Starting phenix.real_space_refine
on Wed Sep 17 03:24:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jrn_61761/09_2025/9jrn_61761.map"
  }
  resolution = 3.74
  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=   0.004 sd=   0.055
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      11      5.16       5
     C    2088      2.51       5
     N     512      2.21       5
     O     516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3129
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3103
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 12, 'TRANS': 373}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'TPP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.99, per 1000 atoms: 0.32
  Number of scatterers: 3129
  At special positions: 0
  Unit cell: (68, 65, 75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      11     16.00
     P       2     15.00
     O     516      8.00
     N     512      7.00
     C    2088      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: 0.31
  Conformation dependent library (CDL) restraints added in 116.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  730

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      89.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 40
      removed outlier: 4.213A  pdb=" N   VAL A  29 " --> pdb=" O   TRP A  25 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR A  31 " --> pdb=" O   HIS A  27 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 68
    Processing helix  chain 'A' and resid 68 through 90
      removed outlier: 3.580A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 4.063A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   TYR A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 4.338A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.594A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.823A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 148 through 176
      removed outlier: 3.501A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 201
    Processing helix  chain 'A' and resid 250 through 264
      removed outlier: 3.945A  pdb=" N   ARG A 264 " --> pdb=" O   ASP A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 287
      removed outlier: 3.777A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 304 through 325
      removed outlier: 3.554A  pdb=" N   ALA A 308 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ASP A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 355
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 390
      removed outlier: 3.597A  pdb=" N   LEU A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 395 through 419
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 3.746A  pdb=" N   GLN A 433 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    723 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: 0.59

  Time building geometry restraints manager: 0.35 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: 921
        1.34 -     1.46: 708
        1.46 -     1.57: 1566
        1.57 -     1.69: 4
        1.69 -     1.81: 17
  Bond restraints: 3216
  Sorted by residual:
  bond pdb=" N   THR A  49 "
       pdb=" CA  THR A  49 "
    ideal  model  delta    sigma   weight residual
    1.461  1.487 -0.026 9.20e-03 1.18e+04 7.74e+00
  bond pdb=" C   THR A  49 "
       pdb=" N   PRO A  50 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.36e-02 5.41e+03 2.13e+00
  bond pdb=" CA  THR A  49 "
       pdb=" C   THR A  49 "
    ideal  model  delta    sigma   weight residual
    1.520  1.536 -0.016 1.23e-02 6.61e+03 1.65e+00
  bond pdb=" CG  LEU A 426 "
       pdb=" CD1 LEU A 426 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.61e-01
  bond pdb=" C   THR A  69 "
       pdb=" N   PRO A  70 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.48e-01
  ... (remaining 3211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 4311
        1.90 -     3.81: 59
        3.81 -     5.71: 12
        5.71 -     7.61: 0
        7.61 -     9.52: 2
  Bond angle restraints: 4384
  Sorted by residual:
  angle pdb=" CA  LEU A 426 "
        pdb=" CB  LEU A 426 "
        pdb=" CG  LEU A 426 "
      ideal   model   delta    sigma   weight residual
     116.30  125.82   -9.52 3.50e+00 8.16e-02 7.39e+00
  angle pdb=" C   LEU A  28 "
        pdb=" N   VAL A  29 "
        pdb=" CA  VAL A  29 "
      ideal   model   delta    sigma   weight residual
     122.63  119.80    2.83 1.19e+00 7.06e-01 5.67e+00
  angle pdb=" CA  LEU A 112 "
        pdb=" CB  LEU A 112 "
        pdb=" CG  LEU A 112 "
      ideal   model   delta    sigma   weight residual
     116.30  124.20   -7.90 3.50e+00 8.16e-02 5.09e+00
  angle pdb=" N   GLY A 325 "
        pdb=" CA  GLY A 325 "
        pdb=" C   GLY A 325 "
      ideal   model   delta    sigma   weight residual
     115.62  111.97    3.65 1.71e+00 3.42e-01 4.56e+00
  angle pdb=" CA  THR A  49 "
        pdb=" C   THR A  49 "
        pdb=" O   THR A  49 "
      ideal   model   delta    sigma   weight residual
     118.73  116.81    1.92 9.80e-01 1.04e+00 3.83e+00
  ... (remaining 4379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 1546
       17.68 -    35.36: 228
       35.36 -    53.05: 50
       53.05 -    70.73: 8
       70.73 -    88.41: 5
  Dihedral angle restraints: 1837
    sinusoidal: 701
      harmonic: 1136
  Sorted by residual:
  dihedral pdb=" CB  GLU A 257 "
           pdb=" CG  GLU A 257 "
           pdb=" CD  GLU A 257 "
           pdb=" OE1 GLU A 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.60   83.60     1      3.00e+01 1.11e-03 9.48e+00
  dihedral pdb=" CA  GLU A  62 "
           pdb=" CB  GLU A  62 "
           pdb=" CG  GLU A  62 "
           pdb=" CD  GLU A  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.35  -54.35     3      1.50e+01 4.44e-03 9.28e+00
  dihedral pdb=" N   LYS A 336 "
           pdb=" CA  LYS A 336 "
           pdb=" CB  LYS A 336 "
           pdb=" CG  LYS A 336 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.02   54.02     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 1834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 318
       0.028 -    0.056: 135
       0.056 -    0.084: 42
       0.084 -    0.113: 11
       0.113 -    0.141: 3
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE A  41 "
            pdb=" N   ILE A  41 "
            pdb=" C   ILE A  41 "
            pdb=" CB  ILE A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.69e-01
  chirality pdb=" CA  ILE A 329 "
            pdb=" N   ILE A 329 "
            pdb=" C   ILE A 329 "
            pdb=" CB  ILE A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  ... (remaining 506 not shown)

  Planarity restraints: 521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 103 "   -0.009 2.00e-02 2.50e+03   1.11e-02 2.15e+00
        pdb=" CG  PHE A 103 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 103 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 103 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 103 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 103 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 103 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 145 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO A 146 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.53e+00
        pdb=" N   PRO A  82 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "    0.018 5.00e-02 4.00e+02
  ... (remaining 518 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 478
        2.75 -     3.29: 3176
        3.29 -     3.83: 5465
        3.83 -     4.36: 6242
        4.36 -     4.90: 10508
  Nonbonded interactions: 25869
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" O   LYS A 204 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ALA A 309 "
            pdb=" OG  SER A 313 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   TYR A 126 "
            pdb=" OG1 THR A 129 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 321 "
            pdb=" O   GLN A 377 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A  31 "
            pdb=" O   LEU A 199 "
     model   vdw
     2.282 3.040
  ... (remaining 25864 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.390
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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   0.036   3216  Z= 0.130
  Angle     :  0.594   9.517   4384  Z= 0.315
  Chirality :  0.036   0.141    509
  Planarity :  0.003   0.032    521
  Dihedral  : 17.663  88.411   1107
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 35.24 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.23 (0.42), residues: 380
  helix:  1.49 (0.28), residues: 313
  sheet:  None (None), residues: 0
  loop : -2.42 (0.64), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 429 
 TYR   0.010   0.001   TYR A 287 
 PHE   0.025   0.001   PHE A 103 
 TRP   0.011   0.001   TRP A 331 
 HIS   0.002   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3216)
  covalent geometry    : angle       0.59388 ( 4384)
  hydrogen bonds       : bond        0.20920 (  241)
  hydrogen bonds       : angle       6.88908 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.120 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0505
  time to fit residues: 4.2625
Evaluate side-chains
  57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 346 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.146101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123489 restraints weight = 4974.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.127108 restraints weight = 2915.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.129349 restraints weight = 2064.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.130811 restraints weight = 1660.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.131956 restraints weight = 1441.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3216  Z= 0.164
  Angle     :  0.590   8.642   4384  Z= 0.302
  Chirality :  0.039   0.153    509
  Planarity :  0.004   0.036    521
  Dihedral  :  7.145  89.409    440
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 29.52 %
    Favored  : 66.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.43), residues: 380
  helix:  1.71 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.92 (0.71), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.036   0.002   PHE A 103 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3216)
  covalent geometry    : angle       0.59043 ( 4384)
  hydrogen bonds       : bond        0.04629 (  241)
  hydrogen bonds       : angle       4.38858 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9155 (mm)
REVERT: A  124 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8129 (tt)
REVERT: A  328 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5413 (ptmt)
  outliers start: 14
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0603
  time to fit residues: 5.3587
Evaluate side-chains
  61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  445 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0170
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.149152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.126435 restraints weight = 5108.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130166 restraints weight = 3021.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.132361 restraints weight = 2148.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.134157 restraints weight = 1737.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134969 restraints weight = 1489.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3216  Z= 0.129
  Angle     :  0.551   7.427   4384  Z= 0.280
  Chirality :  0.039   0.189    509
  Planarity :  0.004   0.035    521
  Dihedral  :  7.014  88.898    440
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 30.42 %
    Favored  : 65.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.43), residues: 380
  helix:  1.79 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.96 (0.75), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.011   0.001   TYR A 287 
 PHE   0.018   0.001   PHE A 103 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3216)
  covalent geometry    : angle       0.55121 ( 4384)
  hydrogen bonds       : bond        0.04108 (  241)
  hydrogen bonds       : angle       4.14579 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9191 (mt)
REVERT: A  124 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8063 (tt)
REVERT: A  328 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5390 (ptmt)
REVERT: A  434 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6740 (mp)
  outliers start: 14
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0458
  time to fit residues: 4.3247
Evaluate side-chains
  58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 24 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.147581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.125282 restraints weight = 5104.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.128804 restraints weight = 3043.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130962 restraints weight = 2177.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.132689 restraints weight = 1760.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.133487 restraints weight = 1508.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3216  Z= 0.137
  Angle     :  0.567   7.875   4384  Z= 0.281
  Chirality :  0.039   0.150    509
  Planarity :  0.004   0.037    521
  Dihedral  :  7.032  88.957    440
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 31.33 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.92 (0.43), residues: 380
  helix:  1.81 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.77 (0.76), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  26 
 TYR   0.010   0.001   TYR A  89 
 PHE   0.018   0.001   PHE A 103 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3216)
  covalent geometry    : angle       0.56704 ( 4384)
  hydrogen bonds       : bond        0.03940 (  241)
  hydrogen bonds       : angle       4.01421 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9238 (mt)
REVERT: A  124 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7996 (tt)
REVERT: A  328 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5268 (ptmt)
  outliers start: 13
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0562
  time to fit residues: 4.7209
Evaluate side-chains
  62 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  328 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   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  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.147478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124762 restraints weight = 5191.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.128098 restraints weight = 3155.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.130593 restraints weight = 2284.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.131750 restraints weight = 1828.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.132940 restraints weight = 1618.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3216  Z= 0.136
  Angle     :  0.561   7.525   4384  Z= 0.280
  Chirality :  0.039   0.147    509
  Planarity :  0.004   0.039    521
  Dihedral  :  6.990  89.163    440
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 29.82 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.43), residues: 380
  helix:  1.89 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.80 (0.73), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  26 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.016   0.001   PHE A 103 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3216)
  covalent geometry    : angle       0.56095 ( 4384)
  hydrogen bonds       : bond        0.03856 (  241)
  hydrogen bonds       : angle       3.89273 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.9012 (t80) cc_final: 0.8801 (t80)
REVERT: A   77 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9275 (mt)
REVERT: A  136 TYR cc_start: 0.8105 (t80) cc_final: 0.7887 (t80)
REVERT: A  328 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5321 (ptmt)
REVERT: A  361 SER cc_start: 0.7347 (p) cc_final: 0.6991 (t)
REVERT: A  433 GLN cc_start: 0.7073 (mt0) cc_final: 0.6697 (mt0)
REVERT: A  434 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6539 (mp)
  outliers start: 23
  outliers final: 12
  residues processed: 77
  average time/residue: 0.0592
  time to fit residues: 5.7092
Evaluate side-chains
  70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0980
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   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  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.146238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124045 restraints weight = 5118.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127328 restraints weight = 3075.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.129629 restraints weight = 2232.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.130762 restraints weight = 1792.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.132118 restraints weight = 1587.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3216  Z= 0.137
  Angle     :  0.574   6.975   4384  Z= 0.283
  Chirality :  0.039   0.149    509
  Planarity :  0.004   0.037    521
  Dihedral  :  6.952  89.263    440
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 30.42 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.08 (0.43), residues: 380
  helix:  1.96 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.79 (0.72), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.014   0.001   TYR A 149 
 PHE   0.012   0.001   PHE A 103 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3216)
  covalent geometry    : angle       0.57440 ( 4384)
  hydrogen bonds       : bond        0.03807 (  241)
  hydrogen bonds       : angle       3.84058 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.9026 (t80) cc_final: 0.8793 (t80)
REVERT: A   77 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9274 (mt)
REVERT: A  136 TYR cc_start: 0.8106 (t80) cc_final: 0.7884 (t80)
REVERT: A  328 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5235 (ptmt)
REVERT: A  361 SER cc_start: 0.7323 (p) cc_final: 0.6926 (t)
REVERT: A  433 GLN cc_start: 0.7124 (mt0) cc_final: 0.6715 (mt0)
REVERT: A  434 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6575 (mp)
  outliers start: 17
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0549
  time to fit residues: 5.0856
Evaluate side-chains
  72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.146453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124548 restraints weight = 5225.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.127930 restraints weight = 3102.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.130323 restraints weight = 2211.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.131588 restraints weight = 1758.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.132674 restraints weight = 1532.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3216  Z= 0.132
  Angle     :  0.583  11.245   4384  Z= 0.282
  Chirality :  0.039   0.151    509
  Planarity :  0.004   0.039    521
  Dihedral  :  6.919  89.422    440
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 31.63 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.43), residues: 380
  helix:  1.97 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.73 (0.71), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 422 
 TYR   0.012   0.001   TYR A 149 
 PHE   0.014   0.001   PHE A 103 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3216)
  covalent geometry    : angle       0.58348 ( 4384)
  hydrogen bonds       : bond        0.03765 (  241)
  hydrogen bonds       : angle       3.78868 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9266 (mt)
REVERT: A   89 TYR cc_start: 0.6738 (t80) cc_final: 0.6400 (t80)
REVERT: A  124 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8069 (tt)
REVERT: A  136 TYR cc_start: 0.8112 (t80) cc_final: 0.7889 (t80)
REVERT: A  328 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5207 (ptmt)
REVERT: A  361 SER cc_start: 0.7250 (p) cc_final: 0.6936 (t)
REVERT: A  430 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7623 (mmmm)
REVERT: A  433 GLN cc_start: 0.7170 (mt0) cc_final: 0.6874 (mt0)
REVERT: A  434 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6663 (mp)
  outliers start: 17
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0549
  time to fit residues: 5.1033
Evaluate side-chains
  72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.122974 restraints weight = 5324.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.126470 restraints weight = 3161.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.128537 restraints weight = 2244.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130163 restraints weight = 1819.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.130618 restraints weight = 1562.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3216  Z= 0.148
  Angle     :  0.589  10.994   4384  Z= 0.287
  Chirality :  0.039   0.161    509
  Planarity :  0.004   0.038    521
  Dihedral  :  6.906  89.731    440
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 31.33 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.43), residues: 380
  helix:  1.98 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.67 (0.72), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.017   0.001   PHE A 103 
 TRP   0.014   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3216)
  covalent geometry    : angle       0.58924 ( 4384)
  hydrogen bonds       : bond        0.03798 (  241)
  hydrogen bonds       : angle       3.79148 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9273 (mt)
REVERT: A   89 TYR cc_start: 0.6748 (t80) cc_final: 0.6462 (t80)
REVERT: A  124 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (tt)
REVERT: A  136 TYR cc_start: 0.8150 (t80) cc_final: 0.7918 (t80)
REVERT: A  328 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.4986 (ptmt)
REVERT: A  361 SER cc_start: 0.7283 (p) cc_final: 0.6975 (t)
REVERT: A  430 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7626 (mmmm)
REVERT: A  434 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6648 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0519
  time to fit residues: 4.6944
Evaluate side-chains
  70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.144195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.122330 restraints weight = 5222.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.125536 restraints weight = 3098.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.127881 restraints weight = 2232.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.129123 restraints weight = 1778.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.130146 restraints weight = 1551.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3216  Z= 0.162
  Angle     :  0.617  10.764   4384  Z= 0.300
  Chirality :  0.041   0.190    509
  Planarity :  0.004   0.037    521
  Dihedral  :  6.911  89.784    440
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 31.93 %
    Favored  : 62.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.43), residues: 380
  helix:  1.92 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.70 (0.71), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.023   0.002   PHE A 351 
 TRP   0.014   0.002   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3216)
  covalent geometry    : angle       0.61678 ( 4384)
  hydrogen bonds       : bond        0.03856 (  241)
  hydrogen bonds       : angle       3.84123 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9294 (mt)
REVERT: A   89 TYR cc_start: 0.6712 (t80) cc_final: 0.6506 (t80)
REVERT: A  124 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: A  136 TYR cc_start: 0.8147 (t80) cc_final: 0.7916 (t80)
REVERT: A  361 SER cc_start: 0.7255 (p) cc_final: 0.6965 (t)
REVERT: A  434 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6679 (mp)
  outliers start: 17
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0458
  time to fit residues: 4.0498
Evaluate side-chains
  67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.152060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130174 restraints weight = 4888.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133886 restraints weight = 2819.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.136158 restraints weight = 1969.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.137422 restraints weight = 1567.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.138754 restraints weight = 1376.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3216  Z= 0.142
  Angle     :  0.609  10.742   4384  Z= 0.295
  Chirality :  0.040   0.185    509
  Planarity :  0.004   0.037    521
  Dihedral  :  6.879  89.493    440
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 33.13 %
    Favored  : 62.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.43), residues: 380
  helix:  1.95 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.67 (0.71), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.035   0.001   TYR A 149 
 PHE   0.015   0.001   PHE A 103 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3216)
  covalent geometry    : angle       0.60852 ( 4384)
  hydrogen bonds       : bond        0.03795 (  241)
  hydrogen bonds       : angle       3.81272 (  723)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9276 (mt)
REVERT: A  124 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: A  136 TYR cc_start: 0.8135 (t80) cc_final: 0.7904 (t80)
REVERT: A  361 SER cc_start: 0.7275 (p) cc_final: 0.6990 (t)
REVERT: A  434 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6672 (mp)
REVERT: A  447 PHE cc_start: 0.7164 (t80) cc_final: 0.6949 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0510
  time to fit residues: 4.1200
Evaluate side-chains
  66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  419 SER
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.151937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129852 restraints weight = 5009.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133595 restraints weight = 2878.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135877 restraints weight = 2005.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137672 restraints weight = 1592.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138529 restraints weight = 1346.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3216  Z= 0.144
  Angle     :  0.615  10.684   4384  Z= 0.296
  Chirality :  0.040   0.168    509
  Planarity :  0.004   0.038    521
  Dihedral  :  6.831  89.164    440
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 32.83 %
    Favored  : 62.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.43), residues: 380
  helix:  1.96 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.68 (0.71), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  42 
 TYR   0.028   0.001   TYR A 149 
 PHE   0.023   0.002   PHE A 351 
 TRP   0.014   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3216)
  covalent geometry    : angle       0.61459 ( 4384)
  hydrogen bonds       : bond        0.03784 (  241)
  hydrogen bonds       : angle       3.79862 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 695.54 seconds
wall clock time: 12 minutes 42.82 seconds (762.82 seconds total)