Starting phenix.real_space_refine
on Mon Nov 17 15:31:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sgy_10188/11_2025/6sgy_10188.map"
  }
  resolution = 4.6
  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=   0.002
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      12      5.16       5
     C    3632      2.51       5
     N     996      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5766
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2883
          Classifications: {'peptide': 402}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360}
    Chain: "B"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2883
          Classifications: {'peptide': 402}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360}
  Time building chain proxies: 1.42, per 1000 atoms: 0.25
  Number of scatterers: 5766
  At special positions: 0
  Unit cell: (148.89, 61.683, 97.842, 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      12     16.00
     O    1126      8.00
     N     996      7.00
     C    3632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 376 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 376 " distance=2.02

  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: 0.34
  Conformation dependent library (CDL) restraints added in 333.1 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      17.2% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
    Processing helix  chain 'A' and resid 142 through 147
      removed outlier: 3.777A  pdb=" N   ILE A 146 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 244
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 319 through 330
    Processing helix  chain 'A' and resid 341 through 348
    Processing helix  chain 'A' and resid 463 through 471
      removed outlier: 4.100A  pdb=" N   VAL A 467 " --> pdb=" O   ASP A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.765A  pdb=" N   LEU A 484 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 133
    Processing helix  chain 'B' and resid 142 through 147
      removed outlier: 3.986A  pdb=" N   ILE B 146 " --> pdb=" O   LYS B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.577A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 264
      removed outlier: 3.746A  pdb=" N   VAL B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 330
    Processing helix  chain 'B' and resid 341 through 348
    Processing helix  chain 'B' and resid 403 through 408
      removed outlier: 3.595A  pdb=" N   THR B 406 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP B 408 " --> pdb=" O   HIS B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 471
      removed outlier: 4.105A  pdb=" N   VAL B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.703A  pdb=" N   LEU B 484 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105
      removed outlier: 6.678A  pdb=" N   ILE A 102 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   VAL A 141 " --> pdb=" O   ILE A 102 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ALA A 104 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 191
    Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232
    Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 297
    Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 409
    Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 479
      removed outlier: 4.258A  pdb=" N   LEU A 477 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET A 446 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 104
    Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 115
    Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 191
    Processing sheet with id=AB2, first strand: chain 'B' and resid 189 through 191
    Processing sheet with id=AB3, first strand: chain 'B' and resid 230 through 232
    Processing sheet with id=AB4, first strand: chain 'B' and resid 315 through 317
      removed outlier: 9.350A  pdb=" N   LEU B 340 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   VAL B 297 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 409 through 410
    Processing sheet with id=AB6, first strand: chain 'B' and resid 477 through 479
      removed outlier: 4.071A  pdb=" N   LEU B 477 " --> pdb=" O   GLY B 428 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 432 " --> pdb=" O   VAL B 479 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET B 446 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    462 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: 0.85

  Time building geometry restraints manager: 0.48 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: 1955
        1.34 -     1.46: 1038
        1.46 -     1.57: 2899
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 5912
  Sorted by residual:
  bond pdb=" C   SER B 440 "
       pdb=" N   PRO B 441 "
    ideal  model  delta    sigma   weight residual
    1.331  1.402 -0.072 1.31e-02 5.83e+03 3.00e+01
  bond pdb=" C   SER A 440 "
       pdb=" N   PRO A 441 "
    ideal  model  delta    sigma   weight residual
    1.332  1.394 -0.062 1.32e-02 5.74e+03 2.24e+01
  bond pdb=" N   ALA A 252 "
       pdb=" CA  ALA A 252 "
    ideal  model  delta    sigma   weight residual
    1.464  1.425  0.039 9.80e-03 1.04e+04 1.60e+01
  bond pdb=" C   LEU A 288 "
       pdb=" N   PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 9.40e-03 1.13e+04 1.15e+01
  bond pdb=" CB  TRP B 226 "
       pdb=" CG  TRP B 226 "
    ideal  model  delta    sigma   weight residual
    1.498  1.420  0.078 3.10e-02 1.04e+03 6.40e+00
  ... (remaining 5907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 7856
        3.06 -     6.11: 244
        6.11 -     9.17: 34
        9.17 -    12.23: 8
       12.23 -    15.29: 4
  Bond angle restraints: 8146
  Sorted by residual:
  angle pdb=" C   ALA B 160 "
        pdb=" N   PRO B 161 "
        pdb=" CA  PRO B 161 "
      ideal   model   delta    sigma   weight residual
     127.00  142.29  -15.29 2.40e+00 1.74e-01 4.06e+01
  angle pdb=" C   ALA B 160 "
        pdb=" N   PRO B 161 "
        pdb=" CD  PRO B 161 "
      ideal   model   delta    sigma   weight residual
     120.60  107.24   13.36 2.20e+00 2.07e-01 3.69e+01
  angle pdb=" N   GLY B 457 "
        pdb=" CA  GLY B 457 "
        pdb=" C   GLY B 457 "
      ideal   model   delta    sigma   weight residual
     110.42  119.33   -8.91 1.49e+00 4.50e-01 3.57e+01
  angle pdb=" N   LEU A 288 "
        pdb=" CA  LEU A 288 "
        pdb=" C   LEU A 288 "
      ideal   model   delta    sigma   weight residual
     113.25  120.06   -6.81 1.30e+00 5.92e-01 2.74e+01
  angle pdb=" N   GLU B 285 "
        pdb=" CA  GLU B 285 "
        pdb=" C   GLU B 285 "
      ideal   model   delta    sigma   weight residual
     110.91  116.88   -5.97 1.17e+00 7.31e-01 2.61e+01
  ... (remaining 8141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 3050
       17.35 -    34.69: 413
       34.69 -    52.03: 67
       52.03 -    69.38: 9
       69.38 -    86.72: 3
  Dihedral angle restraints: 3542
    sinusoidal: 1274
      harmonic: 2268
  Sorted by residual:
  dihedral pdb=" CA  ASN B 184 "
           pdb=" C   ASN B 184 "
           pdb=" N   PRO B 185 "
           pdb=" CA  PRO B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  126.23   53.77     0      5.00e+00 4.00e-02 1.16e+02
  dihedral pdb=" CA  ASP A 215 "
           pdb=" C   ASP A 215 "
           pdb=" N   ALA A 216 "
           pdb=" CA  ALA A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.63  -46.37     0      5.00e+00 4.00e-02 8.60e+01
  dihedral pdb=" CA  ALA B 418 "
           pdb=" C   ALA B 418 "
           pdb=" N   ASN B 419 "
           pdb=" CA  ASN B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.18  -41.82     0      5.00e+00 4.00e-02 7.00e+01
  ... (remaining 3539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 689
       0.061 -    0.122: 212
       0.122 -    0.183: 44
       0.183 -    0.244: 8
       0.244 -    0.304: 3
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CB  ILE A 190 "
            pdb=" CA  ILE A 190 "
            pdb=" CG1 ILE A 190 "
            pdb=" CG2 ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  LEU A 288 "
            pdb=" N   LEU A 288 "
            pdb=" C   LEU A 288 "
            pdb=" CB  LEU A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  PRO A 218 "
            pdb=" N   PRO A 218 "
            pdb=" C   PRO A 218 "
            pdb=" CB  PRO A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 953 not shown)

  Planarity restraints: 1094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 184 "    0.071 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO B 185 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO B 185 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO B 185 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 184 "   -0.062 5.00e-02 4.00e+02   9.37e-02 1.40e+01
        pdb=" N   PRO A 185 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 424 "    0.061 5.00e-02 4.00e+02   9.09e-02 1.32e+01
        pdb=" N   PRO A 425 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "    0.049 5.00e-02 4.00e+02
  ... (remaining 1091 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1051
        2.76 -     3.29: 5861
        3.29 -     3.83: 10491
        3.83 -     4.36: 11088
        4.36 -     4.90: 17833
  Nonbonded interactions: 46324
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 181 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASN B 124 "
            pdb=" OG  SER B 127 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ASN A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR A 433 "
            pdb=" O   ALA A 443 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER A 450 "
            pdb=" OG1 THR A 452 "
     model   vdw
     2.274 3.040
  ... (remaining 46319 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
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:             1.610
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.370
  Find NCS groups from input model:        0.080
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.078   5914  Z= 0.357
  Angle     :  1.351  15.285   8150  Z= 0.735
  Chirality :  0.062   0.304    956
  Planarity :  0.011   0.108   1094
  Dihedral  : 15.714  86.724   2084
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 15.17 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    Twisted General : 1.39 %

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 are not related in a simple way.
  whole: -4.34 (0.24), residues: 800
  helix: -3.19 (0.27), residues: 124
  sheet: -2.86 (0.36), residues: 142
  loop : -2.98 (0.24), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 352 
 TYR   0.025   0.004   TYR B 307 
 PHE   0.025   0.003   PHE B 447 
 TRP   0.018   0.003   TRP A 174 
 HIS   0.010   0.002   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 5912)
  covalent geometry    : angle       1.34877 ( 8146)
  SS BOND              : bond        0.01012 (    2)
  SS BOND              : angle       4.04470 (    4)
  hydrogen bonds       : bond        0.15489 (  162)
  hydrogen bonds       : angle       9.41270 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8378 (mmp) cc_final: 0.8132 (mmp)
REVERT: A  235 LEU cc_start: 0.6790 (pp) cc_final: 0.6579 (pp)
  outliers start: 2
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0755
  time to fit residues: 7.4026
Evaluate side-chains
  62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   overall best weight:    0.4198
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 208 HIS
A 316 GLN
A 419 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.082218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.061873 restraints weight = 12776.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.064320 restraints weight = 8699.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.066301 restraints weight = 6487.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.067833 restraints weight = 5153.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.069000 restraints weight = 4276.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.5704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5914  Z= 0.183
  Angle     :  0.905   8.936   8150  Z= 0.468
  Chirality :  0.047   0.183    956
  Planarity :  0.008   0.075   1094
  Dihedral  :  8.880  32.739    850
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.67 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    Twisted General : 0.56 %

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 are not related in a simple way.
  whole: -3.22 (0.27), residues: 800
  helix: -1.73 (0.38), residues: 106
  sheet: -2.25 (0.38), residues: 148
  loop : -2.32 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 230 
 TYR   0.018   0.003   TYR B 112 
 PHE   0.012   0.002   PHE A 284 
 TRP   0.015   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5912)
  covalent geometry    : angle       0.90338 ( 8146)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       2.84237 (    4)
  hydrogen bonds       : bond        0.04219 (  162)
  hydrogen bonds       : angle       7.80379 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8472 (m-80) cc_final: 0.7577 (m-10)
REVERT: A  119 LEU cc_start: 0.9221 (mt) cc_final: 0.9006 (mt)
REVERT: A  211 LEU cc_start: 0.8850 (pt) cc_final: 0.8416 (pt)
REVERT: A  213 HIS cc_start: 0.8606 (m-70) cc_final: 0.8038 (m-70)
REVERT: A  224 LEU cc_start: 0.9285 (tt) cc_final: 0.8975 (mt)
REVERT: A  229 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8744 (mtmt)
REVERT: A  254 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8197 (ttt180)
REVERT: A  446 MET cc_start: 0.8452 (tpp) cc_final: 0.8237 (tpp)
REVERT: A  477 LEU cc_start: 0.9677 (mt) cc_final: 0.9419 (tt)
REVERT: A  487 PHE cc_start: 0.9110 (m-80) cc_final: 0.7938 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0764
  time to fit residues: 7.9153
Evaluate side-chains
  72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0670
   chunk 50 optimal weight:    0.0170
   chunk 43 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0030
   chunk 38 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 17 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0370
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.0644
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.084748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.064822 restraints weight = 12747.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.067180 restraints weight = 8772.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.069143 restraints weight = 6578.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.070640 restraints weight = 5232.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.071864 restraints weight = 4353.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.6339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5914  Z= 0.160
  Angle     :  0.867   7.846   8150  Z= 0.436
  Chirality :  0.046   0.157    956
  Planarity :  0.009   0.079   1094
  Dihedral  :  7.955  30.112    850
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    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 are not related in a simple way.
  whole: -2.96 (0.28), residues: 800
  helix: -1.40 (0.38), residues: 118
  sheet: -2.24 (0.38), residues: 148
  loop : -2.12 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 151 
 TYR   0.011   0.002   TYR B 429 
 PHE   0.019   0.002   PHE A 487 
 TRP   0.010   0.001   TRP A 379 
 HIS   0.006   0.002   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5912)
  covalent geometry    : angle       0.86380 ( 8146)
  SS BOND              : bond        0.00563 (    2)
  SS BOND              : angle       3.25615 (    4)
  hydrogen bonds       : bond        0.04210 (  162)
  hydrogen bonds       : angle       7.34584 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 HIS cc_start: 0.8416 (m-70) cc_final: 0.7898 (m-70)
REVERT: A  224 LEU cc_start: 0.9158 (tt) cc_final: 0.8894 (mt)
REVERT: A  229 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8718 (mtmt)
REVERT: A  242 ASP cc_start: 0.9395 (t0) cc_final: 0.8579 (p0)
REVERT: A  246 LEU cc_start: 0.9032 (mt) cc_final: 0.8652 (mt)
REVERT: A  254 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8115 (ttt180)
REVERT: A  477 LEU cc_start: 0.9609 (mt) cc_final: 0.9233 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0672
  time to fit residues: 6.5776
Evaluate side-chains
  71 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0870
   chunk 2 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0980
   chunk 67 optimal weight:    0.0870
   chunk 25 optimal weight:    0.0000
   chunk 14 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0570
   overall best weight:    0.0658
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.087811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.067706 restraints weight = 13073.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.070225 restraints weight = 9130.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.072222 restraints weight = 6908.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.073737 restraints weight = 5540.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.074984 restraints weight = 4630.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.6924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5914  Z= 0.162
  Angle     :  0.866   9.705   8150  Z= 0.430
  Chirality :  0.046   0.133    956
  Planarity :  0.008   0.072   1094
  Dihedral  :  7.373  29.350    850
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 are not related in a simple way.
  whole: -2.79 (0.28), residues: 800
  helix: -1.01 (0.41), residues: 118
  sheet: -2.03 (0.37), residues: 148
  loop : -2.11 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 151 
 TYR   0.010   0.002   TYR A 359 
 PHE   0.011   0.002   PHE A 487 
 TRP   0.014   0.002   TRP B 448 
 HIS   0.006   0.002   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5912)
  covalent geometry    : angle       0.86193 ( 8146)
  SS BOND              : bond        0.00562 (    2)
  SS BOND              : angle       3.81247 (    4)
  hydrogen bonds       : bond        0.03576 (  162)
  hydrogen bonds       : angle       7.01032 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8169 (m-10) cc_final: 0.7855 (m-10)
REVERT: A  118 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8327 (tp40)
REVERT: A  213 HIS cc_start: 0.8335 (m-70) cc_final: 0.7847 (m-70)
REVERT: A  254 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8382 (ttt180)
REVERT: A  308 TYR cc_start: 0.8923 (m-80) cc_final: 0.8641 (m-80)
REVERT: A  477 LEU cc_start: 0.9475 (mt) cc_final: 0.9163 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0631
  time to fit residues: 6.3612
Evaluate side-chains
  67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0000
   chunk 18 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0040
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.4396
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.087149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.067429 restraints weight = 12531.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.069939 restraints weight = 8728.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.071938 restraints weight = 6577.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.073482 restraints weight = 5231.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.074734 restraints weight = 4340.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.7182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5914  Z= 0.148
  Angle     :  0.826   9.626   8150  Z= 0.411
  Chirality :  0.045   0.134    956
  Planarity :  0.007   0.070   1094
  Dihedral  :  7.039  27.843    850
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.00 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 are not related in a simple way.
  whole: -2.80 (0.28), residues: 800
  helix: -0.76 (0.41), residues: 118
  sheet: -2.00 (0.35), residues: 176
  loop : -2.17 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 352 
 TYR   0.011   0.002   TYR A 359 
 PHE   0.009   0.001   PHE B 487 
 TRP   0.013   0.002   TRP B 379 
 HIS   0.004   0.001   HIS B 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5912)
  covalent geometry    : angle       0.82223 ( 8146)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       3.74761 (    4)
  hydrogen bonds       : bond        0.03466 (  162)
  hydrogen bonds       : angle       6.77231 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8397 (tp-100)
REVERT: A  175 THR cc_start: 0.8807 (p) cc_final: 0.8517 (p)
REVERT: A  197 ASP cc_start: 0.8977 (t0) cc_final: 0.8675 (t0)
REVERT: A  211 LEU cc_start: 0.8509 (pt) cc_final: 0.8214 (pt)
REVERT: A  213 HIS cc_start: 0.8309 (m-70) cc_final: 0.7855 (m90)
REVERT: A  229 LYS cc_start: 0.9264 (ttmt) cc_final: 0.9010 (tmmt)
REVERT: A  254 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8403 (ttt180)
REVERT: A  308 TYR cc_start: 0.8888 (m-80) cc_final: 0.8644 (m-80)
REVERT: A  446 MET cc_start: 0.7927 (tpp) cc_final: 0.7604 (tpp)
REVERT: A  477 LEU cc_start: 0.9486 (mt) cc_final: 0.9199 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 0.0592
  time to fit residues: 5.8624
Evaluate side-chains
  69 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0070
   chunk 8 optimal weight:    0.1980
   chunk 54 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.4798
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.086866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.067249 restraints weight = 12841.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.069665 restraints weight = 9003.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.071667 restraints weight = 6804.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.073129 restraints weight = 5405.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.074456 restraints weight = 4496.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.7387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5914  Z= 0.143
  Angle     :  0.809   9.649   8150  Z= 0.405
  Chirality :  0.044   0.133    956
  Planarity :  0.007   0.071   1094
  Dihedral  :  6.805  27.691    850
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 are not related in a simple way.
  whole: -2.57 (0.28), residues: 800
  helix: -0.25 (0.42), residues: 106
  sheet: -1.89 (0.36), residues: 180
  loop : -2.04 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 151 
 TYR   0.014   0.002   TYR B 112 
 PHE   0.008   0.001   PHE B 487 
 TRP   0.008   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5912)
  covalent geometry    : angle       0.80372 ( 8146)
  SS BOND              : bond        0.00705 (    2)
  SS BOND              : angle       4.10650 (    4)
  hydrogen bonds       : bond        0.03134 (  162)
  hydrogen bonds       : angle       6.57380 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8367 (tp-100)
REVERT: A  211 LEU cc_start: 0.8634 (pt) cc_final: 0.8409 (pt)
REVERT: A  213 HIS cc_start: 0.8298 (m-70) cc_final: 0.7874 (m90)
REVERT: A  242 ASP cc_start: 0.9328 (t0) cc_final: 0.8591 (p0)
REVERT: A  246 LEU cc_start: 0.9032 (mt) cc_final: 0.8743 (mt)
REVERT: A  254 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8485 (ttt180)
REVERT: A  261 PHE cc_start: 0.8970 (t80) cc_final: 0.8770 (t80)
REVERT: A  308 TYR cc_start: 0.8946 (m-80) cc_final: 0.8535 (m-80)
REVERT: A  350 MET cc_start: 0.8182 (mmp) cc_final: 0.7429 (mmm)
REVERT: A  359 TYR cc_start: 0.8904 (m-80) cc_final: 0.8584 (m-80)
REVERT: A  446 MET cc_start: 0.7949 (tpp) cc_final: 0.7685 (tpp)
REVERT: A  477 LEU cc_start: 0.9500 (mt) cc_final: 0.9265 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0654
  time to fit residues: 6.2107
Evaluate side-chains
  70 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    0.0030
   chunk 44 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0050
   chunk 71 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.3004
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.088425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.068484 restraints weight = 13011.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.071063 restraints weight = 9112.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.073048 restraints weight = 6922.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.074605 restraints weight = 5555.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.075736 restraints weight = 4620.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.7679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5914  Z= 0.136
  Angle     :  0.816   9.654   8150  Z= 0.400
  Chirality :  0.045   0.135    956
  Planarity :  0.007   0.070   1094
  Dihedral  :  6.543  30.290    850
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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 are not related in a simple way.
  whole: -2.38 (0.28), residues: 800
  helix: -0.02 (0.45), residues: 106
  sheet: -1.87 (0.38), residues: 146
  loop : -1.92 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 151 
 TYR   0.008   0.001   TYR B 429 
 PHE   0.008   0.001   PHE B 284 
 TRP   0.019   0.002   TRP A 379 
 HIS   0.005   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5912)
  covalent geometry    : angle       0.81159 ( 8146)
  SS BOND              : bond        0.00676 (    2)
  SS BOND              : angle       4.07139 (    4)
  hydrogen bonds       : bond        0.03151 (  162)
  hydrogen bonds       : angle       6.62133 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8316 (tp-100)
REVERT: A  213 HIS cc_start: 0.8255 (m-70) cc_final: 0.7876 (m90)
REVERT: A  242 ASP cc_start: 0.9303 (t0) cc_final: 0.8588 (p0)
REVERT: A  246 LEU cc_start: 0.9005 (mt) cc_final: 0.8749 (mt)
REVERT: A  254 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8491 (ttt180)
REVERT: A  261 PHE cc_start: 0.8930 (t80) cc_final: 0.8726 (t80)
REVERT: A  308 TYR cc_start: 0.8912 (m-80) cc_final: 0.8485 (m-80)
REVERT: A  359 TYR cc_start: 0.8982 (m-80) cc_final: 0.8563 (m-80)
REVERT: A  446 MET cc_start: 0.7907 (tpp) cc_final: 0.7552 (tpp)
REVERT: A  477 LEU cc_start: 0.9429 (mt) cc_final: 0.9124 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0578
  time to fit residues: 5.5468
Evaluate side-chains
  69 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 71 optimal weight:    0.0980
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0050
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0470
   overall best weight:    0.1110
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.089593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.069120 restraints weight = 12398.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.071704 restraints weight = 8647.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.073705 restraints weight = 6501.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.075209 restraints weight = 5189.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.076460 restraints weight = 4325.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.7857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5914  Z= 0.134
  Angle     :  0.805   9.723   8150  Z= 0.395
  Chirality :  0.044   0.133    956
  Planarity :  0.007   0.069   1094
  Dihedral  :  6.311  31.208    850
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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 are not related in a simple way.
  whole: -2.33 (0.29), residues: 800
  helix:  0.08 (0.46), residues: 106
  sheet: -1.65 (0.37), residues: 176
  loop : -1.94 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 238 
 TYR   0.007   0.001   TYR A 429 
 PHE   0.009   0.001   PHE B 284 
 TRP   0.015   0.002   TRP A 379 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5912)
  covalent geometry    : angle       0.79900 ( 8146)
  SS BOND              : bond        0.00851 (    2)
  SS BOND              : angle       4.50574 (    4)
  hydrogen bonds       : bond        0.03027 (  162)
  hydrogen bonds       : angle       6.36026 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8305 (tp40)
REVERT: A  211 LEU cc_start: 0.8517 (pt) cc_final: 0.7996 (tp)
REVERT: A  213 HIS cc_start: 0.8217 (m-70) cc_final: 0.7802 (m-70)
REVERT: A  242 ASP cc_start: 0.9239 (t0) cc_final: 0.8574 (p0)
REVERT: A  246 LEU cc_start: 0.8965 (mt) cc_final: 0.8753 (mt)
REVERT: A  254 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8574 (ttt180)
REVERT: A  261 PHE cc_start: 0.8925 (t80) cc_final: 0.8712 (t80)
REVERT: A  308 TYR cc_start: 0.8877 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  359 TYR cc_start: 0.9021 (m-80) cc_final: 0.8588 (m-80)
REVERT: A  446 MET cc_start: 0.7893 (tpp) cc_final: 0.7576 (tpp)
REVERT: A  477 LEU cc_start: 0.9310 (mt) cc_final: 0.8970 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0530
  time to fit residues: 5.1483
Evaluate side-chains
  66 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0770
   chunk 66 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0370
   chunk 34 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0000
   chunk 56 optimal weight:    0.0060
   overall best weight:    0.1236
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.090998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.070077 restraints weight = 11952.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.072704 restraints weight = 8330.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.074792 restraints weight = 6266.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.076253 restraints weight = 4981.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.077556 restraints weight = 4152.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.8063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5914  Z= 0.137
  Angle     :  0.829   9.491   8150  Z= 0.401
  Chirality :  0.046   0.263    956
  Planarity :  0.007   0.067   1094
  Dihedral  :  6.180  29.415    850
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 are not related in a simple way.
  whole: -2.20 (0.29), residues: 800
  helix:  0.15 (0.46), residues: 106
  sheet: -1.50 (0.37), residues: 176
  loop : -1.87 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 238 
 TYR   0.008   0.001   TYR B 429 
 PHE   0.009   0.001   PHE A 284 
 TRP   0.015   0.002   TRP A 379 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5912)
  covalent geometry    : angle       0.82320 ( 8146)
  SS BOND              : bond        0.00789 (    2)
  SS BOND              : angle       4.59745 (    4)
  hydrogen bonds       : bond        0.02959 (  162)
  hydrogen bonds       : angle       6.06255 (  462)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8244 (tp-100)
REVERT: A  154 LEU cc_start: 0.8672 (tp) cc_final: 0.8246 (pt)
REVERT: A  211 LEU cc_start: 0.8513 (pt) cc_final: 0.8026 (tp)
REVERT: A  213 HIS cc_start: 0.8169 (m-70) cc_final: 0.7739 (m-70)
REVERT: A  254 ARG cc_start: 0.8851 (ttm110) cc_final: 0.8578 (ttt180)
REVERT: A  308 TYR cc_start: 0.8902 (m-80) cc_final: 0.8412 (m-80)
REVERT: A  359 TYR cc_start: 0.9122 (m-80) cc_final: 0.8621 (m-80)
REVERT: A  477 LEU cc_start: 0.9343 (mt) cc_final: 0.8987 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0547
  time to fit residues: 5.2613
Evaluate side-chains
  63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    0.0020
   chunk 20 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0020
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:    0.3980
   chunk 16 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0270
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.0932
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 219 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.091429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.070571 restraints weight = 12604.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.073322 restraints weight = 8683.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.075474 restraints weight = 6517.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.077119 restraints weight = 5170.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.078315 restraints weight = 4272.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.8261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5914  Z= 0.136
  Angle     :  0.833  10.136   8150  Z= 0.396
  Chirality :  0.045   0.208    956
  Planarity :  0.007   0.066   1094
  Dihedral  :  6.047  28.918    850
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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 are not related in a simple way.
  whole: -2.20 (0.29), residues: 800
  helix:  0.06 (0.46), residues: 106
  sheet: -1.52 (0.37), residues: 176
  loop : -1.84 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 238 
 TYR   0.007   0.001   TYR B 429 
 PHE   0.010   0.002   PHE A 284 
 TRP   0.016   0.002   TRP B 379 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5912)
  covalent geometry    : angle       0.82803 ( 8146)
  SS BOND              : bond        0.00815 (    2)
  SS BOND              : angle       4.02974 (    4)
  hydrogen bonds       : bond        0.02993 (  162)
  hydrogen bonds       : angle       6.12646 (  462)

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

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

  800 Ramachandran restraints generated.
    400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  800 Ramachandran restraints generated.
    400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  112 TYR cc_start: 0.7857 (m-10) cc_final: 0.7571 (m-10)
REVERT: B  142 LYS cc_start: 0.9440 (tptp) cc_final: 0.8710 (mptt)
REVERT: B  154 LEU cc_start: 0.8732 (tp) cc_final: 0.8232 (pt)
REVERT: B  213 HIS cc_start: 0.8112 (m-70) cc_final: 0.7873 (m-70)
REVERT: B  261 PHE cc_start: 0.8827 (t80) cc_final: 0.8590 (t80)
REVERT: B  308 TYR cc_start: 0.8845 (m-80) cc_final: 0.8405 (m-80)
REVERT: B  359 TYR cc_start: 0.9158 (m-80) cc_final: 0.8542 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0621
  time to fit residues: 5.6209
Evaluate side-chains
  60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0050
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0170
   chunk 67 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0370
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.3312
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.089983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.069777 restraints weight = 12718.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.072205 restraints weight = 9215.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.074108 restraints weight = 7164.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.075465 restraints weight = 5858.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.076682 restraints weight = 4995.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.8486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5914  Z= 0.136
  Angle     :  0.842  12.799   8150  Z= 0.397
  Chirality :  0.044   0.175    956
  Planarity :  0.007   0.061   1094
  Dihedral  :  6.095  30.503    850
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.67 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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 are not related in a simple way.
  whole: -2.53 (0.28), residues: 800
  helix: -0.39 (0.43), residues: 106
  sheet: -1.62 (0.34), residues: 196
  loop : -2.08 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 238 
 TYR   0.014   0.001   TYR A 429 
 PHE   0.009   0.002   PHE A 284 
 TRP   0.016   0.002   TRP B 174 
 HIS   0.004   0.001   HIS B 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5912)
  covalent geometry    : angle       0.83432 ( 8146)
  SS BOND              : bond        0.00724 (    2)
  SS BOND              : angle       5.09786 (    4)
  hydrogen bonds       : bond        0.02957 (  162)
  hydrogen bonds       : angle       6.39198 (  462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 931.47 seconds
wall clock time: 16 minutes 45.01 seconds (1005.01 seconds total)