Starting phenix.real_space_refine
on Fri Aug 22 15:32:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wqd_37740/08_2025/8wqd_37740.map"
  }
  resolution = 3.55
  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=   0.019
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      29      5.16       5
     C    3166      2.51       5
     N     905      2.21       5
     O     946      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 5046
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 4929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4929
          Classifications: {'peptide': 627}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "G"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 117
          Classifications: {'peptide': 14}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
          Chain breaks: 1
  Time building chain proxies: 1.34, per 1000 atoms: 0.27
  Number of scatterers: 5046
  At special positions: 0
  Unit cell: (104.14, 98.4, 85.28, 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      29     16.00
     O     946      8.00
     N     905      7.00
     C    3166      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: 0.31
  Conformation dependent library (CDL) restraints added in 157.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 1 sheets defined
      66.0% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'D' and resid 1 through 14
      removed outlier: 3.707A  pdb=" N   ALA D   5 " --> pdb=" O   MET D   1 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 24
    Processing helix  chain 'D' and resid 28 through 38
    Processing helix  chain 'D' and resid 48 through 56
    Processing helix  chain 'D' and resid 58 through 68
      removed outlier: 3.857A  pdb=" N   HIS D  68 " --> pdb=" O   LEU D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 99
    Processing helix  chain 'D' and resid 100 through 109
      removed outlier: 3.860A  pdb=" N   LEU D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 132
      removed outlier: 3.598A  pdb=" N   ALA D 127 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 133 through 143
    Processing helix  chain 'D' and resid 156 through 164
    Processing helix  chain 'D' and resid 167 through 175
    Processing helix  chain 'D' and resid 189 through 198
      removed outlier: 4.098A  pdb=" N   PHE D 193 " --> pdb=" O   THR D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 209
    Processing helix  chain 'D' and resid 221 through 229
    Processing helix  chain 'D' and resid 231 through 239
      removed outlier: 3.520A  pdb=" N   VAL D 235 " --> pdb=" O   LYS D 231 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LEU D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LEU D 238 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU D 239 " --> pdb=" O   VAL D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 242
      No H-bonds generated for 'chain 'D' and resid 240 through 242'
    Processing helix  chain 'D' and resid 246 through 262
    Processing helix  chain 'D' and resid 269 through 285
    Processing helix  chain 'D' and resid 299 through 303
    Processing helix  chain 'D' and resid 310 through 315
      removed outlier: 3.502A  pdb=" N   LEU D 314 " --> pdb=" O   ASN D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 337
      removed outlier: 3.616A  pdb=" N   LEU D 324 " --> pdb=" O   ASP D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 344 through 357
    Processing helix  chain 'D' and resid 359 through 378
    Processing helix  chain 'D' and resid 382 through 398
      removed outlier: 3.765A  pdb=" N   LEU D 386 " --> pdb=" O   HIS D 382 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 428
    Processing helix  chain 'D' and resid 432 through 456
    Processing helix  chain 'D' and resid 460 through 478
    Processing helix  chain 'D' and resid 488 through 493
    Processing helix  chain 'D' and resid 501 through 506
    Processing helix  chain 'D' and resid 511 through 520
    Processing helix  chain 'D' and resid 534 through 540
      removed outlier: 3.760A  pdb=" N   ILE D 538 " --> pdb=" O   SER D 534 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ILE D 539 " --> pdb=" O   ALA D 535 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 563
      removed outlier: 3.963A  pdb=" N   ILE D 555 " --> pdb=" O   THR D 551 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER D 558 " --> pdb=" O   SER D 554 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU D 559 " --> pdb=" O   ILE D 555 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL D 560 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 582 through 591
    Processing helix  chain 'D' and resid 596 through 608
      removed outlier: 3.833A  pdb=" N   ASN D 608 " --> pdb=" O   ALA D 604 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 617 through 627
      removed outlier: 4.179A  pdb=" N   GLU D 622 " --> pdb=" O   ARG D 618 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE D 623 " --> pdb=" O   THR D 619 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   HIS D 627 " --> pdb=" O   PHE D 623 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -21 through -17
      removed outlier: 3.622A  pdb=" N   ASP G -18 " --> pdb=" O   HIS G -21 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU G -17 " --> pdb=" O   SER G -20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid -21 through -17'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 40 through 41

    260 hydrogen bonds defined for protein.
    762 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: 0.45

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1721
        1.34 -     1.46: 768
        1.46 -     1.57: 2603
        1.57 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 5133
  Sorted by residual:
  bond pdb=" C   ALA D 404 "
       pdb=" N   PRO D 405 "
    ideal  model  delta    sigma   weight residual
    1.335  1.364 -0.030 1.28e-02 6.10e+03 5.37e+00
  bond pdb=" CB  ILE D 555 "
       pdb=" CG2 ILE D 555 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.29e+00
  bond pdb=" CA  GLU D 307 "
       pdb=" CB  GLU D 307 "
    ideal  model  delta    sigma   weight residual
    1.522  1.541 -0.019 1.86e-02 2.89e+03 1.08e+00
  bond pdb=" CB  PHE D 388 "
       pdb=" CG  PHE D 388 "
    ideal  model  delta    sigma   weight residual
    1.502  1.478  0.024 2.30e-02 1.89e+03 1.07e+00
  bond pdb=" CA  ILE D 616 "
       pdb=" CB  ILE D 616 "
    ideal  model  delta    sigma   weight residual
    1.547  1.536  0.011 1.10e-02 8.26e+03 1.01e+00
  ... (remaining 5128 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 6729
        1.49 -     2.97: 187
        2.97 -     4.46: 23
        4.46 -     5.94: 12
        5.94 -     7.43: 4
  Bond angle restraints: 6955
  Sorted by residual:
  angle pdb=" C   ASN D 289 "
        pdb=" CA  ASN D 289 "
        pdb=" CB  ASN D 289 "
      ideal   model   delta    sigma   weight residual
     116.54  111.16    5.38 1.15e+00 7.56e-01 2.19e+01
  angle pdb=" N   ASP G -18 "
        pdb=" CA  ASP G -18 "
        pdb=" C   ASP G -18 "
      ideal   model   delta    sigma   weight residual
     114.75  109.27    5.48 1.26e+00 6.30e-01 1.89e+01
  angle pdb=" N   THR D 306 "
        pdb=" CA  THR D 306 "
        pdb=" C   THR D 306 "
      ideal   model   delta    sigma   weight residual
     111.55  107.45    4.10 1.37e+00 5.33e-01 8.96e+00
  angle pdb=" CA  ASN D 289 "
        pdb=" C   ASN D 289 "
        pdb=" N   ILE D 290 "
      ideal   model   delta    sigma   weight residual
     119.52  117.24    2.28 7.90e-01 1.60e+00 8.31e+00
  angle pdb=" CA  ASP G -18 "
        pdb=" C   ASP G -18 "
        pdb=" N   LEU G -17 "
      ideal   model   delta    sigma   weight residual
     119.80  116.12    3.68 1.34e+00 5.57e-01 7.53e+00
  ... (remaining 6950 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 2744
       16.80 -    33.60: 292
       33.60 -    50.40: 57
       50.40 -    67.19: 13
       67.19 -    83.99: 4
  Dihedral angle restraints: 3110
    sinusoidal: 1231
      harmonic: 1879
  Sorted by residual:
  dihedral pdb=" CA  ASP D 478 "
           pdb=" CB  ASP D 478 "
           pdb=" CG  ASP D 478 "
           pdb=" OD1 ASP D 478 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.59   55.59     1      2.00e+01 2.50e-03 1.04e+01
  dihedral pdb=" CB  GLU D 586 "
           pdb=" CG  GLU D 586 "
           pdb=" CD  GLU D 586 "
           pdb=" OE1 GLU D 586 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.99  -83.99     1      3.00e+01 1.11e-03 9.55e+00
  dihedral pdb=" CG  ARG D  80 "
           pdb=" CD  ARG D  80 "
           pdb=" NE  ARG D  80 "
           pdb=" CZ  ARG D  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.50   41.50     2      1.50e+01 4.44e-03 9.37e+00
  ... (remaining 3107 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 426
       0.029 -    0.057: 264
       0.057 -    0.086: 81
       0.086 -    0.115: 28
       0.115 -    0.143: 5
  Chirality restraints: 804
  Sorted by residual:
  chirality pdb=" CG  LEU D 238 "
            pdb=" CB  LEU D 238 "
            pdb=" CD1 LEU D 238 "
            pdb=" CD2 LEU D 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE D 616 "
            pdb=" N   ILE D 616 "
            pdb=" C   ILE D 616 "
            pdb=" CB  ILE D 616 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  PRO D 576 "
            pdb=" N   PRO D 576 "
            pdb=" C   PRO D 576 "
            pdb=" CB  PRO D 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 801 not shown)

  Planarity restraints: 902
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 221 "    0.037 5.00e-02 4.00e+02   5.64e-02 5.09e+00
        pdb=" N   PRO D 222 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO D 222 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 222 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 404 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO D 405 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO D 405 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 405 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 123 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO D 124 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 124 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 124 "    0.028 5.00e-02 4.00e+02
  ... (remaining 899 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1233
        2.79 -     3.32: 4988
        3.32 -     3.85: 8291
        3.85 -     4.37: 9423
        4.37 -     4.90: 16449
  Nonbonded interactions: 40384
  Sorted by model distance:
  nonbonded pdb=" O   ASP D  87 "
            pdb=" OG1 THR D 118 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OH  TYR D 449 "
            pdb=" O   PRO D 497 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE2 GLU D   2 "
            pdb=" OH  TYR D  38 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NH2 ARG D 126 "
            pdb=" O   SER G  -2 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OG  SER D  28 "
            pdb=" OD2 ASP D  31 "
     model   vdw
     2.327 3.040
  ... (remaining 40379 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.600
  Find NCS groups from input model:        0.120
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
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      :  0.004   0.039   5133  Z= 0.179
  Angle     :  0.624   7.431   6955  Z= 0.344
  Chirality :  0.041   0.143    804
  Planarity :  0.005   0.056    902
  Dihedral  : 14.561  83.992   1892
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.33), residues: 635
  helix:  0.05 (0.26), residues: 394
  sheet:  None (None), residues: 0
  loop : -1.36 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 283 
 TYR   0.013   0.001   TYR D 440 
 PHE   0.010   0.002   PHE D 388 
 TRP   0.002   0.001   TRP D  93 
 HIS   0.005   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 5133)
  covalent geometry    : angle       0.62409 ( 6955)
  hydrogen bonds       : bond        0.16862 (  260)
  hydrogen bonds       : angle       5.23883 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.202 
Fit side-chains
REVERT: D  135 ASP cc_start: 0.8123 (m-30) cc_final: 0.7669 (m-30)
REVERT: D  172 TYR cc_start: 0.8386 (t80) cc_final: 0.7901 (t80)
REVERT: D  300 HIS cc_start: 0.7876 (t70) cc_final: 0.7500 (t70)
REVERT: D  307 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7453 (tm-30)
REVERT: D  419 GLU cc_start: 0.7940 (tp30) cc_final: 0.7688 (tp30)
REVERT: D  472 TYR cc_start: 0.7457 (t80) cc_final: 0.7171 (t80)
REVERT: D  517 LEU cc_start: 0.8861 (tp) cc_final: 0.8642 (tp)
REVERT: D  622 GLU cc_start: 0.6999 (mp0) cc_final: 0.6734 (mp0)
REVERT: G  -18 ASP cc_start: 0.8083 (t0) cc_final: 0.7827 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0642
  time to fit residues: 8.2822
Evaluate side-chains
  60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.2554

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

Flipped N/Q/H residues before XYZ refinement:
D 262 ASN
D 476 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.145853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.121261 restraints weight = 6818.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.122478 restraints weight = 10206.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.123365 restraints weight = 8359.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.124031 restraints weight = 6167.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.124394 restraints weight = 5429.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5133  Z= 0.104
  Angle     :  0.486   5.374   6955  Z= 0.260
  Chirality :  0.037   0.131    804
  Planarity :  0.004   0.050    902
  Dihedral  :  3.992  27.143    698
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.29 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.35), residues: 635
  helix:  0.67 (0.26), residues: 413
  sheet:  None (None), residues: 0
  loop : -1.26 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 126 
 TYR   0.020   0.001   TYR D 472 
 PHE   0.007   0.001   PHE D 101 
 TRP   0.004   0.001   TRP D  93 
 HIS   0.003   0.001   HIS D 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5133)
  covalent geometry    : angle       0.48562 ( 6955)
  hydrogen bonds       : bond        0.03541 (  260)
  hydrogen bonds       : angle       3.89465 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8282 (t80) cc_final: 0.7784 (t80)
REVERT: D  280 MET cc_start: 0.7584 (tmm) cc_final: 0.6872 (tmt)
REVERT: D  419 GLU cc_start: 0.7894 (tp30) cc_final: 0.7662 (tp30)
REVERT: D  472 TYR cc_start: 0.7209 (t80) cc_final: 0.6959 (t80)
REVERT: D  517 LEU cc_start: 0.8918 (tp) cc_final: 0.8716 (tp)
REVERT: D  622 GLU cc_start: 0.7053 (mp0) cc_final: 0.6788 (mp0)
REVERT: G  -18 ASP cc_start: 0.8531 (t0) cc_final: 0.8161 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0650
  time to fit residues: 6.9274
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  218 HIS
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  455 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0970
   chunk 60 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
D 262 ASN
D 504 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.154117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.132058 restraints weight = 6685.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.132323 restraints weight = 9228.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.133066 restraints weight = 8112.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.133715 restraints weight = 6049.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.133926 restraints weight = 5780.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5133  Z= 0.116
  Angle     :  0.473   5.759   6955  Z= 0.251
  Chirality :  0.037   0.131    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.872  25.031    698
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.75 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.35), residues: 635
  helix:  0.96 (0.27), residues: 413
  sheet:  None (None), residues: 0
  loop : -1.31 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 283 
 TYR   0.018   0.001   TYR D 472 
 PHE   0.008   0.001   PHE D 388 
 TRP   0.003   0.001   TRP D  93 
 HIS   0.003   0.001   HIS D 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5133)
  covalent geometry    : angle       0.47281 ( 6955)
  hydrogen bonds       : bond        0.03234 (  260)
  hydrogen bonds       : angle       3.76089 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8289 (t80) cc_final: 0.7660 (t80)
REVERT: D  472 TYR cc_start: 0.7227 (t80) cc_final: 0.6820 (t80)
REVERT: G  -18 ASP cc_start: 0.8573 (t0) cc_final: 0.8192 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 71
  average time/residue: 0.0659
  time to fit residues: 6.3249
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  262 ASN
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0470
   chunk 60 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** D  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 262 ASN
D 504 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.153442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.131934 restraints weight = 6645.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131752 restraints weight = 9269.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.132485 restraints weight = 8474.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.133533 restraints weight = 6090.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.133772 restraints weight = 5392.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5133  Z= 0.122
  Angle     :  0.474   6.043   6955  Z= 0.252
  Chirality :  0.037   0.129    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.838  25.092    698
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.93 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.35), residues: 635
  helix:  1.09 (0.27), residues: 413
  sheet:  None (None), residues: 0
  loop : -1.30 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 283 
 TYR   0.016   0.001   TYR D 472 
 PHE   0.008   0.001   PHE D 388 
 TRP   0.003   0.001   TRP D  93 
 HIS   0.002   0.001   HIS D 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5133)
  covalent geometry    : angle       0.47369 ( 6955)
  hydrogen bonds       : bond        0.03119 (  260)
  hydrogen bonds       : angle       3.71888 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8287 (t80) cc_final: 0.7659 (t80)
REVERT: D  472 TYR cc_start: 0.7257 (t80) cc_final: 0.6846 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0637
  time to fit residues: 6.4707
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  218 HIS
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  262 ASN
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0060
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
D  45 GLN
D 262 ASN
D 504 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.142132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.117557 restraints weight = 6891.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117385 restraints weight = 9386.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.118806 restraints weight = 7899.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.119586 restraints weight = 5925.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119918 restraints weight = 5762.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5133  Z= 0.129
  Angle     :  0.482   6.591   6955  Z= 0.255
  Chirality :  0.038   0.130    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.802  22.675    698
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.30 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.35), residues: 635
  helix:  1.15 (0.27), residues: 413
  sheet:  None (None), residues: 0
  loop : -1.29 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 283 
 TYR   0.015   0.001   TYR D 472 
 PHE   0.008   0.001   PHE D 101 
 TRP   0.003   0.001   TRP D  93 
 HIS   0.002   0.001   HIS D 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5133)
  covalent geometry    : angle       0.48181 ( 6955)
  hydrogen bonds       : bond        0.03115 (  260)
  hydrogen bonds       : angle       3.70377 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8327 (t80) cc_final: 0.7717 (t80)
REVERT: D  280 MET cc_start: 0.7668 (tmm) cc_final: 0.6946 (tmm)
REVERT: D  472 TYR cc_start: 0.7300 (t80) cc_final: 0.6839 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0612
  time to fit residues: 5.6045
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  262 ASN
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Chi-restraints excluded: chain G residue   -3 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0010
   chunk 60 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4186

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.142595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.117983 restraints weight = 6935.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119487 restraints weight = 10602.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121342 restraints weight = 7237.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.121255 restraints weight = 6104.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.122526 restraints weight = 4998.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5133  Z= 0.115
  Angle     :  0.472   6.564   6955  Z= 0.250
  Chirality :  0.037   0.131    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.732  20.497    698
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.48 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.35), residues: 635
  helix:  1.18 (0.27), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.26 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 283 
 TYR   0.014   0.001   TYR D 472 
 PHE   0.010   0.001   PHE D 447 
 TRP   0.004   0.001   TRP D  93 
 HIS   0.002   0.000   HIS D 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5133)
  covalent geometry    : angle       0.47226 ( 6955)
  hydrogen bonds       : bond        0.03015 (  260)
  hydrogen bonds       : angle       3.65726 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8322 (t80) cc_final: 0.7744 (t80)
REVERT: D  280 MET cc_start: 0.7587 (tmm) cc_final: 0.6858 (tmm)
REVERT: D  368 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8243 (mp)
REVERT: D  472 TYR cc_start: 0.7279 (t80) cc_final: 0.6766 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0605
  time to fit residues: 5.7687
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  218 HIS
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  475 ILE
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:    0.0670
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 17 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0470
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.143180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.118549 restraints weight = 6771.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.118991 restraints weight = 9653.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.119883 restraints weight = 8935.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121186 restraints weight = 6388.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.121432 restraints weight = 5857.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5133  Z= 0.109
  Angle     :  0.474   6.658   6955  Z= 0.250
  Chirality :  0.037   0.140    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.670  18.528    698
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.58 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.35), residues: 635
  helix:  1.14 (0.27), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.26 (0.44), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 283 
 TYR   0.014   0.001   TYR D 472 
 PHE   0.020   0.001   PHE D 101 
 TRP   0.003   0.000   TRP D  93 
 HIS   0.002   0.000   HIS D 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5133)
  covalent geometry    : angle       0.47399 ( 6955)
  hydrogen bonds       : bond        0.02969 (  260)
  hydrogen bonds       : angle       3.61046 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8324 (t80) cc_final: 0.7752 (t80)
REVERT: D  280 MET cc_start: 0.7714 (tmm) cc_final: 0.7034 (tmt)
REVERT: D  368 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0694
  time to fit residues: 6.7978
Evaluate side-chains
  63 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 181 ASN
D 504 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.140172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.116031 restraints weight = 6963.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.115519 restraints weight = 10692.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.117431 restraints weight = 8308.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.117838 restraints weight = 5901.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.118736 restraints weight = 5448.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5133  Z= 0.164
  Angle     :  0.531   7.903   6955  Z= 0.277
  Chirality :  0.039   0.155    804
  Planarity :  0.004   0.049    902
  Dihedral  :  3.850  18.838    698
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.85 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.35), residues: 635
  helix:  1.08 (0.27), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.28 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  46 
 TYR   0.015   0.001   TYR D 472 
 PHE   0.020   0.001   PHE D 101 
 TRP   0.004   0.001   TRP D  93 
 HIS   0.003   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5133)
  covalent geometry    : angle       0.53059 ( 6955)
  hydrogen bonds       : bond        0.03246 (  260)
  hydrogen bonds       : angle       3.73230 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8428 (t80) cc_final: 0.7856 (t80)
REVERT: D  280 MET cc_start: 0.7704 (tmm) cc_final: 0.6999 (tmt)
REVERT: D  368 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8280 (mp)
REVERT: D  472 TYR cc_start: 0.7297 (t80) cc_final: 0.6943 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0517
  time to fit residues: 4.6129
Evaluate side-chains
  63 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  218 HIS
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0370
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   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 = 0.3568 r_free = 0.3568 target = 0.141841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.117104 restraints weight = 6863.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117676 restraints weight = 9598.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119099 restraints weight = 7961.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.119604 restraints weight = 6057.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.119973 restraints weight = 5649.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5133  Z= 0.124
  Angle     :  0.503   7.621   6955  Z= 0.262
  Chirality :  0.038   0.131    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.728  16.630    698
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.40 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.35), residues: 635
  helix:  1.07 (0.27), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.32 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  46 
 TYR   0.017   0.001   TYR D 472 
 PHE   0.023   0.001   PHE D 101 
 TRP   0.004   0.001   TRP D  93 
 HIS   0.003   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5133)
  covalent geometry    : angle       0.50291 ( 6955)
  hydrogen bonds       : bond        0.03049 (  260)
  hydrogen bonds       : angle       3.63910 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8365 (t80) cc_final: 0.7808 (t80)
REVERT: D  280 MET cc_start: 0.7832 (tmm) cc_final: 0.7058 (tmt)
REVERT: D  368 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (mp)
REVERT: D  472 TYR cc_start: 0.7211 (t80) cc_final: 0.6790 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0586
  time to fit residues: 4.9991
Evaluate side-chains
  63 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  475 ILE
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D 504 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.116389 restraints weight = 6885.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.116772 restraints weight = 9724.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117541 restraints weight = 9203.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119342 restraints weight = 6518.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119449 restraints weight = 5912.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5133  Z= 0.136
  Angle     :  0.512   7.779   6955  Z= 0.267
  Chirality :  0.038   0.135    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.778  20.084    698
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.58 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.35), residues: 635
  helix:  1.12 (0.27), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.35 (0.43), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  46 
 TYR   0.016   0.001   TYR D 472 
 PHE   0.024   0.001   PHE D 101 
 TRP   0.003   0.001   TRP D  93 
 HIS   0.003   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5133)
  covalent geometry    : angle       0.51153 ( 6955)
  hydrogen bonds       : bond        0.03112 (  260)
  hydrogen bonds       : angle       3.65988 (  762)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: D  172 TYR cc_start: 0.8374 (t80) cc_final: 0.7790 (t80)
REVERT: D  280 MET cc_start: 0.7822 (tmm) cc_final: 0.7057 (tmt)
REVERT: D  368 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8286 (mp)
REVERT: D  472 TYR cc_start: 0.7233 (t80) cc_final: 0.6808 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0609
  time to fit residues: 5.3054
Evaluate side-chains
  64 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  230 CYS
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  475 ILE
Chi-restraints excluded: chain D residue  551 THR
Chi-restraints excluded: chain D residue  561 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0170
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
D 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.141403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.116744 restraints weight = 6962.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.118702 restraints weight = 10893.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.120062 restraints weight = 7267.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.120229 restraints weight = 6000.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.121145 restraints weight = 4970.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5133  Z= 0.130
  Angle     :  0.510   7.636   6955  Z= 0.265
  Chirality :  0.038   0.135    804
  Planarity :  0.004   0.047    902
  Dihedral  :  3.771  19.271    698
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.58 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.35), residues: 635
  helix:  1.12 (0.27), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.35 (0.43), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 544 
 TYR   0.016   0.001   TYR D 472 
 PHE   0.024   0.001   PHE D 101 
 TRP   0.003   0.000   TRP D  93 
 HIS   0.003   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5133)
  covalent geometry    : angle       0.51048 ( 6955)
  hydrogen bonds       : bond        0.03086 (  260)
  hydrogen bonds       : angle       3.64062 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1128.08 seconds
wall clock time: 20 minutes 9.13 seconds (1209.13 seconds total)