Starting phenix.real_space_refine
on Fri Aug 22 13:30:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xq0_33387/08_2025/7xq0_33387_neut.cif"
  }
  resolution = 3.0
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      10      5.16       5
     C    2189      2.51       5
     N     553      2.21       5
     O     564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 3320
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3232
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 14, 'TRANS': 387}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 88
          Unusual residues: {'2BA': 2}
          Classifications: {'RNA_mixed': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.28, per 1000 atoms: 0.39
  Number of scatterers: 3320
  At special positions: 0
  Unit cell: (78, 75, 67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P       4     15.00
     O     564      8.00
     N     553      7.00
     C    2189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 131.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      83.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 27
      removed outlier: 3.621A  pdb=" N   TRP A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 39
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 69 through 90
      removed outlier: 3.923A  pdb=" N   SER A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 3.879A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 113
      removed outlier: 3.531A  pdb=" N   LEU A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.582A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 4.414A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 176
      removed outlier: 3.686A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 202
      removed outlier: 3.712A  pdb=" N   PHE A 195 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 264 through 275
      removed outlier: 3.540A  pdb=" N   LEU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 296
      removed outlier: 4.142A  pdb=" N   LEU A 283 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR A 286 " --> pdb=" O   TYR A 282 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN A 293 " --> pdb=" O   HIS A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 324
      removed outlier: 3.797A  pdb=" N   THR A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 4.070A  pdb=" N   ALA A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ARG A 333 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 3.586A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 377
      removed outlier: 3.682A  pdb=" N   CYS A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 367 " --> pdb=" O   TRP A 363 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 392 through 418
      removed outlier: 3.765A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 3.962A  pdb=" N   ILE A 445 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    645 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: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 973
        1.34 -     1.45: 637
        1.45 -     1.57: 1781
        1.57 -     1.69: 12
        1.69 -     1.80: 18
  Bond restraints: 3421
  Sorted by residual:
  bond pdb="C1'1 2BA A 601 "
       pdb="C2'1 2BA A 601 "
    ideal  model  delta    sigma   weight residual
    1.532  1.294  0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb="C1'1 2BA A 602 "
       pdb="C2'1 2BA A 602 "
    ideal  model  delta    sigma   weight residual
    1.532  1.297  0.235 2.00e-02 2.50e+03 1.39e+02
  bond pdb=" C1' 2BA A 601 "
       pdb=" C2' 2BA A 601 "
    ideal  model  delta    sigma   weight residual
    1.541  1.317  0.224 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" C1' 2BA A 602 "
       pdb=" C2' 2BA A 602 "
    ideal  model  delta    sigma   weight residual
    1.541  1.318  0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb="C1'1 2BA A 601 "
       pdb="O4'1 2BA A 601 "
    ideal  model  delta    sigma   weight residual
    1.408  1.617 -0.209 2.00e-02 2.50e+03 1.09e+02
  ... (remaining 3416 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 4576
        3.31 -     6.62: 67
        6.62 -     9.93: 22
        9.93 -    13.24: 10
       13.24 -    16.55: 6
  Bond angle restraints: 4681
  Sorted by residual:
  angle pdb=" CA  VAL A 380 "
        pdb=" C   VAL A 380 "
        pdb=" N   PRO A 381 "
      ideal   model   delta    sigma   weight residual
     120.83  116.29    4.54 6.10e-01 2.69e+00 5.53e+01
  angle pdb=" N   LEU A  72 "
        pdb=" CA  LEU A  72 "
        pdb=" C   LEU A  72 "
      ideal   model   delta    sigma   weight residual
     112.23  105.18    7.05 1.26e+00 6.30e-01 3.13e+01
  angle pdb=" O1P 2BA A 601 "
        pdb=" P   2BA A 601 "
        pdb=" O2P 2BA A 601 "
      ideal   model   delta    sigma   weight residual
     121.18  104.63   16.55 3.00e+00 1.11e-01 3.04e+01
  angle pdb=" O1P 2BA A 602 "
        pdb=" P   2BA A 602 "
        pdb=" O2P 2BA A 602 "
      ideal   model   delta    sigma   weight residual
     121.18  104.64   16.54 3.00e+00 1.11e-01 3.04e+01
  angle pdb="O1P1 2BA A 602 "
        pdb=" P1  2BA A 602 "
        pdb="O2P1 2BA A 602 "
      ideal   model   delta    sigma   weight residual
     122.22  106.86   15.36 3.00e+00 1.11e-01 2.62e+01
  ... (remaining 4676 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 1870
       17.70 -    35.39: 137
       35.39 -    53.09: 24
       53.09 -    70.79: 3
       70.79 -    88.48: 3
  Dihedral angle restraints: 2037
    sinusoidal: 854
      harmonic: 1183
  Sorted by residual:
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  VAL A 418 "
           pdb=" C   VAL A 418 "
           pdb=" N   SER A 419 "
           pdb=" CA  SER A 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  TRP A 363 "
           pdb=" C   TRP A 363 "
           pdb=" N   LEU A 364 "
           pdb=" CA  LEU A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 2034 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.099: 514
       0.099 -    0.198: 23
       0.198 -    0.297: 3
       0.297 -    0.396: 0
       0.396 -    0.494: 2
  Chirality restraints: 542
  Sorted by residual:
  chirality pdb=" C2' 2BA A 602 "
            pdb=" C1' 2BA A 602 "
            pdb=" C3' 2BA A 602 "
            pdb=" O2' 2BA A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.31   -0.49 2.00e-01 2.50e+01 6.11e+00
  chirality pdb=" C2' 2BA A 601 "
            pdb=" C1' 2BA A 601 "
            pdb=" C3' 2BA A 601 "
            pdb=" O2' 2BA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.34   -0.46 2.00e-01 2.50e+01 5.39e+00
  chirality pdb="C2'1 2BA A 602 "
            pdb="C1'1 2BA A 602 "
            pdb="C3'1 2BA A 602 "
            pdb="O2'1 2BA A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67   -2.39   -0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 539 not shown)

  Planarity restraints: 552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  71 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   VAL A  71 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   VAL A  71 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A  72 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO A  82 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.037 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO A  70 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.031 5.00e-02 4.00e+02
  ... (remaining 549 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 742
        2.77 -     3.30: 3009
        3.30 -     3.83: 5785
        3.83 -     4.37: 7298
        4.37 -     4.90: 11921
  Nonbonded interactions: 28755
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  83 "
            pdb=" OG1 THR A  87 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   VAL A 304 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O1P 2BA A 601 "
            pdb=" N6  2BA A 602 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   ARG A  61 "
            pdb=" OG1 THR A  65 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" OG  SER A 392 "
            pdb=" OE1 GLU A 394 "
     model   vdw
     2.339 3.040
  ... (remaining 28750 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:             3.190
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.890
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
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      :  0.014   0.238   3421  Z= 0.710
  Angle     :  1.263  16.547   4681  Z= 0.569
  Chirality :  0.057   0.494    542
  Planarity :  0.006   0.057    552
  Dihedral  : 13.005  88.484   1277
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.36 %
    Favored  : 90.78 %
  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: -6.72 (0.21), residues: 398
  helix: -4.46 (0.12), residues: 313
  sheet:  None (None), residues: 0
  loop : -3.02 (0.49), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.009   0.002   TYR A  76 
 PHE   0.011   0.001   PHE A  37 
 TRP   0.008   0.002   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.01440 ( 3421)
  covalent geometry    : angle       1.26324 ( 4681)
  hydrogen bonds       : bond        0.27598 (  215)
  hydrogen bonds       : angle      11.32005 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7168 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7399 (pp20) cc_final: 0.6862 (tm-30)
REVERT: A  122 MET cc_start: 0.8531 (tmm) cc_final: 0.8278 (ttp)
REVERT: A  333 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7023 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8211 (t80) cc_final: 0.7976 (t80)
REVERT: A  451 MET cc_start: 0.6313 (mmt) cc_final: 0.6057 (mmt)
  outliers start: 3
  outliers final: 0
  residues processed: 56
  average time/residue: 0.4888
  time to fit residues: 28.3081
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0870
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0040
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.2970

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 293 ASN
A 431 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.112141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.094640 restraints weight = 4007.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.83
r_work: 0.2950 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3421  Z= 0.126
  Angle     :  0.570   6.219   4681  Z= 0.297
  Chirality :  0.037   0.109    542
  Planarity :  0.005   0.035    552
  Dihedral  :  6.019  25.101    574
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 10.95 %
    Favored  : 85.88 %
  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: -3.01 (0.33), residues: 398
  helix: -1.76 (0.23), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.09 (0.58), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 429 
 TYR   0.008   0.001   TYR A 438 
 PHE   0.007   0.001   PHE A 432 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3421)
  covalent geometry    : angle       0.56977 ( 4681)
  hydrogen bonds       : bond        0.04562 (  215)
  hydrogen bonds       : angle       4.83879 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7523 (mtp85) cc_final: 0.6672 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7839 (pp20) cc_final: 0.6983 (pm20)
REVERT: A  333 ARG cc_start: 0.7601 (tmt170) cc_final: 0.7034 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8523 (t80) cc_final: 0.8290 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 56
  average time/residue: 0.3271
  time to fit residues: 19.2828
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  321 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0670
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.110567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.092596 restraints weight = 3889.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.85
r_work: 0.2873 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3421  Z= 0.129
  Angle     :  0.530   7.670   4681  Z= 0.267
  Chirality :  0.038   0.124    542
  Planarity :  0.004   0.028    552
  Dihedral  :  5.561  22.951    574
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 12.97 %
    Favored  : 83.57 %
  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: -0.81 (0.39), residues: 398
  helix: -0.07 (0.28), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.05 (0.61), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 157 
 TYR   0.009   0.001   TYR A 438 
 PHE   0.012   0.001   PHE A  84 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3421)
  covalent geometry    : angle       0.52996 ( 4681)
  hydrogen bonds       : bond        0.03834 (  215)
  hydrogen bonds       : angle       4.12327 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6464 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7781 (pp20) cc_final: 0.7305 (pm20)
REVERT: A  333 ARG cc_start: 0.7467 (tmt170) cc_final: 0.6901 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8493 (t80) cc_final: 0.8186 (t80)
REVERT: A  451 MET cc_start: 0.6715 (mmt) cc_final: 0.6384 (mpp)
REVERT: A  452 LEU cc_start: 0.7274 (tt) cc_final: 0.7070 (tm)
  outliers start: 12
  outliers final: 7
  residues processed: 54
  average time/residue: 0.3245
  time to fit residues: 18.4598
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0370
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.110320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.092422 restraints weight = 3856.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.86
r_work: 0.2862 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3421  Z= 0.133
  Angle     :  0.510   6.374   4681  Z= 0.258
  Chirality :  0.039   0.171    542
  Planarity :  0.003   0.026    552
  Dihedral  :  5.501  23.845    574
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 13.26 %
    Favored  : 83.00 %
  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:  0.20 (0.41), residues: 398
  helix:  0.68 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.86 (0.60), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.009   0.001   TYR A  35 
 PHE   0.008   0.001   PHE A 125 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3421)
  covalent geometry    : angle       0.50972 ( 4681)
  hydrogen bonds       : bond        0.03641 (  215)
  hydrogen bonds       : angle       3.94938 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6414 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7873 (pp20) cc_final: 0.7490 (pm20)
REVERT: A  187 TYR cc_start: 0.8440 (m-80) cc_final: 0.8058 (m-80)
REVERT: A  333 ARG cc_start: 0.7456 (tmt170) cc_final: 0.6899 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8500 (t80) cc_final: 0.8097 (t80)
REVERT: A  451 MET cc_start: 0.6622 (mmt) cc_final: 0.6324 (mpp)
  outliers start: 13
  outliers final: 6
  residues processed: 48
  average time/residue: 0.3559
  time to fit residues: 17.9835
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3207 r_free = 0.3207 target = 0.109460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.091570 restraints weight = 3884.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.87
r_work: 0.2850 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3421  Z= 0.145
  Angle     :  0.516   8.768   4681  Z= 0.257
  Chirality :  0.039   0.137    542
  Planarity :  0.003   0.027    552
  Dihedral  :  5.542  24.336    574
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 13.54 %
    Favored  : 81.84 %
  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:  0.60 (0.42), residues: 398
  helix:  0.96 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.75 (0.61), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.014   0.001   PHE A  84 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3421)
  covalent geometry    : angle       0.51550 ( 4681)
  hydrogen bonds       : bond        0.03628 (  215)
  hydrogen bonds       : angle       3.88246 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7292 (mtp85) cc_final: 0.6343 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7805 (pp20) cc_final: 0.6821 (pm20)
REVERT: A  114 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7055 (m-70)
REVERT: A  333 ARG cc_start: 0.7460 (tmt170) cc_final: 0.6909 (tpt-90)
REVERT: A  395 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7611 (tm)
REVERT: A  416 PHE cc_start: 0.8527 (t80) cc_final: 0.8244 (t80)
REVERT: A  451 MET cc_start: 0.6574 (mmt) cc_final: 0.6290 (mpp)
  outliers start: 16
  outliers final: 6
  residues processed: 50
  average time/residue: 0.3431
  time to fit residues: 18.0573
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0670
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0170
   overall best weight:    0.2756

-------------------------------------------------------------------------------
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 = 0.3250 r_free = 0.3250 target = 0.112809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.095286 restraints weight = 3871.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.86
r_work: 0.2907 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3421  Z= 0.106
  Angle     :  0.493   9.178   4681  Z= 0.244
  Chirality :  0.037   0.140    542
  Planarity :  0.003   0.026    552
  Dihedral  :  5.326  24.101    574
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.14 %
    Favored  : 80.69 %
  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:  1.07 (0.42), residues: 398
  helix:  1.32 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.74 (0.63), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  61 
 TYR   0.009   0.001   TYR A  92 
 PHE   0.007   0.001   PHE A 372 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3421)
  covalent geometry    : angle       0.49256 ( 4681)
  hydrogen bonds       : bond        0.03349 (  215)
  hydrogen bonds       : angle       3.69346 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6375 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7783 (pp20) cc_final: 0.7415 (pm20)
REVERT: A  114 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7143 (m-70)
REVERT: A  187 TYR cc_start: 0.8397 (m-80) cc_final: 0.8002 (m-80)
REVERT: A  289 HIS cc_start: 0.8783 (m-70) cc_final: 0.8363 (m170)
REVERT: A  303 ARG cc_start: 0.6974 (mtp180) cc_final: 0.6642 (ptp90)
REVERT: A  333 ARG cc_start: 0.7468 (tmt170) cc_final: 0.6918 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8391 (t80) cc_final: 0.8088 (t80)
  outliers start: 11
  outliers final: 3
  residues processed: 51
  average time/residue: 0.3934
  time to fit residues: 20.9905
Evaluate side-chains
  42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   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 = 0.3205 r_free = 0.3205 target = 0.109425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.091631 restraints weight = 3911.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.86
r_work: 0.2851 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3421  Z= 0.157
  Angle     :  0.553   8.556   4681  Z= 0.270
  Chirality :  0.041   0.191    542
  Planarity :  0.003   0.027    552
  Dihedral  :  5.540  25.566    574
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.56 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.42), residues: 398
  helix:  1.38 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.54 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.022   0.001   PHE A 447 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3421)
  covalent geometry    : angle       0.55300 ( 4681)
  hydrogen bonds       : bond        0.03646 (  215)
  hydrogen bonds       : angle       3.79841 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6304 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7723 (pp20) cc_final: 0.6739 (pm20)
REVERT: A  114 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7183 (m-70)
REVERT: A  289 HIS cc_start: 0.8765 (m-70) cc_final: 0.8359 (m170)
REVERT: A  303 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6643 (ptp90)
REVERT: A  333 ARG cc_start: 0.7427 (tmt170) cc_final: 0.6882 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8474 (t80) cc_final: 0.8205 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 47
  average time/residue: 0.4172
  time to fit residues: 20.4888
Evaluate side-chains
  44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.110295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.092765 restraints weight = 3941.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.85
r_work: 0.2916 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3421  Z= 0.149
  Angle     :  0.564   8.698   4681  Z= 0.271
  Chirality :  0.041   0.187    542
  Planarity :  0.003   0.028    552
  Dihedral  :  5.578  26.038    574
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.85 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.42), residues: 398
  helix:  1.40 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.44 (0.65), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.020   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3421)
  covalent geometry    : angle       0.56416 ( 4681)
  hydrogen bonds       : bond        0.03646 (  215)
  hydrogen bonds       : angle       3.80728 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7453 (mtp85) cc_final: 0.6560 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7880 (pp20) cc_final: 0.6921 (pm20)
REVERT: A  114 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7197 (m-70)
REVERT: A  289 HIS cc_start: 0.8860 (m-70) cc_final: 0.8461 (m170)
REVERT: A  303 ARG cc_start: 0.7110 (mtp180) cc_final: 0.6815 (ptp90)
REVERT: A  333 ARG cc_start: 0.7560 (tmt170) cc_final: 0.7018 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8557 (t80) cc_final: 0.8327 (t80)
REVERT: A  451 MET cc_start: 0.7221 (mmt) cc_final: 0.6904 (mmt)
  outliers start: 10
  outliers final: 5
  residues processed: 48
  average time/residue: 0.4321
  time to fit residues: 21.6305
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0060
   chunk 12 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.110005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.092504 restraints weight = 3890.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.85
r_work: 0.2862 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3421  Z= 0.144
  Angle     :  0.553   8.107   4681  Z= 0.267
  Chirality :  0.040   0.180    542
  Planarity :  0.003   0.029    552
  Dihedral  :  5.569  26.363    574
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.85 %
    Favored  : 81.56 %
  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:  1.31 (0.42), residues: 398
  helix:  1.44 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.48 (0.65), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 214 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.022   0.001   PHE A  84 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3421)
  covalent geometry    : angle       0.55282 ( 4681)
  hydrogen bonds       : bond        0.03624 (  215)
  hydrogen bonds       : angle       3.79310 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6403 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7719 (pp20) cc_final: 0.6696 (pm20)
REVERT: A  114 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7122 (m-70)
REVERT: A  289 HIS cc_start: 0.8675 (m-70) cc_final: 0.8261 (m170)
REVERT: A  303 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6672 (ptp90)
REVERT: A  333 ARG cc_start: 0.7443 (tmt170) cc_final: 0.6897 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8471 (t80) cc_final: 0.8200 (t80)
REVERT: A  451 MET cc_start: 0.7074 (mmt) cc_final: 0.6705 (mmt)
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 0.4209
  time to fit residues: 20.6784
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0000
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.110680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.093143 restraints weight = 3849.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.86
r_work: 0.2885 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3421  Z= 0.130
  Angle     :  0.550   9.185   4681  Z= 0.265
  Chirality :  0.040   0.183    542
  Planarity :  0.003   0.028    552
  Dihedral  :  5.504  26.461    574
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.29 %
    Favored  : 80.98 %
  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:  1.39 (0.42), residues: 398
  helix:  1.49 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.44 (0.65), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 303 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.014   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3421)
  covalent geometry    : angle       0.54955 ( 4681)
  hydrogen bonds       : bond        0.03536 (  215)
  hydrogen bonds       : angle       3.75381 (  645)

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

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

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  796 Ramachandran restraints generated.
    398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6431 (mmp-170)
REVERT: A   62 GLU cc_start: 0.7727 (pp20) cc_final: 0.6699 (pm20)
REVERT: A  114 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7113 (m-70)
REVERT: A  289 HIS cc_start: 0.8725 (m-70) cc_final: 0.8314 (m170)
REVERT: A  303 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6685 (ptp90)
REVERT: A  333 ARG cc_start: 0.7476 (tmt170) cc_final: 0.6929 (tpt-90)
REVERT: A  416 PHE cc_start: 0.8405 (t80) cc_final: 0.8180 (t80)
REVERT: A  451 MET cc_start: 0.7094 (mmt) cc_final: 0.6794 (mmt)
  outliers start: 6
  outliers final: 5
  residues processed: 46
  average time/residue: 0.4261
  time to fit residues: 20.4343
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 11 optimal weight:    0.3980
   chunk 38 optimal weight:    0.0170
   overall best weight:    0.4018

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.111732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.094152 restraints weight = 3896.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.88
r_work: 0.2897 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3421  Z= 0.121
  Angle     :  0.533   7.630   4681  Z= 0.259
  Chirality :  0.039   0.205    542
  Planarity :  0.003   0.028    552
  Dihedral  :  5.464  26.405    574
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.58 %
    Favored  : 80.12 %
  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:  1.49 (0.42), residues: 398
  helix:  1.57 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.44 (0.64), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  91 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.022   0.001   PHE A  84 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3421)
  covalent geometry    : angle       0.53310 ( 4681)
  hydrogen bonds       : bond        0.03486 (  215)
  hydrogen bonds       : angle       3.72928 (  645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1276.73 seconds
wall clock time: 22 minutes 41.72 seconds (1361.72 seconds total)