Starting phenix.real_space_refine
on Sat Apr  4 20:50:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbu_61326/04_2026/9jbu_61326.map"
  }
  resolution = 3.8
  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=   0.018
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      30      5.16       5
     C    2142      2.51       5
     N     501      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3219
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3166
          Classifications: {'peptide': 415}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 15, 'TRANS': 399}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'AJP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 14
  Time building chain proxies: 1.14, per 1000 atoms: 0.35
  Number of scatterers: 3219
  At special positions: 0
  Unit cell: (79.23, 52.542, 72.558, 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      30     16.00
     O     546      8.00
     N     501      7.00
     C    2142      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  81 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 134.2 milliseconds
  

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 1 sheets defined
      93.0% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
      removed outlier: 3.970A  pdb=" N   ARG A  10 " --> pdb=" O   ALA A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 27
      removed outlier: 3.856A  pdb=" N   SER A  27 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 31
    Processing helix  chain 'A' and resid 32 through 44
      removed outlier: 3.786A  pdb=" N   LEU A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 50
    Processing helix  chain 'A' and resid 81 through 102
      removed outlier: 3.753A  pdb=" N   ILE A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 114
      removed outlier: 3.612A  pdb=" N   ILE A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 139
    Processing helix  chain 'A' and resid 139 through 144
      removed outlier: 3.626A  pdb=" N   SER A 144 " --> pdb=" O   PRO A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 168
      removed outlier: 4.005A  pdb=" N   ILE A 149 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 167 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 172
    Processing helix  chain 'A' and resid 175 through 189
    Processing helix  chain 'A' and resid 192 through 204
      removed outlier: 3.503A  pdb=" N   ALA A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 229
      removed outlier: 3.623A  pdb=" N   VAL A 221 " --> pdb=" O   CYS A 217 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   PHE A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 321
    Processing helix  chain 'A' and resid 321 through 344
      removed outlier: 3.595A  pdb=" N   LEU A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 353
    Processing helix  chain 'A' and resid 356 through 371
    Processing helix  chain 'A' and resid 372 through 386
      removed outlier: 3.777A  pdb=" N   LEU A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      Proline residue:  A 379  - end of helix
    Processing helix  chain 'A' and resid 416 through 444
      removed outlier: 3.639A  pdb=" N   LYS A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 434 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 476
      removed outlier: 3.911A  pdb=" N   ILE A 451 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU A 452 " --> pdb=" O   PRO A 448 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   SER A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   HIS A 465 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   SER A 466 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
    Processing helix  chain 'A' and resid 498 through 507
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 514 through 526
    Processing helix  chain 'A' and resid 529 through 543
      removed outlier: 3.818A  pdb=" N   CYS A 537 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75
      removed outlier: 3.589A  pdb=" N   SER A  73 " --> pdb=" O   SER A  80 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    768 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: 0.55

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 947
        1.34 -     1.46: 822
        1.46 -     1.58: 1483
        1.58 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 3299
  Sorted by residual:
  bond pdb=" C39 AJP A 601 "
       pdb=" O40 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.412  1.445 -0.033 2.00e-02 2.50e+03 2.72e+00
  bond pdb=" C26 AJP A 601 "
       pdb=" O25 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.407 -0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" C08 AJP A 601 "
       pdb=" O09 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.410  1.440 -0.030 2.00e-02 2.50e+03 2.18e+00
  bond pdb=" C30 AJP A 601 "
       pdb=" O31 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.412  1.441 -0.029 2.00e-02 2.50e+03 2.15e+00
  bond pdb=" C22 AJP A 601 "
       pdb=" O79 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.408  1.436 -0.028 2.00e-02 2.50e+03 1.95e+00
  ... (remaining 3294 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 4404
        1.36 -     2.72: 70
        2.72 -     4.08: 19
        4.08 -     5.44: 7
        5.44 -     6.80: 2
  Bond angle restraints: 4502
  Sorted by residual:
  angle pdb=" C05 AJP A 601 "
        pdb=" O09 AJP A 601 "
        pdb=" C08 AJP A 601 "
      ideal   model   delta    sigma   weight residual
     108.76  101.96    6.80 3.00e+00 1.11e-01 5.14e+00
  angle pdb=" C24 AJP A 601 "
        pdb=" C23 AJP A 601 "
        pdb=" O25 AJP A 601 "
      ideal   model   delta    sigma   weight residual
     110.79  104.01    6.78 3.00e+00 1.11e-01 5.11e+00
  angle pdb=" C22 AJP A 601 "
        pdb=" C23 AJP A 601 "
        pdb=" O25 AJP A 601 "
      ideal   model   delta    sigma   weight residual
     107.60  112.22   -4.62 3.00e+00 1.11e-01 2.37e+00
  angle pdb=" C07 AJP A 601 "
        pdb=" C08 AJP A 601 "
        pdb=" O09 AJP A 601 "
      ideal   model   delta    sigma   weight residual
     107.32  103.55    3.77 3.00e+00 1.11e-01 1.58e+00
  angle pdb=" C   GLN A 500 "
        pdb=" N   PRO A 501 "
        pdb=" CD  PRO A 501 "
      ideal   model   delta    sigma   weight residual
     125.00  129.97   -4.97 4.10e+00 5.95e-02 1.47e+00
  ... (remaining 4497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.73: 1942
       23.73 -    47.46: 44
       47.46 -    71.20: 3
       71.20 -    94.93: 18
       94.93 -   118.66: 15
  Dihedral angle restraints: 2022
    sinusoidal: 836
      harmonic: 1186
  Sorted by residual:
  dihedral pdb=" C30 AJP A 601 "
           pdb=" C28 AJP A 601 "
           pdb=" C29 AJP A 601 "
           pdb=" O77 AJP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -177.72  -59.06 -118.66     1      3.00e+01 1.11e-03 1.58e+01
  dihedral pdb=" O34 AJP A 601 "
           pdb=" C28 AJP A 601 "
           pdb=" C29 AJP A 601 "
           pdb=" O77 AJP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.96   59.11 -118.07     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C27 AJP A 601 "
           pdb=" C28 AJP A 601 "
           pdb=" C29 AJP A 601 "
           pdb=" C30 AJP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.87  -62.20  116.07     1      3.00e+01 1.11e-03 1.54e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 503
       0.059 -    0.117: 51
       0.117 -    0.176: 2
       0.176 -    0.234: 1
       0.234 -    0.293: 1
  Chirality restraints: 558
  Sorted by residual:
  chirality pdb=" C11 AJP A 601 "
            pdb=" C10 AJP A 601 "
            pdb=" C12 AJP A 601 "
            pdb=" C16 AJP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.50   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" C08 AJP A 601 "
            pdb=" C07 AJP A 601 "
            pdb=" C10 AJP A 601 "
            pdb=" O09 AJP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.77   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C15 AJP A 601 "
            pdb=" C14 AJP A 601 "
            pdb=" C16 AJP A 601 "
            pdb=" C20 AJP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.56    0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 555 not shown)

  Planarity restraints: 530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 194 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO A 195 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 195 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 195 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 378 "   -0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO A 379 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 379 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 379 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 104 "    0.017 5.00e-02 4.00e+02   2.49e-02 9.89e-01
        pdb=" N   PRO A 105 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "    0.014 5.00e-02 4.00e+02
  ... (remaining 527 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 575
        2.76 -     3.29: 3455
        3.29 -     3.83: 5568
        3.83 -     4.36: 6525
        4.36 -     4.90: 10909
  Nonbonded interactions: 27032
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  19 "
            pdb=" ND2 ASN A  23 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   PRO A 140 "
            pdb=" OG  SER A 144 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   LEU A 324 "
            pdb=" OG  SER A 327 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OE1 GLU A  22 "
            pdb=" NH1 ARG A 119 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OE1 GLN A 371 "
            pdb=" NH2 ARG A 461 "
     model   vdw
     2.308 3.120
  ... (remaining 27027 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.220
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.970
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3300  Z= 0.133
  Angle     :  0.492   6.802   4504  Z= 0.220
  Chirality :  0.039   0.293    558
  Planarity :  0.003   0.028    530
  Dihedral  : 18.002 118.659   1257
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  2.92 %
    Favored  : 95.61 %
  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:  3.38 (0.42), residues: 407
  helix:  2.27 (0.27), residues: 350
  sheet:  None (None), residues: 0
  loop :  2.35 (0.93), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 337 
 TYR   0.006   0.001   TYR A 383 
 PHE   0.006   0.001   PHE A 227 
 TRP   0.008   0.001   TRP A  33 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3299)
  covalent geometry    : angle       0.49197 ( 4502)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.33091 (    2)
  hydrogen bonds       : bond        0.25418 (  262)
  hydrogen bonds       : angle       6.13116 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8453 (t0) cc_final: 0.8068 (t0)
REVERT: A  116 ARG cc_start: 0.7387 (ttt180) cc_final: 0.6603 (ptp-170)
REVERT: A  141 ASN cc_start: 0.8971 (m-40) cc_final: 0.8761 (p0)
REVERT: A  179 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7715 (t80)
REVERT: A  183 MET cc_start: 0.9020 (mmt) cc_final: 0.8415 (mmm)
REVERT: A  201 TYR cc_start: 0.8254 (t80) cc_final: 0.7997 (t80)
REVERT: A  316 MET cc_start: 0.6589 (mtt) cc_final: 0.5919 (ppp)
REVERT: A  325 LEU cc_start: 0.8809 (mt) cc_final: 0.8554 (mt)
REVERT: A  384 ILE cc_start: 0.8880 (mt) cc_final: 0.8676 (mm)
REVERT: A  416 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.6885 (tpt170)
REVERT: A  431 THR cc_start: 0.8919 (m) cc_final: 0.8581 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 166
  average time/residue: 0.0561
  time to fit residues: 11.4302
Evaluate side-chains
  130 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  488 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0170
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.135472 restraints weight = 5800.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.139292 restraints weight = 2948.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.142237 restraints weight = 1808.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144054 restraints weight = 1186.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.145395 restraints weight = 851.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3300  Z= 0.153
  Angle     :  0.720   8.345   4504  Z= 0.330
  Chirality :  0.045   0.232    558
  Planarity :  0.005   0.054    530
  Dihedral  : 13.445 102.727    586
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.25 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.20 (0.41), residues: 407
  helix:  2.22 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  1.67 (1.02), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.023   0.002   TYR A 472 
 PHE   0.018   0.002   PHE A  26 
 TRP   0.015   0.001   TRP A  74 
 HIS   0.001   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3299)
  covalent geometry    : angle       0.71915 ( 4502)
  SS BOND              : bond        0.00501 (    1)
  SS BOND              : angle       1.45932 (    2)
  hydrogen bonds       : bond        0.04702 (  262)
  hydrogen bonds       : angle       4.31323 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8169 (t0) cc_final: 0.7851 (t0)
REVERT: A   85 ASP cc_start: 0.8738 (m-30) cc_final: 0.8532 (t0)
REVERT: A  116 ARG cc_start: 0.7288 (ttt180) cc_final: 0.6439 (ptp-170)
REVERT: A  119 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7704 (tpt-90)
REVERT: A  201 TYR cc_start: 0.8521 (t80) cc_final: 0.8233 (t80)
REVERT: A  316 MET cc_start: 0.6578 (mtt) cc_final: 0.5930 (ppp)
REVERT: A  384 ILE cc_start: 0.8659 (mt) cc_final: 0.8346 (mm)
REVERT: A  416 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.6690 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8018 (pp30)
  outliers start: 14
  outliers final: 5
  residues processed: 146
  average time/residue: 0.0496
  time to fit residues: 9.2709
Evaluate side-chains
  127 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 32 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 ASN
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.154008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.138855 restraints weight = 5771.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.142743 restraints weight = 3025.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.145563 restraints weight = 1826.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.147418 restraints weight = 1209.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.148633 restraints weight = 855.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3300  Z= 0.141
  Angle     :  0.686   7.514   4504  Z= 0.314
  Chirality :  0.045   0.354    558
  Planarity :  0.005   0.056    530
  Dihedral  : 10.411  92.948    584
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 19.59 %
    Favored  : 74.85 %
  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:  2.99 (0.42), residues: 407
  helix:  2.08 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop :  1.53 (1.10), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.022   0.002   TYR A 472 
 PHE   0.029   0.002   PHE A 503 
 TRP   0.022   0.001   TRP A  74 
 HIS   0.002   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3299)
  covalent geometry    : angle       0.68544 ( 4502)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.94658 (    2)
  hydrogen bonds       : bond        0.03978 (  262)
  hydrogen bonds       : angle       4.09317 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8049 (t0) cc_final: 0.7805 (t0)
REVERT: A  116 ARG cc_start: 0.7404 (ttt180) cc_final: 0.6452 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7378 (ttt180)
REVERT: A  179 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8018 (t80)
REVERT: A  316 MET cc_start: 0.6550 (mtt) cc_final: 0.6008 (ppp)
REVERT: A  347 ASN cc_start: 0.8776 (m-40) cc_final: 0.8345 (m-40)
REVERT: A  357 GLN cc_start: 0.7713 (pm20) cc_final: 0.7495 (pm20)
REVERT: A  384 ILE cc_start: 0.8663 (mt) cc_final: 0.8451 (mm)
REVERT: A  416 ARG cc_start: 0.7358 (mtt-85) cc_final: 0.6898 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7993 (pp30)
  outliers start: 19
  outliers final: 10
  residues processed: 139
  average time/residue: 0.0416
  time to fit residues: 7.5017
Evaluate side-chains
  135 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0570
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  89 ASN
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.156849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.141462 restraints weight = 5410.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.145128 restraints weight = 2830.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.147935 restraints weight = 1748.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.149694 restraints weight = 1155.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150899 restraints weight = 833.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3300  Z= 0.139
  Angle     :  0.656   7.317   4504  Z= 0.306
  Chirality :  0.043   0.337    558
  Planarity :  0.005   0.054    530
  Dihedral  :  8.490  82.477    584
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 20.76 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.42), residues: 407
  helix:  1.92 (0.27), residues: 350
  sheet:  None (None), residues: 0
  loop :  1.66 (1.09), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.023   0.002   TYR A 472 
 PHE   0.020   0.002   PHE A 503 
 TRP   0.032   0.002   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3299)
  covalent geometry    : angle       0.65547 ( 4502)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       0.72784 (    2)
  hydrogen bonds       : bond        0.03783 (  262)
  hydrogen bonds       : angle       4.09655 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8088 (t0) cc_final: 0.7795 (t0)
REVERT: A  116 ARG cc_start: 0.7478 (ttt180) cc_final: 0.6496 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7388 (ttt180)
REVERT: A  131 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8493 (mm)
REVERT: A  148 PHE cc_start: 0.7809 (m-10) cc_final: 0.6656 (t80)
REVERT: A  179 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: A  316 MET cc_start: 0.6611 (mtt) cc_final: 0.6040 (ppp)
REVERT: A  416 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6723 (mmp-170)
  outliers start: 19
  outliers final: 11
  residues processed: 136
  average time/residue: 0.0461
  time to fit residues: 7.9719
Evaluate side-chains
  129 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  317 HIS
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.157399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.142130 restraints weight = 5462.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.146042 restraints weight = 2856.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.148753 restraints weight = 1715.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.150616 restraints weight = 1139.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151810 restraints weight = 803.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3300  Z= 0.142
  Angle     :  0.690   8.613   4504  Z= 0.315
  Chirality :  0.043   0.229    558
  Planarity :  0.005   0.054    530
  Dihedral  :  7.617  73.786    584
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.81 %
    Favored  : 71.93 %
  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:  2.70 (0.42), residues: 407
  helix:  1.89 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop :  1.48 (1.08), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.025   0.002   TYR A 472 
 PHE   0.030   0.001   PHE A 503 
 TRP   0.031   0.002   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3299)
  covalent geometry    : angle       0.68954 ( 4502)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.59057 (    2)
  hydrogen bonds       : bond        0.03737 (  262)
  hydrogen bonds       : angle       4.15619 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8062 (t0) cc_final: 0.7721 (t0)
REVERT: A   84 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8965 (pp30)
REVERT: A  116 ARG cc_start: 0.7566 (ttt180) cc_final: 0.6512 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7400 (ttt180)
REVERT: A  179 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (t80)
REVERT: A  316 MET cc_start: 0.6620 (mtt) cc_final: 0.6013 (ppp)
REVERT: A  347 ASN cc_start: 0.8833 (m-40) cc_final: 0.8626 (m-40)
REVERT: A  416 ARG cc_start: 0.7130 (mtt-85) cc_final: 0.6926 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8146 (pp30)
  outliers start: 18
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0484
  time to fit residues: 7.9048
Evaluate side-chains
  128 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 423 ASN
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.153186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137509 restraints weight = 5535.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.141469 restraints weight = 2926.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.144217 restraints weight = 1765.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.146011 restraints weight = 1178.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.147326 restraints weight = 852.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3300  Z= 0.151
  Angle     :  0.701   7.829   4504  Z= 0.323
  Chirality :  0.043   0.201    558
  Planarity :  0.005   0.052    530
  Dihedral  :  7.372  73.340    584
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 21.93 %
    Favored  : 72.51 %
  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:  2.68 (0.43), residues: 407
  helix:  1.88 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop :  1.44 (1.07), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 176 
 TYR   0.023   0.002   TYR A 472 
 PHE   0.022   0.002   PHE A 503 
 TRP   0.019   0.001   TRP A  74 
 HIS   0.001   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3299)
  covalent geometry    : angle       0.70095 ( 4502)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.85775 (    2)
  hydrogen bonds       : bond        0.03777 (  262)
  hydrogen bonds       : angle       4.17180 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ASN cc_start: 0.8083 (t0) cc_final: 0.7703 (t0)
REVERT: A   84 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8983 (pp30)
REVERT: A  116 ARG cc_start: 0.7567 (ttt180) cc_final: 0.6461 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7323 (ttt180)
REVERT: A  179 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (t80)
REVERT: A  207 PHE cc_start: 0.8773 (t80) cc_final: 0.8269 (t80)
REVERT: A  316 MET cc_start: 0.6476 (mtt) cc_final: 0.5959 (ppp)
REVERT: A  347 ASN cc_start: 0.8787 (m-40) cc_final: 0.8560 (m-40)
REVERT: A  416 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6961 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7977 (pp30)
  outliers start: 19
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0477
  time to fit residues: 7.7065
Evaluate side-chains
  131 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  317 HIS
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0010
   chunk 0 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.157687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141821 restraints weight = 5667.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145998 restraints weight = 2926.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.148889 restraints weight = 1733.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.150808 restraints weight = 1132.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.152202 restraints weight = 804.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3300  Z= 0.137
  Angle     :  0.703   9.470   4504  Z= 0.323
  Chirality :  0.043   0.289    558
  Planarity :  0.005   0.050    530
  Dihedral  :  7.146  71.033    584
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 23.10 %
    Favored  : 72.22 %
  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:  2.69 (0.43), residues: 407
  helix:  1.86 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop :  1.65 (1.05), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  11 
 TYR   0.023   0.002   TYR A 472 
 PHE   0.027   0.002   PHE A 481 
 TRP   0.017   0.001   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3299)
  covalent geometry    : angle       0.70279 ( 4502)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.64766 (    2)
  hydrogen bonds       : bond        0.03646 (  262)
  hydrogen bonds       : angle       4.21943 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8971 (pp30)
REVERT: A  116 ARG cc_start: 0.7568 (ttt180) cc_final: 0.6433 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7366 (ttt180)
REVERT: A  148 PHE cc_start: 0.7871 (m-10) cc_final: 0.6460 (t80)
REVERT: A  316 MET cc_start: 0.6470 (mtt) cc_final: 0.5914 (ppp)
REVERT: A  416 ARG cc_start: 0.7176 (mtt-85) cc_final: 0.6920 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8142 (pp30)
  outliers start: 16
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0499
  time to fit residues: 8.2302
Evaluate side-chains
  127 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.158573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.142321 restraints weight = 5913.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.146526 restraints weight = 3100.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.149406 restraints weight = 1864.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151433 restraints weight = 1236.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152891 restraints weight = 880.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3300  Z= 0.137
  Angle     :  0.720   9.819   4504  Z= 0.339
  Chirality :  0.044   0.264    558
  Planarity :  0.005   0.051    530
  Dihedral  :  7.064  69.688    584
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 23.98 %
    Favored  : 71.05 %
  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:  2.49 (0.42), residues: 407
  helix:  1.81 (0.27), residues: 350
  sheet:  None (None), residues: 0
  loop :  0.93 (1.02), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  11 
 TYR   0.022   0.002   TYR A 472 
 PHE   0.058   0.002   PHE A 207 
 TRP   0.014   0.001   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3299)
  covalent geometry    : angle       0.71892 ( 4502)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       1.80834 (    2)
  hydrogen bonds       : bond        0.03536 (  262)
  hydrogen bonds       : angle       4.23228 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 VAL cc_start: 0.8288 (m) cc_final: 0.7966 (p)
REVERT: A  116 ARG cc_start: 0.7621 (ttt180) cc_final: 0.6471 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7453 (ttt180)
REVERT: A  179 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8461 (t80)
REVERT: A  316 MET cc_start: 0.6449 (mtt) cc_final: 0.5869 (ppp)
REVERT: A  337 ARG cc_start: 0.8376 (tpt-90) cc_final: 0.7798 (tpm170)
REVERT: A  416 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.7012 (mmp-170)
REVERT: A  488 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8163 (pp30)
REVERT: A  495 PHE cc_start: 0.8288 (t80) cc_final: 0.7988 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 125
  average time/residue: 0.0539
  time to fit residues: 8.4587
Evaluate side-chains
  129 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0170
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.157487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141123 restraints weight = 5785.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.145242 restraints weight = 3065.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148059 restraints weight = 1866.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.150100 restraints weight = 1248.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151561 restraints weight = 895.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3300  Z= 0.148
  Angle     :  0.728   9.535   4504  Z= 0.346
  Chirality :  0.044   0.237    558
  Planarity :  0.005   0.050    530
  Dihedral  :  7.042  68.089    584
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 24.85 %
    Favored  : 70.47 %
  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:  2.44 (0.42), residues: 407
  helix:  1.82 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop :  0.64 (1.01), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  11 
 TYR   0.021   0.002   TYR A 472 
 PHE   0.029   0.002   PHE A 481 
 TRP   0.015   0.001   TRP A  74 
 HIS   0.001   0.001   HIS A   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3299)
  covalent geometry    : angle       0.72799 ( 4502)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       1.42438 (    2)
  hydrogen bonds       : bond        0.03629 (  262)
  hydrogen bonds       : angle       4.32778 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 VAL cc_start: 0.8298 (m) cc_final: 0.7987 (p)
REVERT: A  116 ARG cc_start: 0.7573 (ttt180) cc_final: 0.6452 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8127 (ttt180) cc_final: 0.7463 (ttt180)
REVERT: A  148 PHE cc_start: 0.7810 (m-10) cc_final: 0.6446 (t80)
REVERT: A  179 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8333 (t80)
REVERT: A  316 MET cc_start: 0.6440 (mtt) cc_final: 0.5897 (ppp)
REVERT: A  337 ARG cc_start: 0.8337 (tpt-90) cc_final: 0.7789 (tpm170)
REVERT: A  488 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8187 (pp30)
REVERT: A  495 PHE cc_start: 0.8296 (t80) cc_final: 0.8066 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 120
  average time/residue: 0.0504
  time to fit residues: 7.6589
Evaluate side-chains
  126 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 GLN ** 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 = 0.3922 r_free = 0.3922 target = 0.157338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141080 restraints weight = 5784.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.145246 restraints weight = 3040.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148128 restraints weight = 1827.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.150071 restraints weight = 1209.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.151533 restraints weight = 868.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3300  Z= 0.148
  Angle     :  0.746  14.594   4504  Z= 0.354
  Chirality :  0.043   0.227    558
  Planarity :  0.005   0.050    530
  Dihedral  :  7.169  66.859    584
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 26.32 %
    Favored  : 69.30 %
  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:  2.34 (0.43), residues: 407
  helix:  1.77 (0.28), residues: 349
  sheet:  None (None), residues: 0
  loop :  0.46 (1.01), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 416 
 TYR   0.023   0.002   TYR A 472 
 PHE   0.034   0.002   PHE A 503 
 TRP   0.014   0.001   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3299)
  covalent geometry    : angle       0.74552 ( 4502)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       1.33781 (    2)
  hydrogen bonds       : bond        0.03597 (  262)
  hydrogen bonds       : angle       4.33802 (  768)

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

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6418 (ptp-170)
REVERT: A  119 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7429 (ttt180)
REVERT: A  146 LEU cc_start: 0.8329 (mt) cc_final: 0.8074 (tt)
REVERT: A  148 PHE cc_start: 0.7819 (m-10) cc_final: 0.6454 (t80)
REVERT: A  179 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8381 (t80)
REVERT: A  316 MET cc_start: 0.6399 (mtt) cc_final: 0.5839 (ppp)
REVERT: A  337 ARG cc_start: 0.8335 (tpt-90) cc_final: 0.7791 (tpm170)
REVERT: A  488 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8203 (pp30)
  outliers start: 15
  outliers final: 12
  residues processed: 120
  average time/residue: 0.0574
  time to fit residues: 8.5901
Evaluate side-chains
  124 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   82 GLN
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  523 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0570
   chunk 38 optimal weight:    0.2980
   chunk 34 optimal weight:    0.0060
   chunk 33 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.2714

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.160916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.145638 restraints weight = 5692.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.149464 restraints weight = 3015.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.152114 restraints weight = 1839.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.153881 restraints weight = 1228.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.155189 restraints weight = 891.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.5243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3300  Z= 0.125
  Angle     :  0.693   8.879   4504  Z= 0.327
  Chirality :  0.041   0.212    558
  Planarity :  0.005   0.051    530
  Dihedral  :  6.758  60.509    584
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 27.49 %
    Favored  : 69.01 %
  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:  2.43 (0.43), residues: 407
  helix:  1.85 (0.28), residues: 348
  sheet:  None (None), residues: 0
  loop :  0.38 (0.99), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.024   0.002   TYR A 472 
 PHE   0.030   0.002   PHE A 481 
 TRP   0.013   0.001   TRP A  74 
 HIS   0.001   0.000   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3299)
  covalent geometry    : angle       0.69234 ( 4502)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       1.00244 (    2)
  hydrogen bonds       : bond        0.03417 (  262)
  hydrogen bonds       : angle       4.29525 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 741.75 seconds
wall clock time: 13 minutes 27.09 seconds (807.09 seconds total)