Starting phenix.real_space_refine
on Tue Aug  4 13:17:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/12pb_76659/08_2026/12pb_76659.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      24      5.16       5
     C    2040      2.51       5
     N     538      2.21       5
     O     578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3180
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 967
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 6, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 2213
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 285, 2201
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
      Conformer: "B"
        Number of residues, atoms: 285, 2201
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          bond proxies already assigned to first conformer: 2238
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 201 " occ=0.48
      ... (22 atoms not shown)
      pdb=" OH BTYR A 201 " occ=0.52
  Time building chain proxies: 0.89, per 1000 atoms: 0.28
  Number of scatterers: 3180
  At special positions: 0
  Unit cell: (73.216, 69.056, 101.504, 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      24     16.00
     O     578      8.00
     N     538      7.00
     C    2040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  98 " 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: 0.27
  Conformation dependent library (CDL) restraints added in 191.9 milliseconds
  

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 4 sheets defined
      53.9% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.727A  pdb=" N   SER B  32 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.682A  pdb=" N   THR B  93 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'A' and resid 3 through 31
      Proline residue:  A  20  - end of helix
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 3.503A  pdb=" N   ARG A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 150
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.427A  pdb=" N   GLY A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 164 through 173
      removed outlier: 4.055A  pdb=" N   THR A 168 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 182 through 210
    Processing helix  chain 'A' and resid 216 through 235
    Processing helix  chain 'A' and resid 235 through 248
      removed outlier: 3.739A  pdb=" N   ASP A 239 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 277
    Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 10
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 62
      removed outlier: 6.658A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   MET B  37 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 62
      removed outlier: 6.658A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   MET B  37 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 40 through 41

    206 hydrogen bonds defined for protein.
    562 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: 0.50

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1015
        1.34 -     1.46: 786
        1.46 -     1.58: 1423
        1.58 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 3258
  Sorted by residual:
  bond pdb=" C   PRO A  36 "
       pdb=" N   PRO A  37 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.02e-01
  bond pdb=" CB  PRO A  37 "
       pdb=" CG  PRO A  37 "
    ideal  model  delta    sigma   weight residual
    1.492  1.530 -0.038 5.00e-02 4.00e+02 5.71e-01
  bond pdb=" CB  PRO A 237 "
       pdb=" CG  PRO A 237 "
    ideal  model  delta    sigma   weight residual
    1.492  1.467  0.025 5.00e-02 4.00e+02 2.52e-01
  bond pdb=" CG  PRO A  37 "
       pdb=" CD  PRO A  37 "
    ideal  model  delta    sigma   weight residual
    1.503  1.486  0.017 3.40e-02 8.65e+02 2.42e-01
  bond pdb=" C   VAL A 217 "
       pdb=" N   PRO A 218 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.006 1.36e-02 5.41e+03 2.27e-01
  ... (remaining 3253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 4379
        1.64 -     3.28: 33
        3.28 -     4.91: 5
        4.91 -     6.55: 5
        6.55 -     8.19: 1
  Bond angle restraints: 4423
  Sorted by residual:
  angle pdb=" C   PRO A  36 "
        pdb=" N   PRO A  37 "
        pdb=" CD  PRO A  37 "
      ideal   model   delta    sigma   weight residual
     125.00  133.19   -8.19 4.10e+00 5.95e-02 3.99e+00
  angle pdb=" CA  LEU A   9 "
        pdb=" CB  LEU A   9 "
        pdb=" CG  LEU A   9 "
      ideal   model   delta    sigma   weight residual
     116.30  121.87   -5.57 3.50e+00 8.16e-02 2.53e+00
  angle pdb=" C   PRO A  36 "
        pdb=" N   PRO A  37 "
        pdb=" CA  PRO A  37 "
      ideal   model   delta    sigma   weight residual
     120.53  116.74    3.79 2.52e+00 1.57e-01 2.26e+00
  angle pdb=" CA  PRO A  37 "
        pdb=" N   PRO A  37 "
        pdb=" CD  PRO A  37 "
      ideal   model   delta    sigma   weight residual
     112.00  109.95    2.05 1.40e+00 5.10e-01 2.15e+00
  angle pdb=" C   ASN A 283 "
        pdb=" N   SER A 284 "
        pdb=" CA  SER A 284 "
      ideal   model   delta    sigma   weight residual
     121.54  124.34   -2.80 1.91e+00 2.74e-01 2.15e+00
  ... (remaining 4418 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.60: 1770
       12.60 -    25.21: 100
       25.21 -    37.81: 33
       37.81 -    50.41: 10
       50.41 -    63.02: 3
  Dihedral angle restraints: 1916
    sinusoidal: 740
      harmonic: 1176
  Sorted by residual:
  dihedral pdb=" N   ASN A 248 "
           pdb=" CA  ASN A 248 "
           pdb=" CB  ASN A 248 "
           pdb=" CG  ASN A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.59  -56.59     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" N   TYR A  57 "
           pdb=" CA  TYR A  57 "
           pdb=" CB  TYR A  57 "
           pdb=" CG  TYR A  57 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.59  -56.41     3      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CA  GLU A 156 "
           pdb=" CB  GLU A 156 "
           pdb=" CG  GLU A 156 "
           pdb=" CD  GLU A 156 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.72   44.28     3      1.50e+01 4.44e-03 7.97e+00
  ... (remaining 1913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 260
       0.024 -    0.048: 151
       0.048 -    0.073: 54
       0.073 -    0.097: 12
       0.097 -    0.121: 14
  Chirality restraints: 491
  Sorted by residual:
  chirality pdb=" CA  VAL A 290 "
            pdb=" N   VAL A 290 "
            pdb=" C   VAL A 290 "
            pdb=" CB  VAL A 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  VAL B  95 "
            pdb=" N   VAL B  95 "
            pdb=" C   VAL B  95 "
            pdb=" CB  VAL B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.28e-01
  chirality pdb=" CA  ILE A  39 "
            pdb=" N   ILE A  39 "
            pdb=" C   ILE A  39 "
            pdb=" CB  ILE A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 488 not shown)

  Planarity restraints: 563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  35 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO A  36 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A  36 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  36 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 236 "   -0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO A 237 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 237 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 237 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 217 "   -0.016 5.00e-02 4.00e+02   2.48e-02 9.84e-01
        pdb=" N   PRO A 218 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 560 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.09: 2310
        3.09 -     3.54: 3433
        3.54 -     3.99: 4602
        3.99 -     4.45: 5780
        4.45 -     4.90: 8863
  Nonbonded interactions: 24988
  Sorted by model distance:
  nonbonded pdb=" C   ASN A 248 "
            pdb=" CG  ASN A 248 "
     model   vdw
     2.633 2.800
  nonbonded pdb=" N   ILE A  39 "
            pdb=" O   ILE A  39 "
     model   vdw
     2.637 2.496
  nonbonded pdb=" N   ASP A 216 "
            pdb=" O   ASP A 216 "
     model   vdw
     2.646 2.496
  nonbonded pdb=" N   LYS A 289 "
            pdb=" O   LYS A 289 "
     model   vdw
     2.652 2.496
  nonbonded pdb=" N   ALA B  94 "
            pdb=" O   ALA B  94 "
     model   vdw
     2.658 2.496
  ... (remaining 24983 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=0.48 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:             9.660
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.140
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
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      :  0.003   0.038   3259  Z= 0.117
  Angle     :  0.462   8.191   4425  Z= 0.223
  Chirality :  0.037   0.121    491
  Planarity :  0.003   0.031    563
  Dihedral  :  9.859  63.016   1167
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.43 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.43), residues: 407
  helix:  3.49 (0.37), residues: 185
  sheet:  1.70 (0.75), residues: 42
  loop : -0.03 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.007   0.001   TYR A  32 
 PHE   0.010   0.001   PHE B  50 
 TRP   0.005   0.001   TRP A 266 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 3258)
  covalent geometry    : angle       0.46203 /  0.22 ( 4423)
  SS BOND              : bond        0.00063 /  0.03 (    1)
  SS BOND              : angle       0.63358 /  0.37 (    2)
  hydrogen bonds       : bond        0.14269 /  9.89 (  193)
  hydrogen bonds       : angle       5.31353 /  3.90 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8675 (mp10)
REVERT: B   89 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9012 (mm-30)
REVERT: A   33 GLU cc_start: 0.8437 (tp30) cc_final: 0.8224 (tp30)
REVERT: A   90 LYS cc_start: 0.8301 (tptt) cc_final: 0.7840 (mmmt)
REVERT: A  245 MET cc_start: 0.9026 (mmm) cc_final: 0.8814 (mmm)
REVERT: A  248 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7848 (p0)
REVERT: A  276 GLU cc_start: 0.9399 (tp30) cc_final: 0.9055 (tp30)
REVERT: A  279 MET cc_start: 0.7477 (ttp) cc_final: 0.7093 (tpp)
  outliers start: 3
  outliers final: 2
  residues processed: 47
  average time/residue: 0.0785
  time to fit residues: 4.4674
Evaluate side-chains
  37 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  248 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0470
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.3278

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.088264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.059761 restraints weight = 34595.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 6.39
r_work: 0.2830 rms_B_bonded: 6.38 restraints_weight: 2.0000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3259  Z= 0.123
  Angle     :  0.514   7.992   4425  Z= 0.258
  Chirality :  0.038   0.126    491
  Planarity :  0.004   0.053    563
  Dihedral  :  4.960  56.635    458
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.65 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.43), residues: 407
  helix:  3.63 (0.37), residues: 186
  sheet:  1.51 (0.69), residues: 42
  loop :  0.11 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B   5 
 TYR   0.007   0.001   TYR A 170 
 PHE   0.015   0.001   PHE B  50 
 TRP   0.006   0.001   TRP A 270 
 HIS   0.004   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 3258)
  covalent geometry    : angle       0.51428 /  0.26 ( 4423)
  SS BOND              : bond        0.00066 /  0.03 (    1)
  SS BOND              : angle       0.21878 /  0.13 (    2)
  hydrogen bonds       : bond        0.03386 /  2.37 (  193)
  hydrogen bonds       : angle       3.81277 /  2.74 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: B    6 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8526 (mp10)
REVERT: B  120 TYR cc_start: 0.8591 (m-80) cc_final: 0.8234 (m-80)
REVERT: A   90 LYS cc_start: 0.8321 (tptt) cc_final: 0.7859 (mmmt)
REVERT: A  210 ASN cc_start: 0.9297 (m-40) cc_final: 0.8826 (m110)
REVERT: A  248 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (p0)
REVERT: A  276 GLU cc_start: 0.9309 (tp30) cc_final: 0.9030 (tp30)
REVERT: A  279 MET cc_start: 0.7622 (ttp) cc_final: 0.7316 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 43
  average time/residue: 0.0514
  time to fit residues: 2.7865
Evaluate side-chains
  39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  248 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0170
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   overall best weight:    0.3596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.088281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.060051 restraints weight = 28148.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 5.95
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3259  Z= 0.122
  Angle     :  0.533   8.362   4425  Z= 0.257
  Chirality :  0.037   0.123    491
  Planarity :  0.004   0.029    563
  Dihedral  :  4.826  56.654    458
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.94 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.43), residues: 407
  helix:  3.61 (0.37), residues: 186
  sheet:  1.39 (0.67), residues: 42
  loop :  0.07 (0.49), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   5 
 TYR   0.009   0.001   TYR A 170 
 PHE   0.014   0.001   PHE B  50 
 TRP   0.005   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 3258)
  covalent geometry    : angle       0.53266 /  0.26 ( 4423)
  SS BOND              : bond        0.00088 /  0.05 (    1)
  SS BOND              : angle       0.16042 /  0.09 (    2)
  hydrogen bonds       : bond        0.03046 /  2.11 (  193)
  hydrogen bonds       : angle       3.60027 /  2.59 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
REVERT: B    6 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8451 (mp10)
REVERT: B   89 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8897 (mm-30)
REVERT: A   33 GLU cc_start: 0.7968 (tp30) cc_final: 0.7680 (tp30)
REVERT: A   90 LYS cc_start: 0.8322 (tptt) cc_final: 0.7880 (mmmt)
REVERT: A  210 ASN cc_start: 0.9075 (m-40) cc_final: 0.8698 (m-40)
REVERT: A  276 GLU cc_start: 0.9202 (tp30) cc_final: 0.8995 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 40
  average time/residue: 0.0588
  time to fit residues: 2.9180
Evaluate side-chains
  36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.087802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.059120 restraints weight = 30848.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 6.12
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3259  Z= 0.146
  Angle     :  0.548   8.375   4425  Z= 0.260
  Chirality :  0.037   0.123    491
  Planarity :  0.004   0.029    563
  Dihedral  :  4.088  52.396    456
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.23 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.43), residues: 407
  helix:  3.58 (0.36), residues: 187
  sheet:  1.40 (0.68), residues: 42
  loop :  0.05 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.014   0.001   TYR B 120 
 PHE   0.017   0.001   PHE B  50 
 TRP   0.006   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 3258)
  covalent geometry    : angle       0.54810 /  0.26 ( 4423)
  SS BOND              : bond        0.00115 /  0.06 (    1)
  SS BOND              : angle       0.15359 /  0.09 (    2)
  hydrogen bonds       : bond        0.02951 /  2.05 (  193)
  hydrogen bonds       : angle       3.57298 /  2.57 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.071 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8393 (mp10)
REVERT: B   89 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8893 (mm-30)
REVERT: A   90 LYS cc_start: 0.8343 (tptt) cc_final: 0.7886 (mmmt)
REVERT: A  210 ASN cc_start: 0.9057 (m-40) cc_final: 0.8705 (m-40)
REVERT: A  279 MET cc_start: 0.8562 (tpp) cc_final: 0.8248 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0428
  time to fit residues: 2.0846
Evaluate side-chains
  38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  248 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0670
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.4918

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.087381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.058794 restraints weight = 28761.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 6.01
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3259  Z= 0.142
  Angle     :  0.551   7.988   4425  Z= 0.264
  Chirality :  0.037   0.117    491
  Planarity :  0.004   0.029    563
  Dihedral  :  4.087  51.575    456
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.53 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.43), residues: 407
  helix:  3.56 (0.36), residues: 187
  sheet:  1.42 (0.69), residues: 42
  loop :  0.08 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   5 
 TYR   0.025   0.001   TYR B 120 
 PHE   0.015   0.001   PHE B  50 
 TRP   0.006   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 3258)
  covalent geometry    : angle       0.55126 /  0.26 ( 4423)
  SS BOND              : bond        0.00113 /  0.06 (    1)
  SS BOND              : angle       0.15757 /  0.09 (    2)
  hydrogen bonds       : bond        0.02894 /  2.02 (  193)
  hydrogen bonds       : angle       3.54522 /  2.55 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8873 (mm-30)
REVERT: A   90 LYS cc_start: 0.8346 (tptt) cc_final: 0.7892 (mmmt)
REVERT: A  210 ASN cc_start: 0.9055 (m-40) cc_final: 0.8701 (m-40)
REVERT: A  279 MET cc_start: 0.8598 (tpp) cc_final: 0.8205 (tpp)
  outliers start: 5
  outliers final: 3
  residues processed: 39
  average time/residue: 0.0466
  time to fit residues: 2.3760
Evaluate side-chains
  37 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.087236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.059811 restraints weight = 20820.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 6.70
r_work: 0.2786 rms_B_bonded: 6.32 restraints_weight: 2.0000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3259  Z= 0.192
  Angle     :  0.564   7.944   4425  Z= 0.274
  Chirality :  0.038   0.121    491
  Planarity :  0.004   0.030    563
  Dihedral  :  4.130  50.752    456
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.23 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.43), residues: 407
  helix:  3.53 (0.36), residues: 187
  sheet:  1.34 (0.71), residues: 40
  loop :  0.09 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 120 
 PHE   0.019   0.001   PHE B  50 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.004   0.001   HIS A 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.19 ( 3258)
  covalent geometry    : angle       0.56445 /  0.27 ( 4423)
  SS BOND              : bond        0.00182 /  0.10 (    1)
  SS BOND              : angle       0.13794 /  0.08 (    2)
  hydrogen bonds       : bond        0.03029 /  2.11 (  193)
  hydrogen bonds       : angle       3.59670 /  2.58 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8324 (tptt) cc_final: 0.7864 (mmmt)
REVERT: A  210 ASN cc_start: 0.9202 (m-40) cc_final: 0.8916 (m-40)
REVERT: A  279 MET cc_start: 0.8730 (tpp) cc_final: 0.8325 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0758
  time to fit residues: 3.4897
Evaluate side-chains
  38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  169 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.0020
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.087697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.058441 restraints weight = 26164.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 5.89
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3259  Z= 0.157
  Angle     :  0.565   8.004   4425  Z= 0.275
  Chirality :  0.038   0.118    491
  Planarity :  0.004   0.031    563
  Dihedral  :  4.094  50.115    456
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.11 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.43), residues: 407
  helix:  3.52 (0.36), residues: 187
  sheet:  1.31 (0.72), residues: 40
  loop :  0.02 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.021   0.001   TYR B 120 
 PHE   0.016   0.001   PHE B  50 
 TRP   0.006   0.001   TRP A 194 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 3258)
  covalent geometry    : angle       0.56517 /  0.27 ( 4423)
  SS BOND              : bond        0.00144 /  0.08 (    1)
  SS BOND              : angle       0.15453 /  0.09 (    2)
  hydrogen bonds       : bond        0.02889 /  2.01 (  193)
  hydrogen bonds       : angle       3.56682 /  2.56 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8326 (tptt) cc_final: 0.7883 (mmmt)
REVERT: A  210 ASN cc_start: 0.9011 (m-40) cc_final: 0.8663 (m-40)
REVERT: A  279 MET cc_start: 0.8648 (tpp) cc_final: 0.7981 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0594
  time to fit residues: 2.8442
Evaluate side-chains
  38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.087194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057789 restraints weight = 33566.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 6.35
r_work: 0.2800 rms_B_bonded: 6.30 restraints_weight: 2.0000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3259  Z= 0.180
  Angle     :  0.581   8.023   4425  Z= 0.283
  Chirality :  0.038   0.122    491
  Planarity :  0.004   0.030    563
  Dihedral  :  4.148  49.972    456
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.40 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.43), residues: 407
  helix:  3.47 (0.36), residues: 187
  sheet:  1.31 (0.71), residues: 40
  loop : -0.01 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.020   0.001   TYR B 120 
 PHE   0.017   0.001   PHE B  50 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.003   0.001   HIS A 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.18 ( 3258)
  covalent geometry    : angle       0.58093 /  0.28 ( 4423)
  SS BOND              : bond        0.00175 /  0.09 (    1)
  SS BOND              : angle       0.14025 /  0.08 (    2)
  hydrogen bonds       : bond        0.02960 /  2.06 (  193)
  hydrogen bonds       : angle       3.61757 /  2.59 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.096 
Fit side-chains
REVERT: B   89 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8840 (mm-30)
REVERT: A   90 LYS cc_start: 0.8332 (tptt) cc_final: 0.7872 (mmmt)
REVERT: A  210 ASN cc_start: 0.9195 (m-40) cc_final: 0.8909 (m-40)
REVERT: A  276 GLU cc_start: 0.9206 (tp30) cc_final: 0.8799 (tm-30)
REVERT: A  279 MET cc_start: 0.8759 (tpp) cc_final: 0.8054 (tpp)
  outliers start: 6
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0474
  time to fit residues: 2.3119
Evaluate side-chains
  39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  248 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.7782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.086868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.057519 restraints weight = 31739.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 6.18
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3259  Z= 0.201
  Angle     :  0.602   8.006   4425  Z= 0.295
  Chirality :  0.039   0.121    491
  Planarity :  0.004   0.030    563
  Dihedral  :  4.216  49.906    456
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.70 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.42), residues: 407
  helix:  3.40 (0.37), residues: 187
  sheet:  1.31 (0.71), residues: 40
  loop : -0.03 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.019   0.001   TYR B 120 
 PHE   0.019   0.001   PHE B  50 
 TRP   0.008   0.001   TRP A 270 
 HIS   0.004   0.001   HIS A 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00475 /  0.20 ( 3258)
  covalent geometry    : angle       0.60209 /  0.30 ( 4423)
  SS BOND              : bond        0.00186 /  0.10 (    1)
  SS BOND              : angle       0.17948 /  0.10 (    2)
  hydrogen bonds       : bond        0.03037 /  2.11 (  193)
  hydrogen bonds       : angle       3.64896 /  2.61 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.084 
Fit side-chains
REVERT: B   82 TYR cc_start: 0.8710 (m-10) cc_final: 0.8444 (m-10)
REVERT: A   90 LYS cc_start: 0.8334 (tptt) cc_final: 0.7898 (mmmt)
REVERT: A  210 ASN cc_start: 0.9011 (m-40) cc_final: 0.8661 (m-40)
REVERT: A  272 MET cc_start: 0.8795 (tpp) cc_final: 0.8434 (tpp)
REVERT: A  276 GLU cc_start: 0.9194 (tp30) cc_final: 0.8781 (tm-30)
REVERT: A  279 MET cc_start: 0.8724 (tpp) cc_final: 0.7938 (tpp)
  outliers start: 6
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0536
  time to fit residues: 2.5914
Evaluate side-chains
  39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  248 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 12 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0470
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.3078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 248 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 = 0.3709 r_free = 0.3709 target = 0.088220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.059298 restraints weight = 30015.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 6.16
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3259  Z= 0.127
  Angle     :  0.594   8.440   4425  Z= 0.287
  Chirality :  0.037   0.119    491
  Planarity :  0.004   0.032    563
  Dihedral  :  4.084  48.965    456
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.57 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.43), residues: 407
  helix:  3.44 (0.37), residues: 187
  sheet:  1.36 (0.69), residues: 42
  loop :  0.00 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 126 
 TYR   0.019   0.001   TYR B 120 
 PHE   0.011   0.001   PHE B  50 
 TRP   0.006   0.001   TRP A 266 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 3258)
  covalent geometry    : angle       0.59441 /  0.29 ( 4423)
  SS BOND              : bond        0.00055 /  0.03 (    1)
  SS BOND              : angle       0.12570 /  0.07 (    2)
  hydrogen bonds       : bond        0.02756 /  1.90 (  193)
  hydrogen bonds       : angle       3.56784 /  2.55 (  562)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8328 (tptt) cc_final: 0.7884 (mmmt)
REVERT: A  210 ASN cc_start: 0.8987 (m-40) cc_final: 0.8572 (m-40)
REVERT: A  272 MET cc_start: 0.8745 (tpp) cc_final: 0.8410 (tpp)
REVERT: A  276 GLU cc_start: 0.9213 (tp30) cc_final: 0.8831 (tm-30)
REVERT: A  279 MET cc_start: 0.8724 (tpp) cc_final: 0.7923 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0688
  time to fit residues: 3.3477
Evaluate side-chains
  38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  169 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 14 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 248 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 = 0.3708 r_free = 0.3708 target = 0.088142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.058803 restraints weight = 30370.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 6.27
r_work: 0.2830 rms_B_bonded: 6.26 restraints_weight: 2.0000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3259  Z= 0.149
  Angle     :  0.627   9.683   4425  Z= 0.306
  Chirality :  0.038   0.119    491
  Planarity :  0.004   0.031    563
  Dihedral  :  4.137  49.591    456
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.16 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.43), residues: 407
  helix:  3.40 (0.37), residues: 187
  sheet:  1.44 (0.69), residues: 42
  loop : -0.04 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 171 
 TYR   0.017   0.001   TYR B 120 
 PHE   0.014   0.001   PHE B  50 
 TRP   0.018   0.002   TRP A 194 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 3258)
  covalent geometry    : angle       0.62722 /  0.31 ( 4423)
  SS BOND              : bond        0.00080 /  0.04 (    1)
  SS BOND              : angle       0.12848 /  0.07 (    2)
  hydrogen bonds       : bond        0.02884 /  2.01 (  193)
  hydrogen bonds       : angle       3.62603 /  2.59 (  562)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1090.49 seconds
wall clock time: 19 minutes 16.68 seconds (1156.68 seconds total)