Starting phenix.real_space_refine
on Fri Aug 22 14:05:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/08_2025/8wjh_37580.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     Cl      1      4.86       5
     C    2493      2.51       5
     N     643      2.21       5
     O     658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3824
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3823
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 26, 'TRANS': 478}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.99, per 1000 atoms: 0.26
  Number of scatterers: 3824
  At special positions: 0
  Unit cell: (90.95, 77.04, 88.81, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      29     16.00
     O     658      8.00
     N     643      7.00
     C    2493      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 113 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 136 " 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: 0.21
  Conformation dependent library (CDL) restraints added in 108.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      82.4% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
      removed outlier: 3.618A  pdb=" N   LYS A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 36
      removed outlier: 3.601A  pdb=" N   THR A  18 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
      Proline residue:  A  27  - end of helix
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 140 through 164
    Processing helix  chain 'A' and resid 168 through 187
      removed outlier: 3.522A  pdb=" N   MET A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 192 through 222
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 4.552A  pdb=" N   ALA A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   VAL A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 276
      Proline residue:  A 265  - end of helix
      removed outlier: 3.880A  pdb=" N   LEU A 271 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 288 through 303
    Processing helix  chain 'A' and resid 314 through 320
    Processing helix  chain 'A' and resid 320 through 327
    Processing helix  chain 'A' and resid 335 through 339
    Processing helix  chain 'A' and resid 339 through 366
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 373 through 399
    Processing helix  chain 'A' and resid 400 through 422
    Processing helix  chain 'A' and resid 426 through 456
      removed outlier: 3.716A  pdb=" N   ALA A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 484
      removed outlier: 3.556A  pdb=" N   GLY A 466 " --> pdb=" O   MET A 462 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE A 467 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 485 through 488
    Processing helix  chain 'A' and resid 491 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88
      removed outlier: 4.036A  pdb=" N   ARG A  87 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU A 111 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    289 hydrogen bonds defined for protein.
    858 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: 0.40

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1191
        1.35 -     1.47: 985
        1.47 -     1.60: 1692
        1.60 -     1.72: 0
        1.72 -     1.85: 45
  Bond restraints: 3913
  Sorted by residual:
  bond pdb=" N   ARG A 473 "
       pdb=" CA  ARG A 473 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.23e-02 6.61e+03 6.14e+00
  bond pdb=" N   THR A 470 "
       pdb=" CA  THR A 470 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.23e-02 6.61e+03 5.34e+00
  bond pdb=" CB  CYS A 113 "
       pdb=" SG  CYS A 113 "
    ideal  model  delta    sigma   weight residual
    1.808  1.743  0.065 3.30e-02 9.18e+02 3.88e+00
  bond pdb=" CA  LEU A  26 "
       pdb=" C   LEU A  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.543 -0.021 1.11e-02 8.12e+03 3.69e+00
  bond pdb=" C   VAL A 264 "
       pdb=" N   PRO A 265 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.10e+00
  ... (remaining 3908 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 5118
        2.87 -     5.75: 170
        5.75 -     8.62: 29
        8.62 -    11.50: 6
       11.50 -    14.37: 4
  Bond angle restraints: 5327
  Sorted by residual:
  angle pdb=" C   CYS A 136 "
        pdb=" CA  CYS A 136 "
        pdb=" CB  CYS A 136 "
      ideal   model   delta    sigma   weight residual
     110.42  124.79  -14.37 1.99e+00 2.53e-01 5.22e+01
  angle pdb=" C   VAL A 135 "
        pdb=" N   CYS A 136 "
        pdb=" CA  CYS A 136 "
      ideal   model   delta    sigma   weight residual
     121.54  133.18  -11.64 1.91e+00 2.74e-01 3.71e+01
  angle pdb=" N   VAL A 460 "
        pdb=" CA  VAL A 460 "
        pdb=" C   VAL A 460 "
      ideal   model   delta    sigma   weight residual
     113.43  107.42    6.01 1.09e+00 8.42e-01 3.04e+01
  angle pdb=" C   ALA A 390 "
        pdb=" N   THR A 391 "
        pdb=" CA  THR A 391 "
      ideal   model   delta    sigma   weight residual
     121.14  112.79    8.35 1.75e+00 3.27e-01 2.27e+01
  angle pdb=" N   THR A 392 "
        pdb=" CA  THR A 392 "
        pdb=" C   THR A 392 "
      ideal   model   delta    sigma   weight residual
     111.28  106.36    4.92 1.09e+00 8.42e-01 2.04e+01
  ... (remaining 5322 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2080
       17.34 -    34.68: 149
       34.68 -    52.02: 49
       52.02 -    69.36: 19
       69.36 -    86.70: 8
  Dihedral angle restraints: 2305
    sinusoidal: 864
      harmonic: 1441
  Sorted by residual:
  dihedral pdb=" CB  CYS A  85 "
           pdb=" SG  CYS A  85 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.55   81.45     1      1.00e+01 1.00e-02 8.17e+01
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 113 "
           pdb=" CB  CYS A 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.66   65.66     1      1.00e+01 1.00e-02 5.64e+01
  dihedral pdb=" C   CYS A 136 "
           pdb=" N   CYS A 136 "
           pdb=" CA  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.65   18.05     0      2.50e+00 1.60e-01 5.21e+01
  ... (remaining 2302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 578
       0.116 -    0.232: 47
       0.232 -    0.349: 1
       0.349 -    0.465: 1
       0.465 -    0.581: 2
  Chirality restraints: 629
  Sorted by residual:
  chirality pdb=" CA  CYS A 136 "
            pdb=" N   CYS A 136 "
            pdb=" C   CYS A 136 "
            pdb=" CB  CYS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.43e+00
  chirality pdb=" CG  LEU A 296 "
            pdb=" CB  LEU A 296 "
            pdb=" CD1 LEU A 296 "
            pdb=" CD2 LEU A 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" CB  ILE A 269 "
            pdb=" CA  ILE A 269 "
            pdb=" CG1 ILE A 269 "
            pdb=" CG2 ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 626 not shown)

  Planarity restraints: 662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 459 "   -0.025 2.00e-02 2.50e+03   4.87e-02 2.37e+01
        pdb=" C   PRO A 459 "    0.084 2.00e-02 2.50e+03
        pdb=" O   PRO A 459 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   VAL A 460 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 390 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.70e+00
        pdb=" C   ALA A 390 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ALA A 390 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 391 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  94 "    0.012 2.00e-02 2.50e+03   2.38e-02 5.65e+00
        pdb=" C   GLN A  94 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLN A  94 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  95 "    0.014 2.00e-02 2.50e+03
  ... (remaining 659 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 754
        2.78 -     3.31: 3894
        3.31 -     3.84: 6500
        3.84 -     4.37: 7086
        4.37 -     4.90: 12471
  Nonbonded interactions: 30705
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 366 "
            pdb=" NH2 ARG A 486 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   MET A 218 "
            pdb=" OG1 THR A 222 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   GLN A 424 "
            pdb=" NE2 GLN A 427 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" O   LEU A 212 "
            pdb=" OG1 THR A 216 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" NH2 ARG A  89 "
            pdb=" O   ALA A 108 "
     model   vdw
     2.383 3.120
  ... (remaining 30700 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.720
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   3915  Z= 0.309
  Angle     :  1.272  14.373   5331  Z= 0.720
  Chirality :  0.069   0.581    629
  Planarity :  0.009   0.064    662
  Dihedral  : 15.606  86.704   1367
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 19.75 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.35), residues: 499
  helix:  0.78 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -0.42 (0.55), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.003   ARG A 486 
 TYR   0.021   0.005   TYR A 119 
 PHE   0.031   0.003   PHE A 354 
 TRP   0.032   0.003   TRP A 282 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 3913)
  covalent geometry    : angle       1.26836 ( 5327)
  SS BOND              : bond        0.00528 (    2)
  SS BOND              : angle       3.56806 (    4)
  hydrogen bonds       : bond        0.13655 (  289)
  hydrogen bonds       : angle       6.15032 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  473 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6036 (mtp180)
  outliers start: 4
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0568
  time to fit residues: 2.4837
Evaluate side-chains
  30 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.194434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.138168 restraints weight = 3783.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.26
r_work: 0.3472 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3915  Z= 0.175
  Angle     :  0.655   6.765   5331  Z= 0.337
  Chirality :  0.041   0.185    629
  Planarity :  0.004   0.029    662
  Dihedral  :  5.360  58.096    538
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.75 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.38), residues: 499
  helix:  1.63 (0.27), residues: 375
  sheet: -0.39 (1.52), residues: 10
  loop : -0.17 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 401 
 TYR   0.011   0.002   TYR A 361 
 PHE   0.018   0.002   PHE A 267 
 TRP   0.018   0.002   TRP A 255 
 HIS   0.002   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3913)
  covalent geometry    : angle       0.65381 ( 5327)
  SS BOND              : bond        0.00768 (    2)
  SS BOND              : angle       1.72421 (    4)
  hydrogen bonds       : bond        0.05694 (  289)
  hydrogen bonds       : angle       4.89481 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  473 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6665 (mtt180)
  outliers start: 7
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0461
  time to fit residues: 2.2138
Evaluate side-chains
  32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  473 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.0870
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.187956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131261 restraints weight = 3805.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.26
r_work: 0.3394 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3915  Z= 0.170
  Angle     :  0.642  12.099   5331  Z= 0.318
  Chirality :  0.041   0.159    629
  Planarity :  0.004   0.034    662
  Dihedral  :  5.049  51.873    538
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.00 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.38), residues: 499
  helix:  1.33 (0.27), residues: 387
  sheet: -1.00 (1.49), residues: 10
  loop : -0.01 (0.64), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 200 
 TYR   0.011   0.002   TYR A 361 
 PHE   0.017   0.002   PHE A 205 
 TRP   0.015   0.001   TRP A 282 
 HIS   0.001   0.000   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3913)
  covalent geometry    : angle       0.64106 ( 5327)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       1.12959 (    4)
  hydrogen bonds       : bond        0.05278 (  289)
  hydrogen bonds       : angle       4.74374 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4929 (mtp) cc_final: 0.3805 (pmm)
REVERT: A  136 CYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6751 (t)
REVERT: A  411 MET cc_start: 0.6254 (mmp) cc_final: 0.6019 (tpp)
REVERT: A  482 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7034 (tp)
  outliers start: 10
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0495
  time to fit residues: 2.7938
Evaluate side-chains
  34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  482 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.187983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.132126 restraints weight = 3805.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.21
r_work: 0.3404 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3915  Z= 0.143
  Angle     :  0.556   6.789   5331  Z= 0.279
  Chirality :  0.039   0.164    629
  Planarity :  0.004   0.036    662
  Dihedral  :  4.008  18.078    534
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.00 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.38), residues: 499
  helix:  1.33 (0.27), residues: 390
  sheet: -1.39 (1.46), residues: 10
  loop :  0.20 (0.66), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.010   0.001   TYR A 361 
 PHE   0.014   0.001   PHE A 205 
 TRP   0.010   0.001   TRP A 282 
 HIS   0.001   0.000   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3913)
  covalent geometry    : angle       0.55534 ( 5327)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.74367 (    4)
  hydrogen bonds       : bond        0.04812 (  289)
  hydrogen bonds       : angle       4.62525 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4875 (mtp) cc_final: 0.3762 (pmm)
REVERT: A  136 CYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7145 (t)
REVERT: A  411 MET cc_start: 0.6542 (mmp) cc_final: 0.6275 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 36
  average time/residue: 0.0465
  time to fit residues: 2.3986
Evaluate side-chains
  33 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  136 CYS
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.191114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133173 restraints weight = 3735.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.37
r_work: 0.3243 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6232
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3915  Z= 0.143
  Angle     :  0.554   6.653   5331  Z= 0.276
  Chirality :  0.038   0.149    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.939  17.497    534
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.00 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.38), residues: 499
  helix:  1.45 (0.27), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.31 (0.63), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.013   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3913)
  covalent geometry    : angle       0.55400 ( 5327)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.68819 (    4)
  hydrogen bonds       : bond        0.04764 (  289)
  hydrogen bonds       : angle       4.56742 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4664 (mtp) cc_final: 0.3539 (pmm)
REVERT: A   24 PHE cc_start: 0.7199 (m-80) cc_final: 0.6827 (m-80)
REVERT: A  317 MET cc_start: 0.4867 (pmm) cc_final: 0.4440 (pmm)
REVERT: A  411 MET cc_start: 0.6140 (mmt) cc_final: 0.5860 (tpp)
REVERT: A  482 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6741 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 42
  average time/residue: 0.0449
  time to fit residues: 2.7520
Evaluate side-chains
  37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.190851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.133153 restraints weight = 3775.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.37
r_work: 0.3246 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6204
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3915  Z= 0.136
  Angle     :  0.540   6.230   5331  Z= 0.269
  Chirality :  0.038   0.146    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.871  16.524    534
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.25 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.39), residues: 499
  helix:  1.44 (0.27), residues: 388
  sheet:  None (None), residues: 0
  loop :  0.35 (0.65), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 282 
 HIS   0.001   0.000   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3913)
  covalent geometry    : angle       0.53941 ( 5327)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       1.13093 (    4)
  hydrogen bonds       : bond        0.04602 (  289)
  hydrogen bonds       : angle       4.48926 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4760 (mtp) cc_final: 0.3576 (pmm)
REVERT: A  317 MET cc_start: 0.5194 (pmm) cc_final: 0.4744 (pmm)
REVERT: A  411 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5818 (tpp)
REVERT: A  482 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6744 (tp)
  outliers start: 12
  outliers final: 7
  residues processed: 38
  average time/residue: 0.0438
  time to fit residues: 2.3871
Evaluate side-chains
  36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  411 MET
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0370
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.5058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.192448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134626 restraints weight = 3798.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.37
r_work: 0.3270 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3915  Z= 0.126
  Angle     :  0.525   6.239   5331  Z= 0.261
  Chirality :  0.037   0.141    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.815  15.930    534
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.50 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.39), residues: 499
  helix:  1.52 (0.27), residues: 388
  sheet:  None (None), residues: 0
  loop :  0.41 (0.66), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.009   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3913)
  covalent geometry    : angle       0.52388 ( 5327)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       1.10637 (    4)
  hydrogen bonds       : bond        0.04400 (  289)
  hydrogen bonds       : angle       4.41176 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4819 (mtp) cc_final: 0.3534 (pmm)
REVERT: A  107 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.4236 (tp30)
REVERT: A  120 ASP cc_start: 0.7632 (m-30) cc_final: 0.6482 (p0)
REVERT: A  317 MET cc_start: 0.5176 (pmm) cc_final: 0.4732 (pmm)
REVERT: A  411 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5855 (tpp)
REVERT: A  473 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6496 (mtt180)
REVERT: A  482 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6665 (tp)
  outliers start: 14
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0525
  time to fit residues: 2.9504
Evaluate side-chains
  36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 MET
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.193075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135308 restraints weight = 3817.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.31
r_work: 0.3229 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6230
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3915  Z= 0.151
  Angle     :  0.549   6.839   5331  Z= 0.274
  Chirality :  0.038   0.134    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.851  15.207    534
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.00 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.39), residues: 499
  helix:  1.60 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop :  0.23 (0.63), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 345 
 TYR   0.008   0.001   TYR A 361 
 PHE   0.011   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3913)
  covalent geometry    : angle       0.54837 ( 5327)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       1.28741 (    4)
  hydrogen bonds       : bond        0.04759 (  289)
  hydrogen bonds       : angle       4.43466 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4732 (mtp) cc_final: 0.3549 (pmm)
REVERT: A   24 PHE cc_start: 0.7193 (m-80) cc_final: 0.6760 (m-80)
REVERT: A  107 GLU cc_start: 0.4523 (OUTLIER) cc_final: 0.4286 (tp30)
REVERT: A  317 MET cc_start: 0.5132 (pmm) cc_final: 0.4833 (pmm)
REVERT: A  411 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.5834 (tpp)
REVERT: A  473 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6527 (mtt180)
REVERT: A  482 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6727 (tp)
  outliers start: 13
  outliers final: 8
  residues processed: 41
  average time/residue: 0.0441
  time to fit residues: 2.5541
Evaluate side-chains
  41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 MET
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.193674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.136661 restraints weight = 3829.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.29
r_work: 0.3259 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6259
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3915  Z= 0.139
  Angle     :  0.537   6.468   5331  Z= 0.267
  Chirality :  0.038   0.132    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.842  15.320    534
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.75 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.39), residues: 499
  helix:  1.70 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.35 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.008   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3913)
  covalent geometry    : angle       0.53589 ( 5327)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       1.20228 (    4)
  hydrogen bonds       : bond        0.04619 (  289)
  hydrogen bonds       : angle       4.42053 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 25
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4846 (mtp) cc_final: 0.3552 (pmm)
REVERT: A  107 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.4226 (tp30)
REVERT: A  317 MET cc_start: 0.5116 (pmm) cc_final: 0.4821 (pmm)
REVERT: A  411 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5869 (tpp)
REVERT: A  473 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6535 (mtt180)
REVERT: A  482 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6752 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 36
  average time/residue: 0.0414
  time to fit residues: 2.0554
Evaluate side-chains
  37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 25
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 MET
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.193810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137178 restraints weight = 3803.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.31
r_work: 0.3258 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3915  Z= 0.135
  Angle     :  0.530   6.710   5331  Z= 0.264
  Chirality :  0.038   0.129    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.814  14.931    534
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 22.25 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.39), residues: 499
  helix:  1.73 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.38 (0.63), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3913)
  covalent geometry    : angle       0.52912 ( 5327)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       1.00764 (    4)
  hydrogen bonds       : bond        0.04522 (  289)
  hydrogen bonds       : angle       4.37528 (  858)

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

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

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  998 Ramachandran restraints generated.
    499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4864 (mtp) cc_final: 0.3550 (pmm)
REVERT: A   28 CYS cc_start: 0.7538 (m) cc_final: 0.7081 (p)
REVERT: A  107 GLU cc_start: 0.4477 (OUTLIER) cc_final: 0.4219 (tp30)
REVERT: A  120 ASP cc_start: 0.7710 (m-30) cc_final: 0.6510 (p0)
REVERT: A  317 MET cc_start: 0.5385 (pmm) cc_final: 0.5092 (pmm)
REVERT: A  411 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5854 (tpp)
  outliers start: 10
  outliers final: 8
  residues processed: 35
  average time/residue: 0.0437
  time to fit residues: 2.2956
Evaluate side-chains
  35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 MET
Chi-restraints excluded: chain A residue  500 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.193351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.137038 restraints weight = 3800.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.26
r_work: 0.3250 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6361
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3915  Z= 0.137
  Angle     :  0.534   6.549   5331  Z= 0.265
  Chirality :  0.038   0.129    629
  Planarity :  0.004   0.036    662
  Dihedral  :  3.810  14.738    534
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 22.00 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.39), residues: 499
  helix:  1.71 (0.27), residues: 375
  sheet:  None (None), residues: 0
  loop :  0.36 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.007   0.001   TYR A 361 
 PHE   0.012   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 255 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3913)
  covalent geometry    : angle       0.53301 ( 5327)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       1.04050 (    4)
  hydrogen bonds       : bond        0.04577 (  289)
  hydrogen bonds       : angle       4.36435 (  858)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1077.50 seconds
wall clock time: 19 minutes 2.78 seconds (1142.78 seconds total)