Starting phenix.real_space_refine
on Thu Sep 10 20:33:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/23ig_68992/09_2026/23ig_68992.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
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      20      5.16       5
     C    2030      2.51       5
     N     474      2.21       5
     O     518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3042
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3042
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 14, 'TRANS': 386}
          Chain breaks: 3
  Time building chain proxies: 0.68, per 1000 atoms: 0.22
  Number of scatterers: 3042
  At special positions: 0
  Unit cell: (60.35, 71.4, 75.65, 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      20     16.00
     O     518      8.00
     N     474      7.00
     C    2030      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: 0.25
  Conformation dependent library (CDL) restraints added in 78.0 milliseconds
  

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  718

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      87.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 57
      removed outlier: 4.086A  pdb=" N   VAL A  31 " --> pdb=" O   TYR A  27 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A  48 " --> pdb=" O   MET A  44 " (cutoff:3.500A)
      Proline residue:  A  49  - end of helix
      removed outlier: 3.719A  pdb=" N   LYS A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   SER A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   VAL A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 84
      removed outlier: 3.873A  pdb=" N   ASN A  84 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 111
      removed outlier: 3.687A  pdb=" N   LEU A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   PHE A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   PHE A 109 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 139
    Processing helix  chain 'A' and resid 139 through 144
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 3.652A  pdb=" N   PHE A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 177
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 191 through 208
    Processing helix  chain 'A' and resid 209 through 212
      removed outlier: 7.014A  pdb=" N   TRP A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 209 through 212'
    Processing helix  chain 'A' and resid 213 through 234
      removed outlier: 3.776A  pdb=" N   ILE A 218 " --> pdb=" O   TRP A 214 " (cutoff:3.500A)
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 286 through 312
      Proline residue:  A 306  - end of helix
    Processing helix  chain 'A' and resid 320 through 328
      removed outlier: 3.519A  pdb=" N   SER A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 350
      removed outlier: 4.207A  pdb=" N   ASP A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 374
      removed outlier: 4.328A  pdb=" N   THR A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE A 364 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      Proline residue:  A 365  - end of helix
    Processing helix  chain 'A' and resid 377 through 394
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 4.072A  pdb=" N   LEU A 398 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   THR A 400 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 3.684A  pdb=" N   LEU A 407 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A 408 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   THR A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 418
    Processing helix  chain 'A' and resid 419 through 447
      Proline residue:  A 439  - end of helix
      removed outlier: 3.842A  pdb=" N   SER A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 478
      removed outlier: 4.557A  pdb=" N   GLN A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    678 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: 0.53

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 895
        1.34 -     1.46: 800
        1.46 -     1.58: 1395
        1.58 -     1.70: 0
        1.70 -     1.82: 35
  Bond restraints: 3125
  Sorted by residual:
  bond pdb=" N   THR A 400 "
       pdb=" CA  THR A 400 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.04e+01
  bond pdb=" N   VAL A 403 "
       pdb=" CA  VAL A 403 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.54e+00
  bond pdb=" N   VAL A 173 "
       pdb=" CA  VAL A 173 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 8.09e+00
  bond pdb=" N   HIS A 410 "
       pdb=" CA  HIS A 410 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.23e-02 6.61e+03 7.57e+00
  bond pdb=" N   ILE A 172 "
       pdb=" CA  ILE A 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.21e-02 6.83e+03 7.54e+00
  ... (remaining 3120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 4083
        2.03 -     4.05: 146
        4.05 -     6.08: 26
        6.08 -     8.10: 2
        8.10 -    10.13: 1
  Bond angle restraints: 4258
  Sorted by residual:
  angle pdb=" N   MET A 186 "
        pdb=" CA  MET A 186 "
        pdb=" C   MET A 186 "
      ideal   model   delta    sigma   weight residual
     113.38  107.72    5.66 1.23e+00 6.61e-01 2.12e+01
  angle pdb=" N   ASP A 406 "
        pdb=" CA  ASP A 406 "
        pdb=" C   ASP A 406 "
      ideal   model   delta    sigma   weight residual
     113.20  108.59    4.61 1.21e+00 6.83e-01 1.45e+01
  angle pdb=" CA  THR A 409 "
        pdb=" C   THR A 409 "
        pdb=" O   THR A 409 "
      ideal   model   delta    sigma   weight residual
     122.13  118.14    3.99 1.13e+00 7.83e-01 1.25e+01
  angle pdb=" N   LEU A 407 "
        pdb=" CA  LEU A 407 "
        pdb=" C   LEU A 407 "
      ideal   model   delta    sigma   weight residual
     113.15  109.39    3.76 1.19e+00 7.06e-01 1.00e+01
  angle pdb=" CA  GLY A 178 "
        pdb=" C   GLY A 178 "
        pdb=" O   GLY A 178 "
      ideal   model   delta    sigma   weight residual
     122.31  118.14    4.17 1.34e+00 5.57e-01 9.69e+00
  ... (remaining 4253 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.86: 1578
       12.86 -    25.73: 131
       25.73 -    38.59: 35
       38.59 -    51.45: 5
       51.45 -    64.32: 3
  Dihedral angle restraints: 1752
    sinusoidal: 622
      harmonic: 1130
  Sorted by residual:
  dihedral pdb=" CA  ALA A 285 "
           pdb=" C   ALA A 285 "
           pdb=" N   PRO A 286 "
           pdb=" CA  PRO A 286 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.02   26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  TRP A  80 "
           pdb=" C   TRP A  80 "
           pdb=" N   LEU A  81 "
           pdb=" CA  LEU A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ILE A 164 "
           pdb=" C   ILE A 164 "
           pdb=" N   GLY A 165 "
           pdb=" CA  GLY A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 1749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 441
       0.075 -    0.149: 53
       0.149 -    0.224: 6
       0.224 -    0.298: 0
       0.298 -    0.373: 1
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CB  ILE A 281 "
            pdb=" CA  ILE A 281 "
            pdb=" CG1 ILE A 281 "
            pdb=" CG2 ILE A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  ILE A 188 "
            pdb=" N   ILE A 188 "
            pdb=" C   ILE A 188 "
            pdb=" CB  ILE A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" CA  ILE A 185 "
            pdb=" N   ILE A 185 "
            pdb=" C   ILE A 185 "
            pdb=" CB  ILE A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 498 not shown)

  Planarity restraints: 512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 418 "   -0.267 9.50e-02 1.11e+02   1.20e-01 8.83e+00
        pdb=" NE  ARG A 418 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 418 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 418 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 418 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 292 "    0.013 2.00e-02 2.50e+03   1.40e-02 3.41e+00
        pdb=" CG  PHE A 292 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 292 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 292 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 292 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 292 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 292 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 281 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.06e+00
        pdb=" N   PRO A 282 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 509 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1056
        2.85 -     3.37: 3172
        3.37 -     3.88: 5187
        3.88 -     4.39: 5859
        4.39 -     4.90: 9848
  Nonbonded interactions: 25122
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 399 "
            pdb=" OG1 THR A 400 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   TRP A 189 "
            pdb=" ND1 HIS A 192 "
     model   vdw
     2.444 3.120
  nonbonded pdb=" O   ALA A 419 "
            pdb=" C   LEU A 420 "
     model   vdw
     2.540 3.270
  nonbonded pdb=" O   ALA A 419 "
            pdb=" N   THR A 422 "
     model   vdw
     2.561 3.120
  nonbonded pdb=" OG  SER A 411 "
            pdb=" N   SER A 412 "
     model   vdw
     2.573 3.120
  ... (remaining 25117 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:             5.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.210
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
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      :  0.006   0.047   3125  Z= 0.382
  Angle     :  0.852  10.127   4258  Z= 0.528
  Chirality :  0.054   0.373    501
  Planarity :  0.007   0.120    512
  Dihedral  : 10.705  64.317   1034
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  0.31 %
    Favored  : 99.06 %
  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 are not related in a simple way.
  whole: -0.05 (0.40), residues: 393
  helix:  0.50 (0.28), residues: 295
  sheet:  None (None), residues: 0
  loop : -1.47 (0.62), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 352 
 TYR   0.011   0.002   TYR A 103 
 PHE   0.032   0.002   PHE A 292 
 TRP   0.026   0.002   TRP A 304 
 HIS   0.003   0.001   HIS A 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00604 /  0.38 ( 3125)
  covalent geometry    : angle       0.85193 /  0.53 ( 4258)
  hydrogen bonds       : bond        0.11804 /  8.11 (  229)
  hydrogen bonds       : angle       5.82994 /  4.22 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7407 (ttp) cc_final: 0.7205 (ttp)
REVERT: A  100 LEU cc_start: 0.8080 (mt) cc_final: 0.7738 (mm)
REVERT: A  103 TYR cc_start: 0.7955 (t80) cc_final: 0.7657 (t80)
REVERT: A  117 MET cc_start: 0.5539 (mtp) cc_final: 0.5250 (mtp)
REVERT: A  125 ILE cc_start: 0.8237 (mt) cc_final: 0.7999 (mt)
REVERT: A  137 PHE cc_start: 0.7510 (t80) cc_final: 0.7300 (t80)
REVERT: A  156 MET cc_start: 0.6557 (mtp) cc_final: 0.6288 (mtp)
REVERT: A  161 PHE cc_start: 0.7692 (m-80) cc_final: 0.7385 (m-80)
REVERT: A  172 ILE cc_start: 0.7835 (mt) cc_final: 0.7533 (mt)
REVERT: A  175 ASN cc_start: 0.7234 (m-40) cc_final: 0.6897 (m-40)
REVERT: A  186 MET cc_start: 0.6043 (ptp) cc_final: 0.5797 (ptp)
REVERT: A  194 SER cc_start: 0.7773 (m) cc_final: 0.7534 (p)
REVERT: A  223 MET cc_start: 0.6750 (tpp) cc_final: 0.6146 (tpp)
REVERT: A  307 PHE cc_start: 0.8057 (t80) cc_final: 0.7741 (t80)
REVERT: A  341 LEU cc_start: 0.8083 (mt) cc_final: 0.7636 (tt)
REVERT: A  358 SER cc_start: 0.7819 (m) cc_final: 0.7479 (p)
REVERT: A  370 TYR cc_start: 0.8315 (t80) cc_final: 0.8061 (t80)
REVERT: A  372 THR cc_start: 0.8168 (m) cc_final: 0.7877 (p)
REVERT: A  385 MET cc_start: 0.6597 (tpp) cc_final: 0.6247 (tpp)
REVERT: A  410 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.6248 (p90)
REVERT: A  414 ASN cc_start: 0.7458 (t0) cc_final: 0.7167 (t0)
REVERT: A  462 LEU cc_start: 0.8327 (tp) cc_final: 0.8029 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 138
  average time/residue: 0.0360
  time to fit residues: 6.5160
Evaluate side-chains
  126 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.0020
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.133365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.119587 restraints weight = 5803.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123555 restraints weight = 3011.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.126105 restraints weight = 1777.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.127901 restraints weight = 1152.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.129046 restraints weight = 793.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3125  Z= 0.190
  Angle     :  0.631  10.598   4258  Z= 0.329
  Chirality :  0.044   0.163    501
  Planarity :  0.005   0.036    512
  Dihedral  :  5.884  47.578    424
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.52 %
    Favored  : 82.39 %
  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 are not related in a simple way.
  whole:  0.68 (0.42), residues: 393
  helix:  1.11 (0.30), residues: 304
  sheet:  None (None), residues: 0
  loop : -1.76 (0.63), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 418 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.021   0.002   PHE A 292 
 TRP   0.015   0.002   TRP A 212 
 HIS   0.002   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.19 ( 3125)
  covalent geometry    : angle       0.63093 /  0.33 ( 4258)
  hydrogen bonds       : bond        0.05367 /  3.61 (  229)
  hydrogen bonds       : angle       4.76678 /  3.34 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7415 (ttp) cc_final: 0.7136 (ttp)
REVERT: A   52 VAL cc_start: 0.8158 (t) cc_final: 0.7947 (p)
REVERT: A   54 SER cc_start: 0.8366 (p) cc_final: 0.7989 (t)
REVERT: A  100 LEU cc_start: 0.8083 (mt) cc_final: 0.7800 (mm)
REVERT: A  103 TYR cc_start: 0.8041 (t80) cc_final: 0.7838 (t80)
REVERT: A  117 MET cc_start: 0.5391 (mtp) cc_final: 0.5156 (mtp)
REVERT: A  125 ILE cc_start: 0.8222 (mt) cc_final: 0.7984 (mt)
REVERT: A  156 MET cc_start: 0.6532 (mtp) cc_final: 0.6251 (mtp)
REVERT: A  172 ILE cc_start: 0.7776 (mt) cc_final: 0.7572 (mt)
REVERT: A  175 ASN cc_start: 0.6858 (m-40) cc_final: 0.6486 (m-40)
REVERT: A  194 SER cc_start: 0.8036 (m) cc_final: 0.7503 (p)
REVERT: A  223 MET cc_start: 0.6891 (tpp) cc_final: 0.6483 (tpp)
REVERT: A  301 PHE cc_start: 0.8030 (m-80) cc_final: 0.7796 (m-10)
REVERT: A  341 LEU cc_start: 0.8134 (mt) cc_final: 0.7565 (tt)
REVERT: A  409 THR cc_start: 0.8043 (p) cc_final: 0.7726 (m)
REVERT: A  410 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.6244 (p90)
  outliers start: 13
  outliers final: 9
  residues processed: 130
  average time/residue: 0.0350
  time to fit residues: 5.9304
Evaluate side-chains
  132 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  449 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 381 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.133627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.120188 restraints weight = 5568.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124209 restraints weight = 2937.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.126816 restraints weight = 1739.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.128560 restraints weight = 1117.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.129709 restraints weight = 763.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3125  Z= 0.188
  Angle     :  0.617   8.736   4258  Z= 0.319
  Chirality :  0.043   0.159    501
  Planarity :  0.004   0.032    512
  Dihedral  :  5.350  45.006    422
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.55 %
    Favored  : 77.36 %
  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 are not related in a simple way.
  whole:  0.92 (0.42), residues: 393
  helix:  1.29 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.74 (0.61), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 418 
 TYR   0.014   0.001   TYR A  39 
 PHE   0.019   0.002   PHE A 292 
 TRP   0.014   0.001   TRP A 304 
 HIS   0.005   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.19 ( 3125)
  covalent geometry    : angle       0.61737 /  0.32 ( 4258)
  hydrogen bonds       : bond        0.05136 /  3.51 (  229)
  hydrogen bonds       : angle       4.69329 /  3.27 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7373 (ttp) cc_final: 0.7076 (ttp)
REVERT: A   52 VAL cc_start: 0.8249 (t) cc_final: 0.8033 (p)
REVERT: A   54 SER cc_start: 0.8410 (p) cc_final: 0.8067 (t)
REVERT: A  100 LEU cc_start: 0.8072 (mt) cc_final: 0.7849 (mm)
REVERT: A  156 MET cc_start: 0.6466 (mtp) cc_final: 0.6247 (mtp)
REVERT: A  175 ASN cc_start: 0.6829 (m-40) cc_final: 0.6512 (m-40)
REVERT: A  194 SER cc_start: 0.8023 (m) cc_final: 0.7428 (p)
REVERT: A  216 PHE cc_start: 0.7714 (m-80) cc_final: 0.7513 (m-80)
REVERT: A  223 MET cc_start: 0.6743 (tpp) cc_final: 0.6362 (tpp)
REVERT: A  296 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6539 (tp)
REVERT: A  301 PHE cc_start: 0.8050 (m-80) cc_final: 0.7772 (m-10)
REVERT: A  307 PHE cc_start: 0.7929 (t80) cc_final: 0.7721 (t80)
REVERT: A  341 LEU cc_start: 0.8183 (mt) cc_final: 0.7623 (tt)
REVERT: A  358 SER cc_start: 0.7786 (m) cc_final: 0.7473 (p)
REVERT: A  372 THR cc_start: 0.8226 (m) cc_final: 0.7896 (p)
REVERT: A  409 THR cc_start: 0.8121 (p) cc_final: 0.7793 (m)
  outliers start: 13
  outliers final: 9
  residues processed: 131
  average time/residue: 0.0303
  time to fit residues: 5.2569
Evaluate side-chains
  134 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  477 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 381 ASN
** A 410 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.131812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118563 restraints weight = 5597.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122442 restraints weight = 2960.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.125044 restraints weight = 1769.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.126755 restraints weight = 1140.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.127910 restraints weight = 780.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3125  Z= 0.200
  Angle     :  0.615   8.344   4258  Z= 0.320
  Chirality :  0.043   0.157    501
  Planarity :  0.004   0.031    512
  Dihedral  :  4.582  26.278    420
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 20.13 %
    Favored  : 75.79 %
  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 are not related in a simple way.
  whole:  0.87 (0.42), residues: 393
  helix:  1.26 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.79 (0.59), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 418 
 TYR   0.017   0.001   TYR A 103 
 PHE   0.024   0.002   PHE A 137 
 TRP   0.015   0.001   TRP A 304 
 HIS   0.004   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.20 ( 3125)
  covalent geometry    : angle       0.61501 /  0.32 ( 4258)
  hydrogen bonds       : bond        0.05170 /  3.54 (  229)
  hydrogen bonds       : angle       4.67520 /  3.26 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7362 (ttp) cc_final: 0.7073 (ttp)
REVERT: A   52 VAL cc_start: 0.8264 (t) cc_final: 0.8031 (p)
REVERT: A   54 SER cc_start: 0.8383 (p) cc_final: 0.8003 (t)
REVERT: A  100 LEU cc_start: 0.8069 (mt) cc_final: 0.7839 (mm)
REVERT: A  137 PHE cc_start: 0.7841 (t80) cc_final: 0.7564 (t80)
REVERT: A  156 MET cc_start: 0.6493 (mtp) cc_final: 0.6243 (mtp)
REVERT: A  194 SER cc_start: 0.8004 (m) cc_final: 0.7388 (p)
REVERT: A  203 LEU cc_start: 0.8387 (tp) cc_final: 0.7904 (tt)
REVERT: A  223 MET cc_start: 0.6723 (tpp) cc_final: 0.6430 (tpp)
REVERT: A  296 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6576 (tp)
REVERT: A  301 PHE cc_start: 0.8075 (m-80) cc_final: 0.7772 (m-10)
REVERT: A  308 TYR cc_start: 0.7882 (t80) cc_final: 0.7672 (t80)
REVERT: A  341 LEU cc_start: 0.8209 (mt) cc_final: 0.7633 (tt)
REVERT: A  358 SER cc_start: 0.7799 (m) cc_final: 0.7460 (p)
REVERT: A  372 THR cc_start: 0.8272 (m) cc_final: 0.7884 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 129
  average time/residue: 0.0308
  time to fit residues: 5.2350
Evaluate side-chains
  133 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Chi-restraints excluded: chain A residue  477 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0370
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 381 ASN
** A 410 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.131755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.118731 restraints weight = 5571.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122689 restraints weight = 2902.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.125241 restraints weight = 1710.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.126839 restraints weight = 1092.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.128004 restraints weight = 751.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3125  Z= 0.208
  Angle     :  0.607   8.043   4258  Z= 0.318
  Chirality :  0.043   0.142    501
  Planarity :  0.004   0.032    512
  Dihedral  :  4.654  25.468    420
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 21.38 %
    Favored  : 74.53 %
  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 are not related in a simple way.
  whole:  0.89 (0.42), residues: 393
  helix:  1.29 (0.30), residues: 304
  sheet:  None (None), residues: 0
  loop : -1.82 (0.59), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 352 
 TYR   0.017   0.002   TYR A 103 
 PHE   0.024   0.002   PHE A  83 
 TRP   0.018   0.002   TRP A 304 
 HIS   0.005   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.21 ( 3125)
  covalent geometry    : angle       0.60739 /  0.32 ( 4258)
  hydrogen bonds       : bond        0.05249 /  3.62 (  229)
  hydrogen bonds       : angle       4.73787 /  3.28 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.062 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7287 (ttp) cc_final: 0.7026 (ttp)
REVERT: A   52 VAL cc_start: 0.8280 (t) cc_final: 0.8069 (p)
REVERT: A   54 SER cc_start: 0.8382 (p) cc_final: 0.8033 (t)
REVERT: A   92 LEU cc_start: 0.7873 (mm) cc_final: 0.7620 (mp)
REVERT: A  100 LEU cc_start: 0.8035 (mt) cc_final: 0.7807 (mm)
REVERT: A  107 MET cc_start: 0.7881 (mmm) cc_final: 0.7591 (ttt)
REVERT: A  141 TYR cc_start: 0.7176 (t80) cc_final: 0.6855 (t80)
REVERT: A  148 PHE cc_start: 0.7952 (t80) cc_final: 0.7696 (t80)
REVERT: A  156 MET cc_start: 0.6462 (mtp) cc_final: 0.6225 (mtp)
REVERT: A  194 SER cc_start: 0.8016 (m) cc_final: 0.7378 (p)
REVERT: A  203 LEU cc_start: 0.8391 (tp) cc_final: 0.7886 (tt)
REVERT: A  223 MET cc_start: 0.6696 (tpp) cc_final: 0.6448 (tpp)
REVERT: A  301 PHE cc_start: 0.8118 (m-80) cc_final: 0.7734 (m-10)
REVERT: A  341 LEU cc_start: 0.8228 (mt) cc_final: 0.7666 (tt)
REVERT: A  358 SER cc_start: 0.7796 (m) cc_final: 0.7473 (p)
REVERT: A  410 HIS cc_start: 0.6823 (p90) cc_final: 0.6565 (p90)
  outliers start: 13
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0353
  time to fit residues: 5.9546
Evaluate side-chains
  128 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 ASN
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.132508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.119256 restraints weight = 5564.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.123232 restraints weight = 2923.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.125827 restraints weight = 1736.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.127533 restraints weight = 1115.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.128735 restraints weight = 762.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3125  Z= 0.156
  Angle     :  0.579   7.536   4258  Z= 0.301
  Chirality :  0.042   0.163    501
  Planarity :  0.004   0.033    512
  Dihedral  :  4.542  23.530    420
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 25.47 %
    Favored  : 70.75 %
  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 are not related in a simple way.
  whole:  1.12 (0.43), residues: 393
  helix:  1.47 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -1.73 (0.60), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.018   0.001   TYR A  39 
 PHE   0.027   0.002   PHE A  83 
 TRP   0.018   0.002   TRP A 212 
 HIS   0.005   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.16 ( 3125)
  covalent geometry    : angle       0.57869 /  0.30 ( 4258)
  hydrogen bonds       : bond        0.04944 /  3.41 (  229)
  hydrogen bonds       : angle       4.68421 /  3.22 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7245 (ttp) cc_final: 0.6976 (ttp)
REVERT: A   52 VAL cc_start: 0.8278 (t) cc_final: 0.8041 (p)
REVERT: A   54 SER cc_start: 0.8365 (p) cc_final: 0.7996 (t)
REVERT: A  100 LEU cc_start: 0.8022 (mt) cc_final: 0.7805 (mm)
REVERT: A  107 MET cc_start: 0.7889 (mmm) cc_final: 0.7587 (ttt)
REVERT: A  137 PHE cc_start: 0.7941 (t80) cc_final: 0.7726 (t80)
REVERT: A  141 TYR cc_start: 0.7076 (t80) cc_final: 0.6752 (t80)
REVERT: A  148 PHE cc_start: 0.7897 (t80) cc_final: 0.7620 (t80)
REVERT: A  156 MET cc_start: 0.6429 (mtp) cc_final: 0.6208 (mtp)
REVERT: A  203 LEU cc_start: 0.8305 (tp) cc_final: 0.7820 (tt)
REVERT: A  223 MET cc_start: 0.6675 (tpp) cc_final: 0.6301 (tpp)
REVERT: A  301 PHE cc_start: 0.8095 (m-80) cc_final: 0.7739 (m-80)
REVERT: A  308 TYR cc_start: 0.7949 (t80) cc_final: 0.7709 (t80)
REVERT: A  341 LEU cc_start: 0.8189 (mt) cc_final: 0.7576 (tt)
REVERT: A  358 SER cc_start: 0.7772 (m) cc_final: 0.7437 (p)
REVERT: A  410 HIS cc_start: 0.6849 (p90) cc_final: 0.6546 (p90)
  outliers start: 12
  outliers final: 9
  residues processed: 124
  average time/residue: 0.0415
  time to fit residues: 6.7080
Evaluate side-chains
  127 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0980
   chunk 23 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.3438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3818 r_free = 0.3818 target = 0.132596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.119603 restraints weight = 5642.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123512 restraints weight = 2935.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126096 restraints weight = 1730.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.127708 restraints weight = 1105.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.128854 restraints weight = 763.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3125  Z= 0.154
  Angle     :  0.583   7.879   4258  Z= 0.303
  Chirality :  0.041   0.135    501
  Planarity :  0.004   0.034    512
  Dihedral  :  4.434  22.821    420
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.47 %
    Favored  : 71.07 %
  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 are not related in a simple way.
  whole:  1.43 (0.43), residues: 393
  helix:  1.62 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -1.35 (0.64), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 352 
 TYR   0.019   0.001   TYR A 103 
 PHE   0.027   0.002   PHE A  83 
 TRP   0.014   0.001   TRP A 212 
 HIS   0.004   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 3125)
  covalent geometry    : angle       0.58261 /  0.30 ( 4258)
  hydrogen bonds       : bond        0.04812 /  3.35 (  229)
  hydrogen bonds       : angle       4.63939 /  3.19 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7219 (ttp) cc_final: 0.6963 (ttp)
REVERT: A   52 VAL cc_start: 0.8240 (t) cc_final: 0.7970 (p)
REVERT: A   54 SER cc_start: 0.8355 (p) cc_final: 0.8050 (t)
REVERT: A  100 LEU cc_start: 0.8041 (mt) cc_final: 0.7817 (mm)
REVERT: A  107 MET cc_start: 0.7880 (mmm) cc_final: 0.7577 (ttt)
REVERT: A  130 THR cc_start: 0.8018 (m) cc_final: 0.7544 (t)
REVERT: A  141 TYR cc_start: 0.7064 (t80) cc_final: 0.6759 (t80)
REVERT: A  148 PHE cc_start: 0.7871 (t80) cc_final: 0.7582 (t80)
REVERT: A  223 MET cc_start: 0.6729 (tpp) cc_final: 0.6200 (tpp)
REVERT: A  301 PHE cc_start: 0.8135 (m-80) cc_final: 0.7793 (m-80)
REVERT: A  341 LEU cc_start: 0.8170 (mt) cc_final: 0.7569 (tt)
REVERT: A  358 SER cc_start: 0.7778 (m) cc_final: 0.7452 (p)
REVERT: A  410 HIS cc_start: 0.6862 (p90) cc_final: 0.6622 (p90)
  outliers start: 11
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0354
  time to fit residues: 5.6637
Evaluate side-chains
  128 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  127 MET
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0570
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3799 r_free = 0.3799 target = 0.131464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118621 restraints weight = 5661.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122592 restraints weight = 2923.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.125151 restraints weight = 1704.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.126798 restraints weight = 1078.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.127989 restraints weight = 729.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3125  Z= 0.173
  Angle     :  0.598   7.064   4258  Z= 0.316
  Chirality :  0.042   0.134    501
  Planarity :  0.004   0.034    512
  Dihedral  :  4.381  23.183    420
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 25.79 %
    Favored  : 70.13 %
  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 are not related in a simple way.
  whole:  1.44 (0.43), residues: 393
  helix:  1.63 (0.30), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.34 (0.64), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 352 
 TYR   0.020   0.001   TYR A 103 
 PHE   0.030   0.002   PHE A  83 
 TRP   0.014   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.17 ( 3125)
  covalent geometry    : angle       0.59752 /  0.32 ( 4258)
  hydrogen bonds       : bond        0.04958 /  3.43 (  229)
  hydrogen bonds       : angle       4.59391 /  3.16 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7232 (ttp) cc_final: 0.6975 (ttp)
REVERT: A   52 VAL cc_start: 0.8244 (t) cc_final: 0.8037 (p)
REVERT: A   54 SER cc_start: 0.8312 (p) cc_final: 0.7970 (t)
REVERT: A  100 LEU cc_start: 0.8075 (mt) cc_final: 0.7841 (mm)
REVERT: A  107 MET cc_start: 0.7889 (mmm) cc_final: 0.7641 (ttt)
REVERT: A  130 THR cc_start: 0.8022 (m) cc_final: 0.7549 (t)
REVERT: A  141 TYR cc_start: 0.7060 (t80) cc_final: 0.6750 (t80)
REVERT: A  148 PHE cc_start: 0.7915 (t80) cc_final: 0.7607 (t80)
REVERT: A  194 SER cc_start: 0.8062 (m) cc_final: 0.7430 (p)
REVERT: A  223 MET cc_start: 0.6746 (tpp) cc_final: 0.6226 (tpp)
REVERT: A  301 PHE cc_start: 0.8161 (m-80) cc_final: 0.7707 (m-80)
REVERT: A  304 TRP cc_start: 0.8198 (m100) cc_final: 0.7818 (m100)
REVERT: A  308 TYR cc_start: 0.7915 (t80) cc_final: 0.7649 (t80)
REVERT: A  341 LEU cc_start: 0.8178 (mt) cc_final: 0.7573 (tt)
REVERT: A  358 SER cc_start: 0.7782 (m) cc_final: 0.7435 (p)
REVERT: A  410 HIS cc_start: 0.6952 (p90) cc_final: 0.6717 (p90)
  outliers start: 13
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0305
  time to fit residues: 4.8333
Evaluate side-chains
  128 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  127 MET
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.0040
   chunk 35 optimal weight:    0.1980
   chunk 12 optimal weight:    0.1980
   chunk 7 optimal weight:    0.0020
   chunk 2 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.1800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3846 r_free = 0.3846 target = 0.134720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121561 restraints weight = 5599.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.125506 restraints weight = 2957.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.128112 restraints weight = 1759.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.129740 restraints weight = 1127.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.130948 restraints weight = 777.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3125  Z= 0.130
  Angle     :  0.581   6.735   4258  Z= 0.302
  Chirality :  0.040   0.129    501
  Planarity :  0.004   0.035    512
  Dihedral  :  4.239  19.659    420
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 26.73 %
    Favored  : 70.13 %
  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 are not related in a simple way.
  whole:  1.86 (0.44), residues: 393
  helix:  2.01 (0.31), residues: 297
  sheet:  None (None), residues: 0
  loop : -1.29 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 352 
 TYR   0.021   0.001   TYR A 103 
 PHE   0.028   0.002   PHE A  83 
 TRP   0.018   0.001   TRP A 212 
 HIS   0.004   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 3125)
  covalent geometry    : angle       0.58095 /  0.30 ( 4258)
  hydrogen bonds       : bond        0.04385 /  3.03 (  229)
  hydrogen bonds       : angle       4.51941 /  3.12 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7188 (ttp) cc_final: 0.6944 (ttp)
REVERT: A   51 ILE cc_start: 0.8439 (mm) cc_final: 0.8193 (tp)
REVERT: A   52 VAL cc_start: 0.8178 (t) cc_final: 0.7975 (p)
REVERT: A   54 SER cc_start: 0.8317 (p) cc_final: 0.8048 (t)
REVERT: A   91 LEU cc_start: 0.8053 (mm) cc_final: 0.7403 (tt)
REVERT: A  100 LEU cc_start: 0.8032 (mt) cc_final: 0.7798 (mm)
REVERT: A  107 MET cc_start: 0.7894 (mmm) cc_final: 0.7575 (ttt)
REVERT: A  130 THR cc_start: 0.7992 (m) cc_final: 0.7605 (t)
REVERT: A  203 LEU cc_start: 0.8082 (tp) cc_final: 0.7736 (tt)
REVERT: A  223 MET cc_start: 0.6698 (tpp) cc_final: 0.6297 (tpt)
REVERT: A  301 PHE cc_start: 0.8104 (m-80) cc_final: 0.7689 (m-80)
REVERT: A  304 TRP cc_start: 0.8152 (m100) cc_final: 0.7748 (m100)
REVERT: A  341 LEU cc_start: 0.8070 (mt) cc_final: 0.7600 (tp)
REVERT: A  358 SER cc_start: 0.7739 (m) cc_final: 0.7421 (p)
REVERT: A  372 THR cc_start: 0.8202 (m) cc_final: 0.7825 (p)
REVERT: A  410 HIS cc_start: 0.6912 (p90) cc_final: 0.6681 (p90)
  outliers start: 10
  outliers final: 10
  residues processed: 121
  average time/residue: 0.0354
  time to fit residues: 5.6260
Evaluate side-chains
  123 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  127 MET
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 22 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 34 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.132670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119594 restraints weight = 5645.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123563 restraints weight = 2974.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126142 restraints weight = 1756.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.127879 restraints weight = 1124.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.128972 restraints weight = 761.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3125  Z= 0.157
  Angle     :  0.585   6.159   4258  Z= 0.309
  Chirality :  0.042   0.135    501
  Planarity :  0.004   0.035    512
  Dihedral  :  4.277  21.715    420
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 29.25 %
    Favored  : 67.61 %
  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 are not related in a simple way.
  whole:  1.77 (0.44), residues: 393
  helix:  1.87 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.24 (0.65), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 352 
 TYR   0.020   0.001   TYR A 103 
 PHE   0.035   0.002   PHE A  83 
 TRP   0.014   0.001   TRP A 212 
 HIS   0.004   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 ( 3125)
  covalent geometry    : angle       0.58488 /  0.31 ( 4258)
  hydrogen bonds       : bond        0.04659 /  3.23 (  229)
  hydrogen bonds       : angle       4.56824 /  3.16 (  678)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   44 MET cc_start: 0.7207 (ttp) cc_final: 0.6963 (ttp)
REVERT: A   51 ILE cc_start: 0.8421 (mm) cc_final: 0.8154 (tp)
REVERT: A   52 VAL cc_start: 0.8234 (t) cc_final: 0.8015 (p)
REVERT: A   54 SER cc_start: 0.8265 (p) cc_final: 0.8008 (t)
REVERT: A   91 LEU cc_start: 0.8060 (mm) cc_final: 0.7402 (tt)
REVERT: A  100 LEU cc_start: 0.8032 (mt) cc_final: 0.7792 (mm)
REVERT: A  107 MET cc_start: 0.7900 (mmm) cc_final: 0.7636 (ttt)
REVERT: A  130 THR cc_start: 0.8044 (m) cc_final: 0.7610 (t)
REVERT: A  223 MET cc_start: 0.6734 (tpp) cc_final: 0.6315 (tpt)
REVERT: A  301 PHE cc_start: 0.8098 (m-80) cc_final: 0.7669 (m-80)
REVERT: A  304 TRP cc_start: 0.8143 (m100) cc_final: 0.7806 (m100)
REVERT: A  341 LEU cc_start: 0.8096 (mt) cc_final: 0.7583 (tp)
REVERT: A  358 SER cc_start: 0.7782 (m) cc_final: 0.7461 (p)
REVERT: A  410 HIS cc_start: 0.6927 (p90) cc_final: 0.6724 (p90)
  outliers start: 10
  outliers final: 10
  residues processed: 118
  average time/residue: 0.0365
  time to fit residues: 5.6037
Evaluate side-chains
  124 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  127 MET
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  473 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0370
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 410 HIS ** 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 = 0.3753 r_free = 0.3753 target = 0.128952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.115695 restraints weight = 5688.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.119591 restraints weight = 3000.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.122120 restraints weight = 1790.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.123797 restraints weight = 1160.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124997 restraints weight = 803.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.4387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3125  Z= 0.207
  Angle     :  0.630   6.737   4258  Z= 0.335
  Chirality :  0.044   0.144    501
  Planarity :  0.005   0.045    512
  Dihedral  :  4.515  23.619    420
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 28.30 %
    Favored  : 67.92 %
  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 are not related in a simple way.
  whole:  1.48 (0.44), residues: 393
  helix:  1.66 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.31 (0.67), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 352 
 TYR   0.020   0.002   TYR A 103 
 PHE   0.037   0.002   PHE A  83 
 TRP   0.013   0.001   TRP A 212 
 HIS   0.006   0.002   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.21 ( 3125)
  covalent geometry    : angle       0.63041 /  0.34 ( 4258)
  hydrogen bonds       : bond        0.05177 /  3.57 (  229)
  hydrogen bonds       : angle       4.74795 /  3.29 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 653.26 seconds
wall clock time: 11 minutes 52.96 seconds (712.96 seconds total)