Starting phenix.real_space_refine
on Fri Aug 22 13:01:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jt9_36637/08_2025/8jt9_36637.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    1915      2.51       5
     N     444      2.21       5
     O     485      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 2872
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2843
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 23, 'TRANS': 360}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'UYX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.08, per 1000 atoms: 0.38
  Number of scatterers: 2872
  At special positions: 0
  Unit cell: (54.94, 72.98, 80.36, 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      27     16.00
     F       1      9.00
     O     485      8.00
     N     444      7.00
     C    1915      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: 0.29
  Conformation dependent library (CDL) restraints added in 105.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  692

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      92.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 3.645A  pdb=" N   LEU A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 54
      removed outlier: 3.721A  pdb=" N   TYR A  47 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 157
      Proline residue:  A 147  - end of helix
      removed outlier: 3.909A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 179
    Processing helix  chain 'A' and resid 182 through 211
    Processing helix  chain 'A' and resid 213 through 246
      Proline residue:  A 236  - end of helix
    Processing helix  chain 'A' and resid 249 through 270
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 291 through 323
      removed outlier: 4.008A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      Proline residue:  A 316  - end of helix
    Processing helix  chain 'A' and resid 326 through 334
      removed outlier: 4.085A  pdb=" N   PHE A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
      removed outlier: 4.337A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   HIS A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
    Processing helix  chain 'A' and resid 376 through 378
      No H-bonds generated for 'chain 'A' and resid 376 through 378'
    Processing helix  chain 'A' and resid 380 through 414
      removed outlier: 4.439A  pdb=" N   ALA A 386 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
      Proline residue:  A 387  - end of helix
      Proline residue:  A 404  - end of helix
      removed outlier: 3.726A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 447
      removed outlier: 3.681A  pdb=" N   GLY A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE A 435 " --> pdb=" O   MET A 431 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 4.473A  pdb=" N   GLY A 441 " --> pdb=" O   PRO A 437 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ALA A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.746A  pdb=" N   ARG A 471 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    744 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: 0.50

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 434
        1.28 -     1.42: 750
        1.42 -     1.55: 1711
        1.55 -     1.68: 2
        1.68 -     1.82: 46
  Bond restraints: 2943
  Sorted by residual:
  bond pdb=" C12 UYX A 501 "
       pdb=" N05 UYX A 501 "
    ideal  model  delta    sigma   weight residual
    1.462  1.302  0.160 2.00e-02 2.50e+03 6.39e+01
  bond pdb=" C11 UYX A 501 "
       pdb=" N05 UYX A 501 "
    ideal  model  delta    sigma   weight residual
    1.461  1.304  0.157 2.00e-02 2.50e+03 6.19e+01
  bond pdb=" C13 UYX A 501 "
       pdb=" N05 UYX A 501 "
    ideal  model  delta    sigma   weight residual
    1.455  1.353  0.102 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" C17 UYX A 501 "
       pdb=" C21 UYX A 501 "
    ideal  model  delta    sigma   weight residual
    1.465  1.374  0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C17 UYX A 501 "
       pdb=" N06 UYX A 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.315  0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 2938 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 3913
        2.03 -     4.05: 61
        4.05 -     6.08: 32
        6.08 -     8.10: 1
        8.10 -    10.13: 3
  Bond angle restraints: 4010
  Sorted by residual:
  angle pdb=" CA  LEU A 133 "
        pdb=" CB  LEU A 133 "
        pdb=" CG  LEU A 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.55   -9.25 3.50e+00 8.16e-02 6.98e+00
  angle pdb=" CB  GLU A 321 "
        pdb=" CG  GLU A 321 "
        pdb=" CD  GLU A 321 "
      ideal   model   delta    sigma   weight residual
     112.60  116.97   -4.37 1.70e+00 3.46e-01 6.62e+00
  angle pdb=" C   PRO A 473 "
        pdb=" N   PRO A 474 "
        pdb=" CD  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     125.00  135.13  -10.13 4.10e+00 5.95e-02 6.10e+00
  angle pdb=" N   TYR A 158 "
        pdb=" CA  TYR A 158 "
        pdb=" C   TYR A 158 "
      ideal   model   delta    sigma   weight residual
     109.81  115.06   -5.25 2.21e+00 2.05e-01 5.65e+00
  angle pdb=" CA  GLU A 321 "
        pdb=" CB  GLU A 321 "
        pdb=" CG  GLU A 321 "
      ideal   model   delta    sigma   weight residual
     114.10  118.74   -4.64 2.00e+00 2.50e-01 5.39e+00
  ... (remaining 4005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 1521
       17.98 -    35.96: 157
       35.96 -    53.94: 38
       53.94 -    71.92: 8
       71.92 -    89.90: 3
  Dihedral angle restraints: 1727
    sinusoidal: 641
      harmonic: 1086
  Sorted by residual:
  dihedral pdb=" CA  ASN A 154 "
           pdb=" CB  ASN A 154 "
           pdb=" CG  ASN A 154 "
           pdb=" OD1 ASN A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -168.13  -71.87     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CB  GLU A 216 "
           pdb=" CG  GLU A 216 "
           pdb=" CD  GLU A 216 "
           pdb=" OE1 GLU A 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.77  -88.77     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  TYR A 422 "
           pdb=" C   TYR A 422 "
           pdb=" N   ALA A 423 "
           pdb=" CA  ALA A 423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.25   15.75     0      5.00e+00 4.00e-02 9.92e+00
  ... (remaining 1724 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 276
       0.027 -    0.055: 103
       0.055 -    0.082: 63
       0.082 -    0.109: 27
       0.109 -    0.137: 10
  Chirality restraints: 479
  Sorted by residual:
  chirality pdb=" C08 UYX A 501 "
            pdb=" C09 UYX A 501 "
            pdb=" C10 UYX A 501 "
            pdb=" C14 UYX A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.75    0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  PHE A 348 "
            pdb=" N   PHE A 348 "
            pdb=" C   PHE A 348 "
            pdb=" CB  PHE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  GLU A 312 "
            pdb=" N   GLU A 312 "
            pdb=" C   GLU A 312 "
            pdb=" CB  GLU A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 476 not shown)

  Planarity restraints: 491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 160 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO A 161 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 328 "   -0.012 2.00e-02 2.50e+03   1.02e-02 2.61e+00
        pdb=" CG  TRP A 328 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 328 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 328 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 328 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 328 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 328 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 328 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 328 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 328 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  44 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A  45 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "    0.022 5.00e-02 4.00e+02
  ... (remaining 488 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 639
        2.78 -     3.31: 2920
        3.31 -     3.84: 4988
        3.84 -     4.37: 5610
        4.37 -     4.90: 9984
  Nonbonded interactions: 24141
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" OG  SER A 196 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   MET A 175 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   LEU A  30 "
            pdb=" ND2 ASN A  34 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OH  TYR A  47 "
            pdb=" OH  TYR A 243 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   VAL A 141 "
            pdb=" OG1 THR A 145 "
     model   vdw
     2.410 3.040
  ... (remaining 24136 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:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.290
  Find NCS groups from input model:        0.010
  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:9.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
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      :  0.007   0.160   2943  Z= 0.337
  Angle     :  0.763  10.130   4010  Z= 0.354
  Chirality :  0.043   0.137    479
  Planarity :  0.006   0.045    491
  Dihedral  : 15.908  89.895   1035
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 26.09 %
    Favored  : 73.24 %
  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:  2.28 (0.44), residues: 380
  helix:  1.86 (0.30), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.32 (0.82), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 413 
 TYR   0.017   0.001   TYR A 422 
 PHE   0.018   0.002   PHE A  27 
 TRP   0.028   0.002   TRP A 328 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00691 ( 2943)
  covalent geometry    : angle       0.76331 ( 4010)
  hydrogen bonds       : bond        0.09343 (  251)
  hydrogen bonds       : angle       5.72255 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  206 MET cc_start: 0.8828 (ttt) cc_final: 0.8428 (ttt)
REVERT: A  431 MET cc_start: 0.7735 (mmt) cc_final: 0.7361 (tpt)
REVERT: A  453 MET cc_start: 0.8498 (mmt) cc_final: 0.8151 (mmt)
  outliers start: 2
  outliers final: 2
  residues processed: 54
  average time/residue: 0.5691
  time to fit residues: 31.4950
Evaluate side-chains
  48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0270
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.105022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.089216 restraints weight = 4726.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.16
r_work: 0.2975 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2943  Z= 0.133
  Angle     :  0.666  10.035   4010  Z= 0.310
  Chirality :  0.041   0.118    479
  Planarity :  0.005   0.047    491
  Dihedral  :  5.075  28.852    427
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.08 %
    Favored  : 72.91 %
  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:  2.62 (0.44), residues: 380
  helix:  2.09 (0.30), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.41 (0.81), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 413 
 TYR   0.013   0.001   TYR A 422 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.018   0.002   TRP A 328 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2943)
  covalent geometry    : angle       0.66553 ( 4010)
  hydrogen bonds       : bond        0.04099 (  251)
  hydrogen bonds       : angle       4.64486 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  206 MET cc_start: 0.8776 (ttt) cc_final: 0.8437 (ttt)
REVERT: A  243 TYR cc_start: 0.7987 (t80) cc_final: 0.7784 (t80)
  outliers start: 12
  outliers final: 3
  residues processed: 63
  average time/residue: 0.4795
  time to fit residues: 31.0303
Evaluate side-chains
  58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  420 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.104156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.088273 restraints weight = 4793.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.14
r_work: 0.2967 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2943  Z= 0.132
  Angle     :  0.654   9.956   4010  Z= 0.301
  Chirality :  0.041   0.117    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.905  29.944    426
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.41 %
    Favored  : 72.58 %
  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:  2.77 (0.44), residues: 380
  helix:  2.21 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.54 (0.79), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 413 
 TYR   0.012   0.001   TYR A 243 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.017   0.002   TRP A 328 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2943)
  covalent geometry    : angle       0.65399 ( 4010)
  hydrogen bonds       : bond        0.03893 (  251)
  hydrogen bonds       : angle       4.46532 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  206 MET cc_start: 0.8831 (ttt) cc_final: 0.8481 (ttt)
REVERT: A  243 TYR cc_start: 0.8015 (t80) cc_final: 0.7799 (t80)
  outliers start: 12
  outliers final: 3
  residues processed: 66
  average time/residue: 0.4836
  time to fit residues: 32.8557
Evaluate side-chains
  56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  435 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.103080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.087411 restraints weight = 4784.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.08
r_work: 0.2957 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2943  Z= 0.141
  Angle     :  0.658   9.928   4010  Z= 0.304
  Chirality :  0.042   0.121    479
  Planarity :  0.005   0.051    491
  Dihedral  :  4.855  30.371    426
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.08 %
    Favored  : 73.24 %
  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:  2.78 (0.44), residues: 380
  helix:  2.19 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.28 (0.83), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 413 
 TYR   0.014   0.001   TYR A 422 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.019   0.002   TRP A 328 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2943)
  covalent geometry    : angle       0.65790 ( 4010)
  hydrogen bonds       : bond        0.03979 (  251)
  hydrogen bonds       : angle       4.36062 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  243 TYR cc_start: 0.8027 (t80) cc_final: 0.7813 (t80)
REVERT: A  453 MET cc_start: 0.8656 (mmt) cc_final: 0.8367 (mmt)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 0.4828
  time to fit residues: 32.2512
Evaluate side-chains
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  375 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0020
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.104570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.088916 restraints weight = 4705.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.07
r_work: 0.2981 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2943  Z= 0.128
  Angle     :  0.655   9.995   4010  Z= 0.301
  Chirality :  0.041   0.116    479
  Planarity :  0.005   0.052    491
  Dihedral  :  4.833  30.617    426
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 22.74 %
    Favored  : 72.58 %
  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:  2.78 (0.44), residues: 380
  helix:  2.20 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.39 (0.83), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 413 
 TYR   0.011   0.001   TYR A 243 
 PHE   0.016   0.001   PHE A  27 
 TRP   0.018   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2943)
  covalent geometry    : angle       0.65457 ( 4010)
  hydrogen bonds       : bond        0.03788 (  251)
  hydrogen bonds       : angle       4.31209 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6014 (mm-40)
REVERT: A  243 TYR cc_start: 0.8018 (t80) cc_final: 0.7801 (t80)
REVERT: A  377 PHE cc_start: 0.8765 (m-80) cc_final: 0.8493 (m-10)
REVERT: A  406 MET cc_start: 0.8810 (mmm) cc_final: 0.8210 (mmt)
  outliers start: 14
  outliers final: 6
  residues processed: 70
  average time/residue: 0.3986
  time to fit residues: 28.6925
Evaluate side-chains
  64 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  420 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0770
   overall best weight:    1.7744

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.100696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.084925 restraints weight = 4847.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.15
r_work: 0.2913 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2943  Z= 0.174
  Angle     :  0.692   9.973   4010  Z= 0.324
  Chirality :  0.043   0.130    479
  Planarity :  0.005   0.052    491
  Dihedral  :  4.988  30.539    426
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 21.74 %
    Favored  : 73.24 %
  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:  2.65 (0.44), residues: 380
  helix:  2.10 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.30 (0.85), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 413 
 TYR   0.015   0.001   TYR A 422 
 PHE   0.020   0.001   PHE A  27 
 TRP   0.020   0.002   TRP A 328 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2943)
  covalent geometry    : angle       0.69243 ( 4010)
  hydrogen bonds       : bond        0.04349 (  251)
  hydrogen bonds       : angle       4.51528 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6032 (mm-40)
REVERT: A  243 TYR cc_start: 0.8024 (t80) cc_final: 0.7821 (t80)
REVERT: A  245 PHE cc_start: 0.6575 (m-10) cc_final: 0.5967 (m-80)
REVERT: A  346 ASN cc_start: 0.8692 (m-40) cc_final: 0.8451 (m110)
REVERT: A  453 MET cc_start: 0.8666 (mmt) cc_final: 0.8305 (mmt)
  outliers start: 15
  outliers final: 5
  residues processed: 64
  average time/residue: 0.4663
  time to fit residues: 30.7225
Evaluate side-chains
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  420 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.103328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.087921 restraints weight = 4785.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.08
r_work: 0.2958 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2943  Z= 0.135
  Angle     :  0.664   9.890   4010  Z= 0.307
  Chirality :  0.041   0.124    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.889  31.083    426
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.75 %
    Favored  : 72.58 %
  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:  2.81 (0.44), residues: 380
  helix:  2.22 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.41 (0.83), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 413 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.020   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2943)
  covalent geometry    : angle       0.66380 ( 4010)
  hydrogen bonds       : bond        0.03878 (  251)
  hydrogen bonds       : angle       4.39416 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6021 (mm-40)
REVERT: A  245 PHE cc_start: 0.6603 (m-10) cc_final: 0.5988 (m-80)
REVERT: A  310 MET cc_start: 0.8949 (mmm) cc_final: 0.8612 (mpt)
REVERT: A  346 ASN cc_start: 0.8703 (m-40) cc_final: 0.8473 (m110)
REVERT: A  417 VAL cc_start: 0.8626 (t) cc_final: 0.8400 (m)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 0.4674
  time to fit residues: 31.7140
Evaluate side-chains
  61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  405 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0870
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4936

-------------------------------------------------------------------------------
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 = 0.3325 r_free = 0.3325 target = 0.104734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.089094 restraints weight = 4775.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.10
r_work: 0.2983 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2943  Z= 0.128
  Angle     :  0.674  10.003   4010  Z= 0.309
  Chirality :  0.041   0.126    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.786  31.141    426
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 26.76 %
    Favored  : 71.24 %
  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:  2.84 (0.44), residues: 380
  helix:  2.25 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.46 (0.84), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 413 
 TYR   0.009   0.001   TYR A 243 
 PHE   0.015   0.001   PHE A  27 
 TRP   0.020   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2943)
  covalent geometry    : angle       0.67361 ( 4010)
  hydrogen bonds       : bond        0.03705 (  251)
  hydrogen bonds       : angle       4.32157 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5986 (mm-40)
REVERT: A  155 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7644 (mtp180)
REVERT: A  310 MET cc_start: 0.8964 (mmm) cc_final: 0.8736 (mpt)
REVERT: A  327 LYS cc_start: 0.8470 (mppt) cc_final: 0.8123 (tppt)
REVERT: A  346 ASN cc_start: 0.8665 (m-40) cc_final: 0.8441 (m110)
REVERT: A  406 MET cc_start: 0.8783 (mmm) cc_final: 0.8167 (mmt)
REVERT: A  417 VAL cc_start: 0.8609 (t) cc_final: 0.8344 (m)
  outliers start: 6
  outliers final: 4
  residues processed: 61
  average time/residue: 0.4923
  time to fit residues: 30.8775
Evaluate side-chains
  61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.3320 r_free = 0.3320 target = 0.104554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.089134 restraints weight = 4790.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.09
r_work: 0.2988 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2943  Z= 0.133
  Angle     :  0.691  10.075   4010  Z= 0.315
  Chirality :  0.041   0.131    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.794  31.426    426
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.42 %
    Favored  : 70.90 %
  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:  2.51 (0.44), residues: 380
  helix:  2.09 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.53 (0.81), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 413 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.016   0.001   PHE A  27 
 TRP   0.026   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2943)
  covalent geometry    : angle       0.69095 ( 4010)
  hydrogen bonds       : bond        0.03754 (  251)
  hydrogen bonds       : angle       4.31001 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6011 (mm-40)
REVERT: A  155 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7634 (mtp180)
REVERT: A  245 PHE cc_start: 0.6630 (m-10) cc_final: 0.6020 (m-80)
REVERT: A  327 LYS cc_start: 0.8509 (mppt) cc_final: 0.8216 (tptt)
REVERT: A  379 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7940 (mtmm)
REVERT: A  417 VAL cc_start: 0.8572 (t) cc_final: 0.8329 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 65
  average time/residue: 0.5368
  time to fit residues: 35.9016
Evaluate side-chains
  65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  379 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.089028 restraints weight = 4765.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.08
r_work: 0.2981 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2943  Z= 0.136
  Angle     :  0.700  10.112   4010  Z= 0.317
  Chirality :  0.041   0.138    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.755  31.310    426
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.76 %
    Favored  : 69.90 %
  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:  2.49 (0.44), residues: 380
  helix:  2.08 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.53 (0.82), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 413 
 TYR   0.010   0.001   TYR A 422 
 PHE   0.016   0.001   PHE A  27 
 TRP   0.028   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2943)
  covalent geometry    : angle       0.70002 ( 4010)
  hydrogen bonds       : bond        0.03777 (  251)
  hydrogen bonds       : angle       4.30964 (  744)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6034 (mm-40)
REVERT: A  133 LEU cc_start: 0.8651 (tm) cc_final: 0.8422 (tt)
REVERT: A  155 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7646 (mtp180)
REVERT: A  245 PHE cc_start: 0.6617 (m-10) cc_final: 0.6001 (m-80)
REVERT: A  346 ASN cc_start: 0.8657 (m-40) cc_final: 0.8416 (m110)
REVERT: A  379 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7906 (mtmm)
REVERT: A  417 VAL cc_start: 0.8620 (t) cc_final: 0.8382 (m)
REVERT: A  445 LYS cc_start: 0.8530 (tttm) cc_final: 0.8313 (tppp)
  outliers start: 10
  outliers final: 5
  residues processed: 71
  average time/residue: 0.4836
  time to fit residues: 35.3246
Evaluate side-chains
  65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  379 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.104155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.088403 restraints weight = 4748.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.14
r_work: 0.2975 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2943  Z= 0.142
  Angle     :  0.727  10.127   4010  Z= 0.328
  Chirality :  0.042   0.138    479
  Planarity :  0.005   0.050    491
  Dihedral  :  4.793  31.429    426
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 27.76 %
    Favored  : 69.90 %
  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:  2.50 (0.44), residues: 380
  helix:  2.10 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.61 (0.80), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 413 
 TYR   0.010   0.001   TYR A 422 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.031   0.002   TRP A 328 
 HIS   0.000   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2943)
  covalent geometry    : angle       0.72732 ( 4010)
  hydrogen bonds       : bond        0.03824 (  251)
  hydrogen bonds       : angle       4.28789 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1204.53 seconds
wall clock time: 21 minutes 17.15 seconds (1277.15 seconds total)