Starting phenix.real_space_refine
on Fri Aug 22 20:40:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ytw_34094/08_2025/7ytw_34094.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     Na      4      4.78       5
     C    5074      2.51       5
     N    1238      2.21       5
     O    1364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  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: 7744
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 3857
          Classifications: {'peptide': 507}
          Link IDs: {'PTRANS': 33, 'TRANS': 473}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 14
          Unusual residues: {' NA': 2, 'ASC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.42, per 1000 atoms: 0.31
  Number of scatterers: 7744
  At special positions: 0
  Unit cell: (87.74, 107.42, 76.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      64     16.00
     Na      4     11.00
     O    1364      8.00
     N    1238      7.00
     C    5074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  78 " - pdb=" SG  CYS B 136 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 408.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      64.3% alpha, 0.0% 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 51 through 77
      removed outlier: 3.928A  pdb=" N   GLY A  55 " --> pdb=" O   CYS A  51 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   GLY A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      Proline residue:  A  70  - end of helix
    Processing helix  chain 'A' and resid 82 through 105
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 3.592A  pdb=" N   ALA A 125 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 180
      removed outlier: 3.653A  pdb=" N   TRP A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
      removed outlier: 3.730A  pdb=" N   MET A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
    Processing helix  chain 'A' and resid 191 through 204
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 206 through 215
    Processing helix  chain 'A' and resid 217 through 233
    Processing helix  chain 'A' and resid 262 through 282
      removed outlier: 3.546A  pdb=" N   LEU A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 281 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 353
    Processing helix  chain 'A' and resid 359 through 381
    Processing helix  chain 'A' and resid 389 through 399
      removed outlier: 3.802A  pdb=" N   GLY A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 418
      removed outlier: 4.080A  pdb=" N   VAL A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 428
    Processing helix  chain 'A' and resid 431 through 452
    Processing helix  chain 'A' and resid 453 through 455
      No H-bonds generated for 'chain 'A' and resid 453 through 455'
    Processing helix  chain 'A' and resid 462 through 485
      Proline residue:  A 479  - end of helix
    Processing helix  chain 'A' and resid 493 through 506
    Processing helix  chain 'A' and resid 506 through 511
    Processing helix  chain 'A' and resid 512 through 522
      removed outlier: 3.586A  pdb=" N   VAL A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 77
      removed outlier: 3.928A  pdb=" N   GLY B  55 " --> pdb=" O   CYS B  51 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   GLY B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 82 through 105
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 3.592A  pdb=" N   ALA B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 180
      removed outlier: 3.653A  pdb=" N   TRP B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      Proline residue:  B 158  - end of helix
      removed outlier: 3.730A  pdb=" N   MET B 180 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 190
    Processing helix  chain 'B' and resid 191 through 204
      Proline residue:  B 197  - end of helix
    Processing helix  chain 'B' and resid 206 through 215
    Processing helix  chain 'B' and resid 217 through 233
    Processing helix  chain 'B' and resid 262 through 282
      removed outlier: 3.546A  pdb=" N   LEU B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 267 " --> pdb=" O   PRO B 263 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR B 281 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 353
    Processing helix  chain 'B' and resid 359 through 381
    Processing helix  chain 'B' and resid 389 through 399
      removed outlier: 3.802A  pdb=" N   GLY B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 418
      removed outlier: 4.080A  pdb=" N   VAL B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 428
    Processing helix  chain 'B' and resid 431 through 452
    Processing helix  chain 'B' and resid 453 through 455
      No H-bonds generated for 'chain 'B' and resid 453 through 455'
    Processing helix  chain 'B' and resid 462 through 485
      Proline residue:  B 479  - end of helix
    Processing helix  chain 'B' and resid 493 through 506
    Processing helix  chain 'B' and resid 506 through 511
    Processing helix  chain 'B' and resid 512 through 522
      removed outlier: 3.586A  pdb=" N   VAL B 522 " --> pdb=" O   LEU B 518 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1344 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: 1.02

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1816
        1.33 -     1.45: 1622
        1.45 -     1.57: 4398
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 7936
  Sorted by residual:
  bond pdb=" C1  ASC A 703 "
       pdb=" O4  ASC A 703 "
    ideal  model  delta    sigma   weight residual
    1.346  1.449 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C1  ASC B 703 "
       pdb=" O4  ASC B 703 "
    ideal  model  delta    sigma   weight residual
    1.346  1.449 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" CG  PRO A 197 "
       pdb=" CD  PRO A 197 "
    ideal  model  delta    sigma   weight residual
    1.503  1.369  0.134 3.40e-02 8.65e+02 1.55e+01
  bond pdb=" CG  PRO B 197 "
       pdb=" CD  PRO B 197 "
    ideal  model  delta    sigma   weight residual
    1.503  1.369  0.134 3.40e-02 8.65e+02 1.55e+01
  bond pdb=" CG1 ILE A  93 "
       pdb=" CD1 ILE A  93 "
    ideal  model  delta    sigma   weight residual
    1.513  1.424  0.089 3.90e-02 6.57e+02 5.16e+00
  ... (remaining 7931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 10088
        1.87 -     3.75: 570
        3.75 -     5.62: 104
        5.62 -     7.50: 48
        7.50 -     9.37: 22
  Bond angle restraints: 10832
  Sorted by residual:
  angle pdb=" CA  PRO B 197 "
        pdb=" N   PRO B 197 "
        pdb=" CD  PRO B 197 "
      ideal   model   delta    sigma   weight residual
     112.00  105.69    6.31 1.40e+00 5.10e-01 2.03e+01
  angle pdb=" CA  PRO A 197 "
        pdb=" N   PRO A 197 "
        pdb=" CD  PRO A 197 "
      ideal   model   delta    sigma   weight residual
     112.00  105.69    6.31 1.40e+00 5.10e-01 2.03e+01
  angle pdb=" N   PRO A 197 "
        pdb=" CD  PRO A 197 "
        pdb=" CG  PRO A 197 "
      ideal   model   delta    sigma   weight residual
     103.20   96.54    6.66 1.50e+00 4.44e-01 1.97e+01
  angle pdb=" N   PRO B 197 "
        pdb=" CD  PRO B 197 "
        pdb=" CG  PRO B 197 "
      ideal   model   delta    sigma   weight residual
     103.20   96.54    6.66 1.50e+00 4.44e-01 1.97e+01
  angle pdb=" CA  THR A 196 "
        pdb=" CB  THR A 196 "
        pdb=" CG2 THR A 196 "
      ideal   model   delta    sigma   weight residual
     110.50  117.87   -7.37 1.70e+00 3.46e-01 1.88e+01
  ... (remaining 10827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4206
       17.46 -    34.93: 386
       34.93 -    52.39: 44
       52.39 -    69.86: 8
       69.86 -    87.32: 4
  Dihedral angle restraints: 4648
    sinusoidal: 1782
      harmonic: 2866
  Sorted by residual:
  dihedral pdb=" CA  LEU B 201 "
           pdb=" C   LEU B 201 "
           pdb=" N   ILE B 202 "
           pdb=" CA  ILE B 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.43   24.57     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  LEU A 201 "
           pdb=" C   LEU A 201 "
           pdb=" N   ILE A 202 "
           pdb=" CA  ILE A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.43   24.57     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  VAL A 510 "
           pdb=" C   VAL A 510 "
           pdb=" N   GLY A 511 "
           pdb=" CA  GLY A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.84   21.16     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 4645 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1058
       0.079 -    0.157: 196
       0.157 -    0.236: 14
       0.236 -    0.315: 6
       0.315 -    0.394: 8
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" C5  ASC A 703 "
            pdb=" C4  ASC A 703 "
            pdb=" C6  ASC A 703 "
            pdb=" O5  ASC A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.26    2.65   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" C5  ASC B 703 "
            pdb=" C4  ASC B 703 "
            pdb=" C6  ASC B 703 "
            pdb=" O5  ASC B 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.26    2.65   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CB  ILE B 569 "
            pdb=" CA  ILE B 569 "
            pdb=" CG1 ILE B 569 "
            pdb=" CG2 ILE B 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.74e+00
  ... (remaining 1279 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 287 "   -0.057 5.00e-02 4.00e+02   8.66e-02 1.20e+01
        pdb=" N   PRO B 288 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO B 288 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 288 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 287 "   -0.057 5.00e-02 4.00e+02   8.66e-02 1.20e+01
        pdb=" N   PRO A 288 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 262 "   -0.019 2.00e-02 2.50e+03   2.56e-02 1.15e+01
        pdb=" CG  PHE A 262 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 262 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 262 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 262 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 262 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 262 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1442
        2.76 -     3.30: 7518
        3.30 -     3.83: 13648
        3.83 -     4.37: 16474
        4.37 -     4.90: 28229
  Nonbonded interactions: 67311
  Sorted by model distance:
  nonbonded pdb="NA    NA B 701 "
            pdb=" O1  ASC B 703 "
     model   vdw
     2.230 2.470
  nonbonded pdb="NA    NA A 701 "
            pdb=" O1  ASC A 703 "
     model   vdw
     2.230 2.470
  nonbonded pdb=" O   SER A 117 "
            pdb=" O3  ASC A 703 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER B 117 "
            pdb=" O3  ASC B 703 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   CYS A 275 "
            pdb=" OG1 THR A 279 "
     model   vdw
     2.303 3.040
  ... (remaining 67306 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
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.770
  Find NCS groups from input model:        0.040
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
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      :  0.009   0.134   7938  Z= 0.342
  Angle     :  1.112   9.372  10836  Z= 0.586
  Chirality :  0.068   0.394   1282
  Planarity :  0.010   0.087   1346
  Dihedral  : 13.301  87.320   2814
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.06 (0.23), residues: 1002
  helix: -1.97 (0.16), residues: 656
  sheet: -4.36 (0.58), residues: 20
  loop : -1.55 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 463 
 TYR   0.015   0.002   TYR B 143 
 PHE   0.059   0.003   PHE A 262 
 TRP   0.014   0.002   TRP A  48 
 HIS   0.010   0.003   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00860 ( 7936)
  covalent geometry    : angle       1.11218 (10832)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.96212 (    4)
  hydrogen bonds       : bond        0.14790 (  448)
  hydrogen bonds       : angle       6.81052 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  212 ASP cc_start: 0.6573 (m-30) cc_final: 0.6370 (m-30)
REVERT: B  212 ASP cc_start: 0.6572 (m-30) cc_final: 0.6366 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0670
  time to fit residues: 9.5782
Evaluate side-chains
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 ASN
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.176063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.151422 restraints weight = 7330.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 1.35
r_work: 0.3720 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7938  Z= 0.177
  Angle     :  0.681   8.186  10836  Z= 0.357
  Chirality :  0.045   0.164   1282
  Planarity :  0.007   0.062   1346
  Dihedral  :  7.800  85.977   1108
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.31 %
    Favored  : 90.74 %
  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: -1.42 (0.25), residues: 1002
  helix: -0.61 (0.18), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.37 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 529 
 TYR   0.010   0.001   TYR B 481 
 PHE   0.021   0.002   PHE A 262 
 TRP   0.004   0.001   TRP A 146 
 HIS   0.006   0.002   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7936)
  covalent geometry    : angle       0.68037 (10832)
  SS BOND              : bond        0.00091 (    2)
  SS BOND              : angle       1.27972 (    4)
  hydrogen bonds       : bond        0.05605 (  448)
  hydrogen bonds       : angle       4.86376 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6618 (mmm) cc_final: 0.6137 (mmm)
REVERT: B  148 MET cc_start: 0.6607 (mmm) cc_final: 0.6136 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 100
  average time/residue: 0.0689
  time to fit residues: 10.2027
Evaluate side-chains
  98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.3993 r_free = 0.3993 target = 0.171260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.146663 restraints weight = 7387.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.34
r_work: 0.3682 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3551 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7938  Z= 0.224
  Angle     :  0.699   7.916  10836  Z= 0.364
  Chirality :  0.048   0.185   1282
  Planarity :  0.006   0.056   1346
  Dihedral  :  7.815  81.312   1108
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.88 %
    Favored  : 86.46 %
  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: -0.99 (0.26), residues: 1002
  helix: -0.24 (0.19), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.31 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 529 
 TYR   0.011   0.001   TYR A 481 
 PHE   0.020   0.002   PHE A 207 
 TRP   0.005   0.001   TRP A 534 
 HIS   0.004   0.002   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 7936)
  covalent geometry    : angle       0.69881 (10832)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       1.15955 (    4)
  hydrogen bonds       : bond        0.05674 (  448)
  hydrogen bonds       : angle       4.73956 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6645 (mmm) cc_final: 0.6170 (mmm)
REVERT: A  434 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7751 (mp)
REVERT: B  148 MET cc_start: 0.6631 (mmm) cc_final: 0.6167 (mmm)
REVERT: B  434 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7763 (mp)
  outliers start: 14
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0673
  time to fit residues: 10.4363
Evaluate side-chains
  98 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0980
   chunk 81 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 92 optimal weight:    0.0870
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4064 r_free = 0.4064 target = 0.178615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154559 restraints weight = 7333.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 1.34
r_work: 0.3750 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7938  Z= 0.140
  Angle     :  0.607   7.147  10836  Z= 0.314
  Chirality :  0.044   0.156   1282
  Planarity :  0.006   0.053   1346
  Dihedral  :  7.299  83.850   1108
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.83 %
    Favored  : 84.80 %
  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: -0.31 (0.26), residues: 1002
  helix:  0.38 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.27 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 236 
 TYR   0.010   0.001   TYR B 481 
 PHE   0.010   0.001   PHE A 207 
 TRP   0.005   0.001   TRP B 134 
 HIS   0.003   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7936)
  covalent geometry    : angle       0.60660 (10832)
  SS BOND              : bond        0.00041 (    2)
  SS BOND              : angle       1.01102 (    4)
  hydrogen bonds       : bond        0.04856 (  448)
  hydrogen bonds       : angle       4.43230 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6510 (mmm) cc_final: 0.6109 (mmm)
REVERT: A  480 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7069 (m-40)
REVERT: B  148 MET cc_start: 0.6467 (mmm) cc_final: 0.6086 (mmm)
REVERT: B  480 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7049 (m-40)
  outliers start: 20
  outliers final: 10
  residues processed: 98
  average time/residue: 0.0568
  time to fit residues: 8.4975
Evaluate side-chains
  90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  559 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.0770
   chunk 42 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 92 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4033 r_free = 0.4033 target = 0.175923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.151603 restraints weight = 7380.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.34
r_work: 0.3739 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7938  Z= 0.165
  Angle     :  0.623   7.202  10836  Z= 0.322
  Chirality :  0.046   0.173   1282
  Planarity :  0.006   0.051   1346
  Dihedral  :  7.252  81.348   1108
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.96 %
    Favored  : 83.14 %
  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: -0.14 (0.27), residues: 1002
  helix:  0.51 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.21 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 529 
 TYR   0.009   0.001   TYR B 481 
 PHE   0.014   0.001   PHE B 207 
 TRP   0.003   0.001   TRP B 146 
 HIS   0.003   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7936)
  covalent geometry    : angle       0.62260 (10832)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       1.31083 (    4)
  hydrogen bonds       : bond        0.05064 (  448)
  hydrogen bonds       : angle       4.45305 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6470 (mmm) cc_final: 0.6071 (mmm)
REVERT: A  434 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: B  148 MET cc_start: 0.6464 (mmm) cc_final: 0.6079 (mmm)
REVERT: B  434 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7716 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0596
  time to fit residues: 8.7495
Evaluate side-chains
  90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0070
   chunk 53 optimal weight:    0.0370
   chunk 73 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0570
   chunk 82 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0050
   chunk 39 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.1208

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4117 r_free = 0.4117 target = 0.184556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.160625 restraints weight = 7234.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 1.33
r_work: 0.3828 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7938  Z= 0.121
  Angle     :  0.573   6.604  10836  Z= 0.295
  Chirality :  0.043   0.159   1282
  Planarity :  0.005   0.051   1346
  Dihedral  :  6.671  82.418   1108
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.73 %
    Favored  : 83.14 %
  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:  0.22 (0.27), residues: 1002
  helix:  0.82 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.009   0.001   TYR B 481 
 PHE   0.009   0.001   PHE B 566 
 TRP   0.005   0.001   TRP A 134 
 HIS   0.003   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7936)
  covalent geometry    : angle       0.57263 (10832)
  SS BOND              : bond        0.00003 (    2)
  SS BOND              : angle       1.07752 (    4)
  hydrogen bonds       : bond        0.04513 (  448)
  hydrogen bonds       : angle       4.25761 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6314 (mmm) cc_final: 0.6005 (mmm)
REVERT: A  168 MET cc_start: 0.7776 (mmm) cc_final: 0.7536 (mmm)
REVERT: A  434 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7592 (mp)
REVERT: A  480 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6980 (m-40)
REVERT: B  148 MET cc_start: 0.6274 (mmm) cc_final: 0.5983 (mmm)
REVERT: B  168 MET cc_start: 0.7775 (mmm) cc_final: 0.7534 (mmm)
REVERT: B  434 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7595 (mp)
REVERT: B  480 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6976 (m-40)
  outliers start: 18
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0663
  time to fit residues: 9.9344
Evaluate side-chains
  90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0070
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 76 optimal weight:    0.3980
   chunk 80 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4054 r_free = 0.4054 target = 0.179501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155337 restraints weight = 7303.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.35
r_work: 0.3786 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7938  Z= 0.143
  Angle     :  0.593   6.919  10836  Z= 0.307
  Chirality :  0.045   0.181   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  6.775  78.039   1108
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.39 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.27), residues: 1002
  helix:  0.93 (0.20), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.09 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 529 
 TYR   0.008   0.001   TYR B 481 
 PHE   0.012   0.001   PHE B 207 
 TRP   0.005   0.001   TRP A 534 
 HIS   0.003   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7936)
  covalent geometry    : angle       0.59301 (10832)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       1.16093 (    4)
  hydrogen bonds       : bond        0.04737 (  448)
  hydrogen bonds       : angle       4.25424 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7281 (mt0)
REVERT: A  148 MET cc_start: 0.6323 (mmm) cc_final: 0.6019 (mmm)
REVERT: A  168 MET cc_start: 0.7731 (mmm) cc_final: 0.7501 (mmm)
REVERT: A  434 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7636 (mp)
REVERT: A  480 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7012 (m-40)
REVERT: B  104 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7299 (mt0)
REVERT: B  148 MET cc_start: 0.6288 (mmm) cc_final: 0.5996 (mmm)
REVERT: B  168 MET cc_start: 0.7740 (mmm) cc_final: 0.7511 (mmm)
REVERT: B  434 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7645 (mp)
REVERT: B  480 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7017 (m-40)
  outliers start: 20
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0616
  time to fit residues: 9.6025
Evaluate side-chains
  96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.3997 r_free = 0.3997 target = 0.173577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149203 restraints weight = 7395.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.33
r_work: 0.3682 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7938  Z= 0.187
  Angle     :  0.638   7.224  10836  Z= 0.331
  Chirality :  0.046   0.179   1282
  Planarity :  0.006   0.054   1346
  Dihedral  :  7.166  78.074   1108
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.39 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.27), residues: 1002
  helix:  0.80 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.08 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 529 
 TYR   0.008   0.001   TYR B 481 
 PHE   0.017   0.001   PHE B 207 
 TRP   0.004   0.001   TRP B 534 
 HIS   0.003   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7936)
  covalent geometry    : angle       0.63793 (10832)
  SS BOND              : bond        0.00008 (    2)
  SS BOND              : angle       0.98121 (    4)
  hydrogen bonds       : bond        0.05150 (  448)
  hydrogen bonds       : angle       4.44699 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7399 (mt0)
REVERT: A  148 MET cc_start: 0.6339 (mmm) cc_final: 0.6075 (mmm)
REVERT: A  168 MET cc_start: 0.7802 (mmm) cc_final: 0.7574 (mmm)
REVERT: A  434 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: A  480 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (m-40)
REVERT: B  104 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7416 (mt0)
REVERT: B  148 MET cc_start: 0.6332 (mmm) cc_final: 0.6069 (mmm)
REVERT: B  168 MET cc_start: 0.7811 (mmm) cc_final: 0.7589 (mmm)
REVERT: B  434 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7730 (mp)
REVERT: B  480 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7081 (m-40)
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.0564
  time to fit residues: 10.0387
Evaluate side-chains
  110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4024 r_free = 0.4024 target = 0.174699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.150340 restraints weight = 7369.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.34
r_work: 0.3682 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7938  Z= 0.178
  Angle     :  0.631   7.130  10836  Z= 0.325
  Chirality :  0.046   0.174   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  7.194  79.687   1108
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.91 %
    Favored  : 81.71 %
  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:  0.19 (0.27), residues: 1002
  helix:  0.77 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.11 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 529 
 TYR   0.008   0.001   TYR B 481 
 PHE   0.014   0.001   PHE B 207 
 TRP   0.006   0.001   TRP B 534 
 HIS   0.003   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 7936)
  covalent geometry    : angle       0.63054 (10832)
  SS BOND              : bond        0.00024 (    2)
  SS BOND              : angle       1.12435 (    4)
  hydrogen bonds       : bond        0.05063 (  448)
  hydrogen bonds       : angle       4.45958 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7366 (mt0)
REVERT: A  148 MET cc_start: 0.6324 (mmm) cc_final: 0.6093 (mmm)
REVERT: A  168 MET cc_start: 0.7738 (mmm) cc_final: 0.7523 (mmm)
REVERT: A  434 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7719 (mp)
REVERT: A  480 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7099 (m-40)
REVERT: B  104 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7381 (mt0)
REVERT: B  148 MET cc_start: 0.6292 (mmm) cc_final: 0.6073 (mmm)
REVERT: B  168 MET cc_start: 0.7753 (mmm) cc_final: 0.7542 (mmm)
REVERT: B  434 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: B  480 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7084 (m-40)
  outliers start: 20
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0629
  time to fit residues: 10.6718
Evaluate side-chains
  106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0010
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4024 r_free = 0.4024 target = 0.174823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.150607 restraints weight = 7362.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.33
r_work: 0.3687 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7938  Z= 0.171
  Angle     :  0.630   7.110  10836  Z= 0.325
  Chirality :  0.045   0.172   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  7.161  79.692   1108
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.63 %
    Favored  : 81.47 %
  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:  0.22 (0.27), residues: 1002
  helix:  0.80 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.11 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 529 
 TYR   0.008   0.001   TYR A 481 
 PHE   0.013   0.001   PHE B 207 
 TRP   0.007   0.001   TRP B 534 
 HIS   0.003   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 7936)
  covalent geometry    : angle       0.62975 (10832)
  SS BOND              : bond        0.00031 (    2)
  SS BOND              : angle       1.16298 (    4)
  hydrogen bonds       : bond        0.05014 (  448)
  hydrogen bonds       : angle       4.44570 ( 1344)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7374 (mt0)
REVERT: A  148 MET cc_start: 0.6308 (mmm) cc_final: 0.6087 (mmm)
REVERT: A  168 MET cc_start: 0.7722 (mmm) cc_final: 0.7519 (mmm)
REVERT: A  434 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7715 (mp)
REVERT: A  480 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7089 (m-40)
REVERT: B  104 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7394 (mt0)
REVERT: B  148 MET cc_start: 0.6278 (mmm) cc_final: 0.6065 (mmm)
REVERT: B  434 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7722 (mp)
REVERT: B  480 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7076 (m-40)
  outliers start: 16
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0630
  time to fit residues: 10.3074
Evaluate side-chains
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0010
   chunk 96 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0970
   overall best weight:    0.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 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 = 0.4024 r_free = 0.4024 target = 0.176633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152363 restraints weight = 7306.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.34
r_work: 0.3716 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7938  Z= 0.146
  Angle     :  0.605   6.901  10836  Z= 0.312
  Chirality :  0.044   0.166   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  6.970  80.826   1108
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.91 %
    Favored  : 81.71 %
  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:  0.33 (0.27), residues: 1002
  helix:  0.86 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.09 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 529 
 TYR   0.009   0.001   TYR B 481 
 PHE   0.010   0.001   PHE B 207 
 TRP   0.008   0.001   TRP B 534 
 HIS   0.003   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7936)
  covalent geometry    : angle       0.60447 (10832)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       1.17216 (    4)
  hydrogen bonds       : bond        0.04796 (  448)
  hydrogen bonds       : angle       4.36409 ( 1344)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1864.67 seconds
wall clock time: 32 minutes 51.03 seconds (1971.03 seconds total)