Starting phenix.real_space_refine
on Fri Aug 22 14:10:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzs_41768/08_2025/8tzs_41768.cif"
  }
  resolution = 3.84
  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=   0.012
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      36      5.16       5
     C    2594      2.51       5
     N     637      2.21       5
     O     647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 3914
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3914
          Classifications: {'peptide': 480}
          Link IDs: {'PTRANS': 20, 'TRANS': 459}
          Chain breaks: 2
  Time building chain proxies: 1.17, per 1000 atoms: 0.30
  Number of scatterers: 3914
  At special positions: 0
  Unit cell: (86.346, 103.32, 78.228, 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      36     16.00
     O     647      8.00
     N     637      7.00
     C    2594      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 179 " distance=2.04

  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: 0.38
  Conformation dependent library (CDL) restraints added in 163.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  902

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 2 sheets defined
      54.4% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
    Processing helix  chain 'A' and resid 10 through 36
      removed outlier: 3.868A  pdb=" N   ILE A  16 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 4.043A  pdb=" N   GLN A 125 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 173
    Processing helix  chain 'A' and resid 227 through 258
      removed outlier: 3.588A  pdb=" N   LYS A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      Proline residue:  A 243  - end of helix
    Processing helix  chain 'A' and resid 264 through 282
      removed outlier: 3.630A  pdb=" N   PHE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 286 through 291
      removed outlier: 4.112A  pdb=" N   GLY A 290 " --> pdb=" O   TRP A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 322
      removed outlier: 3.708A  pdb=" N   ASP A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 334
    Processing helix  chain 'A' and resid 335 through 360
      Proline residue:  A 341  - end of helix
      removed outlier: 3.753A  pdb=" N   VAL A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   PHE A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 351 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   PHE A 352 " --> pdb=" O   CYS A 348 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   ASP A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 413
      removed outlier: 3.611A  pdb=" N   SER A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   GLY A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LYS A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 456
    Processing helix  chain 'A' and resid 473 through 493
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46
      removed outlier: 5.976A  pdb=" N   ILE A 216 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ALA A 119 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   MET A 110 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLU A 186 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   PHE A 112 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.991A  pdb=" N   MET A 134 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ARG A 155 " --> pdb=" O   MET A 134 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A 136 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   HIS A 153 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A 138 " --> pdb=" O   MET A 151 " (cutoff:3.500A)

    219 hydrogen bonds defined for protein.
    633 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: 0.56

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1185
        1.35 -     1.46: 1036
        1.46 -     1.58: 1747
        1.58 -     1.70: 2
        1.70 -     1.81: 60
  Bond restraints: 4030
  Sorted by residual:
  bond pdb=" CB  PRO A 263 "
       pdb=" CG  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.492  1.667 -0.175 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" CG  PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.503  1.390  0.113 3.40e-02 8.65e+02 1.10e+01
  bond pdb=" N   PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.473  1.514 -0.041 1.40e-02 5.10e+03 8.64e+00
  bond pdb=" N   PRO A 263 "
       pdb=" CA  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.465  1.444  0.020 1.11e-02 8.12e+03 3.36e+00
  bond pdb=" CB  PRO A 170 "
       pdb=" CG  PRO A 170 "
    ideal  model  delta    sigma   weight residual
    1.492  1.580 -0.088 5.00e-02 4.00e+02 3.08e+00
  ... (remaining 4025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 5404
        3.21 -     6.41: 40
        6.41 -     9.62: 7
        9.62 -    12.82: 4
       12.82 -    16.03: 2
  Bond angle restraints: 5457
  Sorted by residual:
  angle pdb=" CA  PRO A 263 "
        pdb=" N   PRO A 263 "
        pdb=" CD  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     112.00   95.97   16.03 1.40e+00 5.10e-01 1.31e+02
  angle pdb=" N   PRO A 263 "
        pdb=" CD  PRO A 263 "
        pdb=" CG  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     103.20   93.36    9.84 1.50e+00 4.44e-01 4.30e+01
  angle pdb=" CA  PRO A 170 "
        pdb=" N   PRO A 170 "
        pdb=" CD  PRO A 170 "
      ideal   model   delta    sigma   weight residual
     112.00  105.41    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" CA  LEU A 440 "
        pdb=" CB  LEU A 440 "
        pdb=" CG  LEU A 440 "
      ideal   model   delta    sigma   weight residual
     116.30  131.82  -15.52 3.50e+00 8.16e-02 1.97e+01
  angle pdb=" CA  CYS A 179 "
        pdb=" CB  CYS A 179 "
        pdb=" SG  CYS A 179 "
      ideal   model   delta    sigma   weight residual
     114.40  124.10   -9.70 2.30e+00 1.89e-01 1.78e+01
  ... (remaining 5452 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 2018
       16.01 -    32.02: 233
       32.02 -    48.04: 78
       48.04 -    64.05: 10
       64.05 -    80.06: 5
  Dihedral angle restraints: 2344
    sinusoidal: 951
      harmonic: 1393
  Sorted by residual:
  dihedral pdb=" CA  CYS A 179 "
           pdb=" C   CYS A 179 "
           pdb=" N   ASP A 180 "
           pdb=" CA  ASP A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.97  -48.03     0      5.00e+00 4.00e-02 9.23e+01
  dihedral pdb=" CA  LYS A 161 "
           pdb=" C   LYS A 161 "
           pdb=" N   CYS A 162 "
           pdb=" CA  CYS A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.29  -31.71     0      5.00e+00 4.00e-02 4.02e+01
  dihedral pdb=" CA  GLU A 178 "
           pdb=" C   GLU A 178 "
           pdb=" N   CYS A 179 "
           pdb=" CA  CYS A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.47  -22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 2341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 457
       0.053 -    0.106: 128
       0.106 -    0.158: 8
       0.158 -    0.211: 1
       0.211 -    0.264: 3
  Chirality restraints: 597
  Sorted by residual:
  chirality pdb=" CB  ILE A 216 "
            pdb=" CA  ILE A 216 "
            pdb=" CG1 ILE A 216 "
            pdb=" CG2 ILE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  CYS A 179 "
            pdb=" N   CYS A 179 "
            pdb=" C   CYS A 179 "
            pdb=" CB  CYS A 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  PRO A 263 "
            pdb=" N   PRO A 263 "
            pdb=" C   PRO A 263 "
            pdb=" CB  PRO A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 594 not shown)

  Planarity restraints: 672
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 169 "    0.070 5.00e-02 4.00e+02   1.03e-01 1.68e+01
        pdb=" N   PRO A 170 "   -0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 262 "   -0.068 5.00e-02 4.00e+02   9.20e-02 1.35e+01
        pdb=" N   PRO A 263 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 263 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 263 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 490 "    0.010 2.00e-02 2.50e+03   1.10e-02 2.12e+00
        pdb=" CG  PHE A 490 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 490 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 490 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 490 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 490 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 490 "    0.001 2.00e-02 2.50e+03
  ... (remaining 669 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 155
        2.72 -     3.26: 4179
        3.26 -     3.81: 6425
        3.81 -     4.35: 7251
        4.35 -     4.90: 12405
  Nonbonded interactions: 30415
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A   8 "
            pdb=" OG  SER A 495 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" NH1 ARG A 158 "
            pdb=" O   PRO A 183 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   MET A   9 "
            pdb=" NH2 ARG A 431 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" O   THR A 371 "
            pdb=" N   GLY A 374 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   GLN A 326 "
            pdb=" NH1 ARG A 329 "
     model   vdw
     2.289 3.120
  ... (remaining 30410 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 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:             1.960
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.770
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
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      :  0.005   0.175   4032  Z= 0.206
  Angle     :  0.882  16.031   5461  Z= 0.482
  Chirality :  0.047   0.264    597
  Planarity :  0.007   0.103    672
  Dihedral  : 15.830  80.062   1436
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 20.57 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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:  0.65 (0.38), residues: 474
  helix:  1.37 (0.32), residues: 223
  sheet:  0.18 (0.61), residues: 67
  loop : -0.56 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 200 
 TYR   0.016   0.002   TYR A  45 
 PHE   0.026   0.002   PHE A 490 
 TRP   0.021   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 4030)
  covalent geometry    : angle       0.87118 ( 5457)
  SS BOND              : bond        0.00476 (    2)
  SS BOND              : angle       5.13274 (    4)
  hydrogen bonds       : bond        0.14113 (  219)
  hydrogen bonds       : angle       6.31322 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0502
  time to fit residues: 6.5054
Evaluate side-chains
  92 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.157480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127538 restraints weight = 8496.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.131105 restraints weight = 4895.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.133582 restraints weight = 3451.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134803 restraints weight = 2745.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.136084 restraints weight = 2401.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   4032  Z= 0.135
  Angle     :  0.639  10.250   5461  Z= 0.331
  Chirality :  0.044   0.255    597
  Planarity :  0.005   0.061    672
  Dihedral  :  5.290  38.495    511
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.73 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.39), residues: 474
  helix:  1.58 (0.32), residues: 229
  sheet:  0.55 (0.61), residues: 65
  loop : -0.40 (0.50), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 200 
 TYR   0.013   0.002   TYR A  45 
 PHE   0.016   0.001   PHE A 318 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4030)
  covalent geometry    : angle       0.63725 ( 5457)
  SS BOND              : bond        0.00736 (    2)
  SS BOND              : angle       1.66790 (    4)
  hydrogen bonds       : bond        0.04553 (  219)
  hydrogen bonds       : angle       4.64934 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 TYR cc_start: 0.7967 (t80) cc_final: 0.7631 (t80)
  outliers start: 14
  outliers final: 10
  residues processed: 111
  average time/residue: 0.0576
  time to fit residues: 8.4496
Evaluate side-chains
  106 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  348 CYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  439 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 331 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.151947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123078 restraints weight = 8274.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.126238 restraints weight = 5020.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128481 restraints weight = 3601.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129783 restraints weight = 2916.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130964 restraints weight = 2542.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4032  Z= 0.225
  Angle     :  0.689  13.509   5461  Z= 0.360
  Chirality :  0.045   0.181    597
  Planarity :  0.005   0.050    672
  Dihedral  :  5.429  39.070    511
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 18.91 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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:  0.88 (0.38), residues: 474
  helix:  1.63 (0.33), residues: 224
  sheet:  0.45 (0.59), residues: 69
  loop : -0.65 (0.49), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 158 
 TYR   0.021   0.002   TYR A  45 
 PHE   0.023   0.003   PHE A 401 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 4030)
  covalent geometry    : angle       0.68696 ( 5457)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       2.10822 (    4)
  hydrogen bonds       : bond        0.04912 (  219)
  hydrogen bonds       : angle       4.65340 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8585 (pt)
REVERT: A  432 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.5876 (t80)
REVERT: A  478 TYR cc_start: 0.8178 (t80) cc_final: 0.7872 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0462
  time to fit residues: 6.6225
Evaluate side-chains
  109 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.155997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.126636 restraints weight = 8404.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.130100 restraints weight = 4869.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132540 restraints weight = 3409.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.133951 restraints weight = 2691.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.135061 restraints weight = 2331.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4032  Z= 0.128
  Angle     :  0.608  11.742   5461  Z= 0.310
  Chirality :  0.042   0.152    597
  Planarity :  0.004   0.038    672
  Dihedral  :  4.993  32.069    511
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 20.33 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.39), residues: 474
  helix:  1.93 (0.33), residues: 227
  sheet:  1.05 (0.62), residues: 59
  loop : -0.51 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.008   0.001   TYR A 492 
 PHE   0.023   0.002   PHE A 490 
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4030)
  covalent geometry    : angle       0.60764 ( 5457)
  SS BOND              : bond        0.00487 (    2)
  SS BOND              : angle       0.96689 (    4)
  hydrogen bonds       : bond        0.04177 (  219)
  hydrogen bonds       : angle       4.19544 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.7905 (m100) cc_final: 0.7520 (m100)
REVERT: A  478 TYR cc_start: 0.8018 (t80) cc_final: 0.7713 (t80)
REVERT: A  489 MET cc_start: 0.8726 (mtm) cc_final: 0.8522 (mtm)
  outliers start: 26
  outliers final: 19
  residues processed: 118
  average time/residue: 0.0512
  time to fit residues: 7.9346
Evaluate side-chains
  118 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.0060
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.157926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.128424 restraints weight = 8285.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131967 restraints weight = 4807.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134467 restraints weight = 3340.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.135922 restraints weight = 2628.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137231 restraints weight = 2269.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.115
  Angle     :  0.614  13.863   5461  Z= 0.302
  Chirality :  0.041   0.130    597
  Planarity :  0.004   0.034    672
  Dihedral  :  4.719  27.842    511
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 20.80 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.39), residues: 474
  helix:  1.93 (0.33), residues: 230
  sheet:  0.67 (0.57), residues: 66
  loop : -0.37 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.008   0.001   TYR A 492 
 PHE   0.026   0.001   PHE A 490 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4030)
  covalent geometry    : angle       0.61415 ( 5457)
  SS BOND              : bond        0.00376 (    2)
  SS BOND              : angle       0.89057 (    4)
  hydrogen bonds       : bond        0.03883 (  219)
  hydrogen bonds       : angle       3.98289 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8182 (ptp) cc_final: 0.7935 (ptt)
REVERT: A  145 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7906 (p90)
REVERT: A  148 TRP cc_start: 0.7903 (m100) cc_final: 0.7485 (m100)
REVERT: A  323 MET cc_start: 0.7632 (mmt) cc_final: 0.7197 (mtt)
REVERT: A  406 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7334 (t0)
REVERT: A  478 TYR cc_start: 0.7943 (t80) cc_final: 0.7693 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0496
  time to fit residues: 7.7726
Evaluate side-chains
  119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0030
   overall best weight:    0.4288

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.158619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.129318 restraints weight = 8582.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.132670 restraints weight = 5190.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.134985 restraints weight = 3713.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136548 restraints weight = 2998.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.137076 restraints weight = 2602.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4032  Z= 0.114
  Angle     :  0.626  12.861   5461  Z= 0.309
  Chirality :  0.041   0.134    597
  Planarity :  0.004   0.041    672
  Dihedral  :  4.575  25.704    511
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 22.46 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.39), residues: 474
  helix:  2.05 (0.33), residues: 230
  sheet:  0.80 (0.58), residues: 73
  loop : -0.07 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 158 
 TYR   0.029   0.002   TYR A 140 
 PHE   0.019   0.001   PHE A 490 
 TRP   0.014   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4030)
  covalent geometry    : angle       0.62580 ( 5457)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       0.85762 (    4)
  hydrogen bonds       : bond        0.03758 (  219)
  hydrogen bonds       : angle       3.88442 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8082 (ptp) cc_final: 0.7848 (ptt)
REVERT: A  145 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7780 (p90)
REVERT: A  148 TRP cc_start: 0.7953 (m100) cc_final: 0.7654 (m100)
REVERT: A  323 MET cc_start: 0.7372 (mmt) cc_final: 0.7129 (mtt)
REVERT: A  406 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7344 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0533
  time to fit residues: 8.5156
Evaluate side-chains
  121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 CYS
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.158044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.128174 restraints weight = 8636.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.131784 restraints weight = 5057.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134297 restraints weight = 3550.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.135727 restraints weight = 2803.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136987 restraints weight = 2427.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.125
  Angle     :  0.640  14.845   5461  Z= 0.313
  Chirality :  0.041   0.128    597
  Planarity :  0.004   0.036    672
  Dihedral  :  4.602  24.847    511
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 22.22 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.39), residues: 474
  helix:  2.03 (0.33), residues: 229
  sheet:  0.80 (0.56), residues: 75
  loop : -0.04 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 141 
 TYR   0.029   0.002   TYR A 140 
 PHE   0.017   0.002   PHE A 490 
 TRP   0.016   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4030)
  covalent geometry    : angle       0.64027 ( 5457)
  SS BOND              : bond        0.00314 (    2)
  SS BOND              : angle       0.74912 (    4)
  hydrogen bonds       : bond        0.03780 (  219)
  hydrogen bonds       : angle       3.92957 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.7968 (m100) cc_final: 0.7589 (m100)
REVERT: A  406 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7287 (t0)
  outliers start: 23
  outliers final: 18
  residues processed: 120
  average time/residue: 0.0523
  time to fit residues: 8.0668
Evaluate side-chains
  119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  477 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0030
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5848

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.158079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.129268 restraints weight = 8470.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.132621 restraints weight = 5107.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.135000 restraints weight = 3625.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.136327 restraints weight = 2884.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137177 restraints weight = 2506.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4032  Z= 0.124
  Angle     :  0.656  14.007   5461  Z= 0.321
  Chirality :  0.042   0.137    597
  Planarity :  0.004   0.033    672
  Dihedral  :  4.631  24.019    511
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 21.75 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.39), residues: 474
  helix:  1.99 (0.33), residues: 229
  sheet:  0.83 (0.55), residues: 75
  loop : -0.02 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 158 
 TYR   0.035   0.002   TYR A 140 
 PHE   0.018   0.002   PHE A 490 
 TRP   0.016   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4030)
  covalent geometry    : angle       0.65568 ( 5457)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.70891 (    4)
  hydrogen bonds       : bond        0.03785 (  219)
  hydrogen bonds       : angle       3.90822 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8428 (mm) cc_final: 0.8179 (mm)
REVERT: A  101 MET cc_start: 0.8119 (ptp) cc_final: 0.7605 (pmm)
REVERT: A  148 TRP cc_start: 0.7971 (m100) cc_final: 0.7639 (m100)
REVERT: A  406 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7243 (t0)
  outliers start: 23
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0523
  time to fit residues: 7.8490
Evaluate side-chains
  120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  477 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.158069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.129894 restraints weight = 8369.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.133195 restraints weight = 5007.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.135535 restraints weight = 3541.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.136909 restraints weight = 2804.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.138123 restraints weight = 2425.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4032  Z= 0.145
  Angle     :  0.666  15.820   5461  Z= 0.327
  Chirality :  0.042   0.128    597
  Planarity :  0.004   0.035    672
  Dihedral  :  4.718  23.589    511
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 21.75 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.39), residues: 474
  helix:  2.00 (0.33), residues: 228
  sheet:  0.89 (0.54), residues: 75
  loop : -0.10 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.029   0.002   TYR A 140 
 PHE   0.020   0.002   PHE A 490 
 TRP   0.018   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4030)
  covalent geometry    : angle       0.66581 ( 5457)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       0.72227 (    4)
  hydrogen bonds       : bond        0.04025 (  219)
  hydrogen bonds       : angle       3.95378 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.7946 (m100) cc_final: 0.7625 (m100)
REVERT: A  259 MET cc_start: 0.8401 (mmm) cc_final: 0.7983 (mmm)
REVERT: A  406 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7605 (t0)
REVERT: A  478 TYR cc_start: 0.8247 (t80) cc_final: 0.7984 (t80)
  outliers start: 22
  outliers final: 18
  residues processed: 113
  average time/residue: 0.0510
  time to fit residues: 7.5555
Evaluate side-chains
  115 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  477 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0670
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.158463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.130395 restraints weight = 8210.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133766 restraints weight = 4888.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.136101 restraints weight = 3449.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.137440 restraints weight = 2740.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.138627 restraints weight = 2371.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4032  Z= 0.141
  Angle     :  0.679  15.528   5461  Z= 0.334
  Chirality :  0.042   0.127    597
  Planarity :  0.004   0.046    672
  Dihedral  :  4.720  22.691    511
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 22.22 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.39), residues: 474
  helix:  1.96 (0.33), residues: 228
  sheet:  0.86 (0.53), residues: 75
  loop : -0.13 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.021   0.002   TYR A 140 
 PHE   0.023   0.002   PHE A 490 
 TRP   0.019   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4030)
  covalent geometry    : angle       0.67932 ( 5457)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.69104 (    4)
  hydrogen bonds       : bond        0.03973 (  219)
  hydrogen bonds       : angle       3.93527 (  633)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.7892 (m100) cc_final: 0.7583 (m100)
REVERT: A  259 MET cc_start: 0.8423 (mmm) cc_final: 0.7975 (mmm)
REVERT: A  406 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7650 (t0)
REVERT: A  478 TYR cc_start: 0.8181 (t80) cc_final: 0.7855 (t80)
  outliers start: 21
  outliers final: 19
  residues processed: 116
  average time/residue: 0.0504
  time to fit residues: 7.6793
Evaluate side-chains
  122 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  406 ASN
Chi-restraints excluded: chain A residue  429 ILE
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  477 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.158217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.130204 restraints weight = 8296.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.133521 restraints weight = 4930.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.135879 restraints weight = 3458.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.137182 restraints weight = 2750.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.138359 restraints weight = 2395.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4032  Z= 0.142
  Angle     :  0.704  15.709   5461  Z= 0.341
  Chirality :  0.042   0.132    597
  Planarity :  0.004   0.041    672
  Dihedral  :  4.727  25.666    511
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 23.40 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.38), residues: 474
  helix:  1.91 (0.33), residues: 229
  sheet:  0.90 (0.52), residues: 75
  loop : -0.20 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.016   0.002   TYR A 140 
 PHE   0.015   0.002   PHE A 398 
 TRP   0.020   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4030)
  covalent geometry    : angle       0.70373 ( 5457)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       0.68137 (    4)
  hydrogen bonds       : bond        0.03989 (  219)
  hydrogen bonds       : angle       3.95619 (  633)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 896.16 seconds
wall clock time: 16 minutes 9.74 seconds (969.74 seconds total)