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 808.15 seconds
wall clock time: 14 minutes 24.70 seconds (864.70 seconds total)