Starting phenix.real_space_refine
on Fri Aug 22 13:52:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sc6_40339/08_2025/8sc6_40339.cif"
  }
  resolution = 3.13
  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=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    2293      2.51       5
     N     565      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3479
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3461
          Classifications: {'peptide': 447}
          Link IDs: {'PTRANS': 22, 'TRANS': 424}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'VIB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.20, per 1000 atoms: 0.34
  Number of scatterers: 3479
  At special positions: 0
  Unit cell: (90.72, 84, 68.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O     590      8.00
     N     565      7.00
     C    2293      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " 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: 0.26
  Conformation dependent library (CDL) restraints added in 93.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  818

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      80.5% alpha, 1.3% 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 19 through 31
      removed outlier: 3.959A  pdb=" N   LEU A  23 " --> pdb=" O   LYS A  19 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.727A  pdb=" N   CYS A  36 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 63
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 147
      removed outlier: 4.520A  pdb=" N   TRP A 146 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 173
      removed outlier: 4.333A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 194
      removed outlier: 3.820A  pdb=" N   ALA A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 3.738A  pdb=" N   VAL A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 258
      removed outlier: 3.612A  pdb=" N   GLN A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 278
      Proline residue:  A 271  - end of helix
      removed outlier: 3.515A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A 276 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 3.504A  pdb=" N   PHE A 338 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 372
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 3.508A  pdb=" N   VAL A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 398
      removed outlier: 4.072A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 420
      removed outlier: 3.542A  pdb=" N   MET A 406 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 3.738A  pdb=" N   ILE A 433 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 491
      removed outlier: 3.788A  pdb=" N   LEU A 472 " --> pdb=" O   VAL A 468 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   CYS A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
      removed outlier: 3.533A  pdb=" N   LEU A 487 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ARG A 488 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 511
      removed outlier: 4.019A  pdb=" N   LEU A 511 " --> pdb=" O   ALA A 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    241 hydrogen bonds defined for protein.
    696 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: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1071
        1.34 -     1.46: 838
        1.46 -     1.58: 1616
        1.58 -     1.69: 1
        1.69 -     1.81: 46
  Bond restraints: 3572
  Sorted by residual:
  bond pdb=" CA  LEU A 427 "
       pdb=" C   LEU A 427 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.14e-02 7.69e+03 5.00e-01
  bond pdb=" N   VAL A  74 "
       pdb=" CA  VAL A  74 "
    ideal  model  delta    sigma   weight residual
    1.468  1.461  0.007 1.05e-02 9.07e+03 4.84e-01
  bond pdb=" CA  THR A 480 "
       pdb=" C   THR A 480 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.008 1.23e-02 6.61e+03 4.75e-01
  bond pdb=" C   ALA A 257 "
       pdb=" N   LEU A 258 "
    ideal  model  delta    sigma   weight residual
    1.327  1.336 -0.009 1.32e-02 5.74e+03 4.45e-01
  bond pdb=" C   VAL A 461 "
       pdb=" O   VAL A 461 "
    ideal  model  delta    sigma   weight residual
    1.226  1.240 -0.013 2.04e-02 2.40e+03 4.30e-01
  ... (remaining 3567 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4682
        1.06 -     2.12: 147
        2.12 -     3.17: 27
        3.17 -     4.23: 7
        4.23 -     5.29: 7
  Bond angle restraints: 4870
  Sorted by residual:
  angle pdb=" C   GLU A 386 "
        pdb=" N   ILE A 387 "
        pdb=" CA  ILE A 387 "
      ideal   model   delta    sigma   weight residual
     120.33  122.81   -2.48 8.00e-01 1.56e+00 9.59e+00
  angle pdb=" C   TYR A  72 "
        pdb=" N   THR A  73 "
        pdb=" CA  THR A  73 "
      ideal   model   delta    sigma   weight residual
     122.46  117.60    4.86 1.80e+00 3.09e-01 7.30e+00
  angle pdb=" CA  CYS A  50 "
        pdb=" CB  CYS A  50 "
        pdb=" SG  CYS A  50 "
      ideal   model   delta    sigma   weight residual
     114.40  119.23   -4.83 2.30e+00 1.89e-01 4.40e+00
  angle pdb=" N   THR A 480 "
        pdb=" CA  THR A 480 "
        pdb=" C   THR A 480 "
      ideal   model   delta    sigma   weight residual
     112.75  115.58   -2.83 1.36e+00 5.41e-01 4.34e+00
  angle pdb=" C   VAL A 461 "
        pdb=" CA  VAL A 461 "
        pdb=" CB  VAL A 461 "
      ideal   model   delta    sigma   weight residual
     112.36  109.75    2.61 1.37e+00 5.33e-01 3.62e+00
  ... (remaining 4865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.01: 1882
       11.01 -    22.02: 141
       22.02 -    33.03: 34
       33.03 -    44.04: 9
       44.04 -    55.05: 1
  Dihedral angle restraints: 2067
    sinusoidal: 788
      harmonic: 1279
  Sorted by residual:
  dihedral pdb=" N   PHE A 273 "
           pdb=" CA  PHE A 273 "
           pdb=" CB  PHE A 273 "
           pdb=" CG  PHE A 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.05   55.05     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" N   LEU A 150 "
           pdb=" CA  LEU A 150 "
           pdb=" CB  LEU A 150 "
           pdb=" CG  LEU A 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -102.93   42.93     3      1.50e+01 4.44e-03 7.71e+00
  dihedral pdb=" N   MET A 239 "
           pdb=" CA  MET A 239 "
           pdb=" CB  MET A 239 "
           pdb=" CG  MET A 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.24  -38.76     3      1.50e+01 4.44e-03 6.84e+00
  ... (remaining 2064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 313
       0.022 -    0.043: 148
       0.043 -    0.065: 63
       0.065 -    0.087: 18
       0.087 -    0.109: 20
  Chirality restraints: 562
  Sorted by residual:
  chirality pdb=" CA  THR A 480 "
            pdb=" N   THR A 480 "
            pdb=" C   THR A 480 "
            pdb=" CB  THR A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.42    0.11 2.00e-01 2.50e+01 2.95e-01
  chirality pdb=" CA  LEU A 270 "
            pdb=" N   LEU A 270 "
            pdb=" C   LEU A 270 "
            pdb=" CB  LEU A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.88e-01
  chirality pdb=" CA  PRO A  53 "
            pdb=" N   PRO A  53 "
            pdb=" C   PRO A  53 "
            pdb=" CB  PRO A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.84e-01
  ... (remaining 559 not shown)

  Planarity restraints: 601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.52e+00
        pdb=" N   PRO A 271 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  74 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.35e+00
        pdb=" N   PRO A  75 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  75 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  75 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  65 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO A  66 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.016 5.00e-02 4.00e+02
  ... (remaining 598 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 868
        2.80 -     3.32: 3411
        3.32 -     3.85: 5504
        3.85 -     4.37: 6251
        4.37 -     4.90: 11184
  Nonbonded interactions: 27218
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 147 "
            pdb=" OH  TYR A 199 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OE1 GLU A 137 "
            pdb=" NE1 TRP A 261 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NZ  LYS A 214 "
            pdb=" OD1 ASP A 474 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   GLN A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.363 3.040
  ... (remaining 27213 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.630
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:    8.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3575  Z= 0.124
  Angle     :  0.505   5.291   4876  Z= 0.289
  Chirality :  0.035   0.109    562
  Planarity :  0.004   0.031    601
  Dihedral  :  8.707  55.052   1240
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  2.96 %
    Favored  : 96.23 %
  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:  2.80 (0.41), residues: 443
  helix:  2.09 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop :  1.57 (0.57), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 234 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3572)
  covalent geometry    : angle       0.50190 ( 4870)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       1.60395 (    6)
  hydrogen bonds       : bond        0.15680 (  241)
  hydrogen bonds       : angle       5.43125 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7672 (m-80)
REVERT: A  351 MET cc_start: 0.8709 (mtt) cc_final: 0.8385 (mtp)
REVERT: A  357 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0796
  time to fit residues: 6.4613
Evaluate side-chains
  41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
A 447 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.195548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.137095 restraints weight = 3584.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.55
r_work: 0.3211 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3575  Z= 0.115
  Angle     :  0.474   6.408   4876  Z= 0.244
  Chirality :  0.036   0.133    562
  Planarity :  0.004   0.034    601
  Dihedral  :  4.661  53.261    487
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.63 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.42), residues: 443
  helix:  2.45 (0.31), residues: 304
  sheet:  None (None), residues: 0
  loop :  1.38 (0.58), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.009   0.001   PHE A 355 
 TRP   0.009   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3572)
  covalent geometry    : angle       0.47275 ( 4870)
  SS BOND              : bond        0.00076 (    3)
  SS BOND              : angle       1.13698 (    6)
  hydrogen bonds       : bond        0.04366 (  241)
  hydrogen bonds       : angle       4.27319 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  273 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7541 (m-80)
REVERT: A  357 ASP cc_start: 0.7689 (m-30) cc_final: 0.7488 (m-30)
REVERT: A  395 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6482 (mm)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0682
  time to fit residues: 4.1554
Evaluate side-chains
  51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0170
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.195696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.137312 restraints weight = 3535.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.14
r_work: 0.3126 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3575  Z= 0.109
  Angle     :  0.444   4.810   4876  Z= 0.229
  Chirality :  0.036   0.127    562
  Planarity :  0.004   0.030    601
  Dihedral  :  4.562  54.321    487
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.89 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.13 (0.41), residues: 443
  helix:  2.48 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop :  1.29 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.009   0.001   PHE A 355 
 TRP   0.010   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3572)
  covalent geometry    : angle       0.44243 ( 4870)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       1.15548 (    6)
  hydrogen bonds       : bond        0.03894 (  241)
  hydrogen bonds       : angle       4.04032 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7430 (mmt) cc_final: 0.7183 (mmp)
REVERT: A  273 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7318 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0658
  time to fit residues: 4.4456
Evaluate side-chains
  50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 27 optimal weight:    0.6980
   chunk 14 optimal weight:    0.1980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.195422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.136931 restraints weight = 3525.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.13
r_work: 0.3107 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3575  Z= 0.108
  Angle     :  0.441   5.003   4876  Z= 0.227
  Chirality :  0.036   0.128    562
  Planarity :  0.004   0.030    601
  Dihedral  :  4.549  55.371    487
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.24 %
    Favored  : 87.60 %
  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:  3.14 (0.41), residues: 443
  helix:  2.48 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop :  1.33 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.009   0.001   PHE A 355 
 TRP   0.010   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3572)
  covalent geometry    : angle       0.43928 ( 4870)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       1.08495 (    6)
  hydrogen bonds       : bond        0.03808 (  241)
  hydrogen bonds       : angle       4.01138 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  200 MET cc_start: 0.7459 (mmt) cc_final: 0.7257 (mmp)
REVERT: A  273 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7301 (m-80)
REVERT: A  357 ASP cc_start: 0.7790 (m-30) cc_final: 0.7546 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 50
  average time/residue: 0.0699
  time to fit residues: 4.4271
Evaluate side-chains
  48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   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 = 0.4100 r_free = 0.4100 target = 0.194383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135770 restraints weight = 3554.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.12
r_work: 0.3105 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3575  Z= 0.123
  Angle     :  0.456   5.087   4876  Z= 0.236
  Chirality :  0.036   0.128    562
  Planarity :  0.004   0.028    601
  Dihedral  :  4.592  57.412    487
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.78 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.03 (0.41), residues: 443
  helix:  2.42 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop :  1.22 (0.57), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.010   0.001   PHE A 355 
 TRP   0.011   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3572)
  covalent geometry    : angle       0.45426 ( 4870)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       1.12260 (    6)
  hydrogen bonds       : bond        0.04053 (  241)
  hydrogen bonds       : angle       4.06382 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6411 (tt)
REVERT: A  273 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7313 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 48
  average time/residue: 0.0712
  time to fit residues: 4.3192
Evaluate side-chains
  49 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   chunk 10 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.196085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137842 restraints weight = 3539.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.09
r_work: 0.3134 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3575  Z= 0.100
  Angle     :  0.428   5.034   4876  Z= 0.220
  Chirality :  0.035   0.129    562
  Planarity :  0.004   0.028    601
  Dihedral  :  4.520  57.517    487
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.59 %
    Favored  : 86.25 %
  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:  3.08 (0.41), residues: 443
  helix:  2.39 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop :  1.37 (0.58), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.008   0.001   PHE A 355 
 TRP   0.008   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 3572)
  covalent geometry    : angle       0.42735 ( 4870)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.91806 (    6)
  hydrogen bonds       : bond        0.03583 (  241)
  hydrogen bonds       : angle       3.94355 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6450 (tt)
REVERT: A   73 THR cc_start: 0.7895 (m) cc_final: 0.7590 (m)
REVERT: A  273 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7238 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0629
  time to fit residues: 4.2610
Evaluate side-chains
  54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.195155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136756 restraints weight = 3564.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.12
r_work: 0.3114 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3575  Z= 0.111
  Angle     :  0.445   5.345   4876  Z= 0.228
  Chirality :  0.036   0.128    562
  Planarity :  0.004   0.027    601
  Dihedral  :  4.542  58.362    487
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.59 %
    Favored  : 85.98 %
  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:  3.12 (0.41), residues: 443
  helix:  2.53 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop :  1.15 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.009   0.001   PHE A 355 
 TRP   0.010   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3572)
  covalent geometry    : angle       0.44354 ( 4870)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       0.98490 (    6)
  hydrogen bonds       : bond        0.03771 (  241)
  hydrogen bonds       : angle       3.97638 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6417 (tt)
REVERT: A   73 THR cc_start: 0.7870 (m) cc_final: 0.7579 (m)
REVERT: A  273 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7236 (m-80)
REVERT: A  357 ASP cc_start: 0.7771 (m-30) cc_final: 0.7438 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0625
  time to fit residues: 4.1339
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0870
   chunk 10 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.195544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136916 restraints weight = 3634.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.16
r_work: 0.3127 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3575  Z= 0.106
  Angle     :  0.437   5.094   4876  Z= 0.225
  Chirality :  0.035   0.128    562
  Planarity :  0.004   0.027    601
  Dihedral  :  4.549  59.452    487
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.86 %
    Favored  : 85.98 %
  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:  3.19 (0.41), residues: 443
  helix:  2.59 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop :  1.14 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.008   0.001   PHE A 355 
 TRP   0.009   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3572)
  covalent geometry    : angle       0.43631 ( 4870)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.97008 (    6)
  hydrogen bonds       : bond        0.03656 (  241)
  hydrogen bonds       : angle       3.95125 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   73 THR cc_start: 0.7887 (m) cc_final: 0.7591 (m)
REVERT: A  273 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7142 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0688
  time to fit residues: 4.2543
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.193895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135355 restraints weight = 3501.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.14
r_work: 0.3113 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3575  Z= 0.127
  Angle     :  0.461   5.115   4876  Z= 0.237
  Chirality :  0.036   0.128    562
  Planarity :  0.004   0.028    601
  Dihedral  :  4.594  59.256    487
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.59 %
    Favored  : 86.25 %
  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:  3.04 (0.41), residues: 443
  helix:  2.50 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop :  1.03 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.010   0.001   PHE A 355 
 TRP   0.011   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3572)
  covalent geometry    : angle       0.45963 ( 4870)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       1.06680 (    6)
  hydrogen bonds       : bond        0.04016 (  241)
  hydrogen bonds       : angle       4.03778 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  273 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7266 (m-80)
REVERT: A  357 ASP cc_start: 0.7884 (m-30) cc_final: 0.7675 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0583
  time to fit residues: 3.7845
Evaluate side-chains
  50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0980
   chunk 43 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0370
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.195230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136561 restraints weight = 3608.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.15
r_work: 0.3122 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3575  Z= 0.101
  Angle     :  0.433   5.134   4876  Z= 0.223
  Chirality :  0.035   0.128    562
  Planarity :  0.004   0.027    601
  Dihedral  :  4.529  59.104    487
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.32 %
    Favored  : 86.25 %
  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:  3.19 (0.41), residues: 443
  helix:  2.60 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop :  1.12 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.008   0.001   PHE A 355 
 TRP   0.009   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3572)
  covalent geometry    : angle       0.43211 ( 4870)
  SS BOND              : bond        0.00239 (    3)
  SS BOND              : angle       0.95405 (    6)
  hydrogen bonds       : bond        0.03588 (  241)
  hydrogen bonds       : angle       3.93482 (  696)

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

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

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  886 Ramachandran restraints generated.
    443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   73 THR cc_start: 0.7845 (m) cc_final: 0.7554 (m)
REVERT: A  273 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7076 (m-80)
REVERT: A  408 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6130 (mtt)
  outliers start: 9
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0740
  time to fit residues: 4.6198
Evaluate side-chains
  54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  273 PHE
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   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 = 0.4102 r_free = 0.4102 target = 0.194595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.136112 restraints weight = 3530.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.11
r_work: 0.3108 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3575  Z= 0.121
  Angle     :  0.454   5.066   4876  Z= 0.234
  Chirality :  0.036   0.128    562
  Planarity :  0.004   0.028    601
  Dihedral  :  4.539  57.987    487
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 11.05 %
    Favored  : 86.25 %
  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:  3.09 (0.41), residues: 443
  helix:  2.53 (0.30), residues: 305
  sheet:  None (None), residues: 0
  loop :  1.06 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.010   0.001   PHE A 355 
 TRP   0.011   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3572)
  covalent geometry    : angle       0.45266 ( 4870)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.06649 (    6)
  hydrogen bonds       : bond        0.03928 (  241)
  hydrogen bonds       : angle       4.00924 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1233.87 seconds
wall clock time: 21 minutes 47.00 seconds (1307.00 seconds total)