Starting phenix.real_space_refine
on Wed Mar 12 11:11:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ytw_34094/03_2025/7ytw_34094.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ytw_34094/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ytw_34094/03_2025/7ytw_34094.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ytw_34094/03_2025/7ytw_34094.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ytw_34094/03_2025/7ytw_34094.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ytw_34094/03_2025/7ytw_34094.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.20, per 1000 atoms: 1.06
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.64
  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: 2.21

  Time building geometry restraints manager: 2.33 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: 0.08
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:             4.730
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.470
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.140
-------------------------------------------------------------------------------
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   7936  Z= 0.560
  Angle     :  1.112   9.372  10832  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.014   0.002   TRP A  48 
 HIS   0.010   0.003   HIS A 157 
 PHE   0.059   0.003   PHE A 262 
 TYR   0.015   0.002   TYR B 143 
 ARG   0.007   0.001   ARG B 463 

*********************** 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  : 0.809 
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: 0.1697
  time to fit residues: 24.3129
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  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0000
   chunk 42 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0000
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.2386

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.180498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.156861 restraints weight = 7211.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.28
r_work: 0.3775 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7936  Z= 0.207
  Angle     :  0.643   8.007  10832  Z= 0.337
  Chirality :  0.044   0.152   1282
  Planarity :  0.007   0.061   1346
  Dihedral  :  7.573  86.904   1108
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  7.36 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.26), residues: 1002
  helix: -0.50 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -1.29 (0.37), residues: 326

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

*********************** 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
  94 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6582 (mmm) cc_final: 0.6148 (mmm)
REVERT: B  148 MET cc_start: 0.6558 (mmm) cc_final: 0.6136 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 90
  average time/residue: 0.1520
  time to fit residues: 20.9549
Evaluate side-chains
  86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.175084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150152 restraints weight = 7468.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.37
r_work: 0.3707 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7936  Z= 0.293
  Angle     :  0.657   7.757  10832  Z= 0.342
  Chirality :  0.047   0.177   1282
  Planarity :  0.006   0.054   1346
  Dihedral  :  7.476  82.030   1108
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.21 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.26), residues: 1002
  helix:  0.02 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.40 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 534 
 HIS   0.004   0.001   HIS A 157 
 PHE   0.016   0.002   PHE A 262 
 TYR   0.010   0.001   TYR B 481 
 ARG   0.002   0.000   ARG A 529 

*********************** 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
  110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6533 (mmm) cc_final: 0.6117 (mmm)
REVERT: B  148 MET cc_start: 0.6528 (mmm) cc_final: 0.6119 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1439
  time to fit residues: 23.8026
Evaluate side-chains
  100 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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 B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  281 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 13 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.177563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153200 restraints weight = 7326.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 1.35
r_work: 0.3740 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7936  Z= 0.230
  Angle     :  0.613   7.298  10832  Z= 0.318
  Chirality :  0.045   0.166   1282
  Planarity :  0.006   0.051   1346
  Dihedral  :  7.142  82.583   1108
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.59 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 1002
  helix:  0.37 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.27 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 134 
 HIS   0.003   0.001   HIS A 157 
 PHE   0.013   0.001   PHE A 207 
 TYR   0.009   0.001   TYR B 481 
 ARG   0.002   0.000   ARG B 529 

*********************** 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
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6509 (mmm) cc_final: 0.6149 (mmm)
REVERT: A  434 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7718 (mp)
REVERT: B  148 MET cc_start: 0.6504 (mmm) cc_final: 0.6157 (mmm)
REVERT: B  434 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7718 (mp)
  outliers start: 18
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1548
  time to fit residues: 23.6265
Evaluate side-chains
  92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
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  434 ILE
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  434 ILE
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 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.147747 restraints weight = 7430.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.34
r_work: 0.3676 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7936  Z= 0.334
  Angle     :  0.668   7.458  10832  Z= 0.346
  Chirality :  0.047   0.189   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  7.381  80.148   1108
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.25 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.26), residues: 1002
  helix:  0.31 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.32 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 309 
 HIS   0.003   0.001   HIS A 361 
 PHE   0.018   0.002   PHE A 207 
 TYR   0.009   0.001   TYR B 481 
 ARG   0.003   0.000   ARG A 529 

*********************** 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
  108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6519 (mmm) cc_final: 0.6112 (mmm)
REVERT: A  434 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7732 (mp)
REVERT: A  480 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7157 (m-40)
REVERT: B  148 MET cc_start: 0.6513 (mmm) cc_final: 0.6116 (mmm)
REVERT: B  434 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: B  480 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7150 (m-40)
  outliers start: 18
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1360
  time to fit residues: 23.1917
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  : 0.755 
-------------------------------------------------------------------------------
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  206 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 60 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.175796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.151472 restraints weight = 7335.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 1.33
r_work: 0.3722 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7936  Z= 0.247
  Angle     :  0.613   7.015  10832  Z= 0.318
  Chirality :  0.045   0.173   1282
  Planarity :  0.006   0.051   1346
  Dihedral  :  7.125  81.837   1108
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.01 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.27), residues: 1002
  helix:  0.51 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.16 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 134 
 HIS   0.003   0.001   HIS A 157 
 PHE   0.013   0.001   PHE A 207 
 TYR   0.009   0.001   TYR B 481 
 ARG   0.002   0.000   ARG A 529 

*********************** 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
  96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 1.666 
Fit side-chains
REVERT: A  148 MET cc_start: 0.6390 (mmm) cc_final: 0.6029 (mmm)
REVERT: A  168 MET cc_start: 0.7800 (mmm) cc_final: 0.7480 (mmm)
REVERT: A  434 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7718 (mp)
REVERT: A  480 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7115 (m-40)
REVERT: B  148 MET cc_start: 0.6341 (mmm) cc_final: 0.6007 (mmm)
REVERT: B  168 MET cc_start: 0.7815 (mmm) cc_final: 0.7494 (mmm)
REVERT: B  434 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: B  480 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7115 (m-40)
  outliers start: 18
  outliers final: 10
  residues processed: 94
  average time/residue: 0.2584
  time to fit residues: 39.3698
Evaluate side-chains
  90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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  320 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
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  320 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 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 = 0.4014 r_free = 0.4014 target = 0.173352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148877 restraints weight = 7406.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.35
r_work: 0.3689 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7936  Z= 0.297
  Angle     :  0.645   7.186  10832  Z= 0.333
  Chirality :  0.046   0.179   1282
  Planarity :  0.006   0.053   1346
  Dihedral  :  7.225  80.873   1108
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.73 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.27), residues: 1002
  helix:  0.48 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 146 
 HIS   0.003   0.001   HIS A 217 
 PHE   0.017   0.001   PHE A 207 
 TYR   0.009   0.001   TYR A 481 
 ARG   0.002   0.000   ARG A 529 

*********************** 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
  106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7347 (mt0)
REVERT: A  148 MET cc_start: 0.6397 (mmm) cc_final: 0.6051 (mmm)
REVERT: A  434 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7729 (mp)
REVERT: A  480 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7145 (m-40)
REVERT: B  104 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7361 (mt0)
REVERT: B  148 MET cc_start: 0.6390 (mmm) cc_final: 0.6054 (mmm)
REVERT: B  434 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7741 (mp)
REVERT: B  480 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7140 (m-40)
  outliers start: 20
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1314
  time to fit residues: 22.1845
Evaluate side-chains
  102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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  206 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
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  206 VAL
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0970
   chunk 68 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.176109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.151569 restraints weight = 7375.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.36
r_work: 0.3727 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7936  Z= 0.238
  Angle     :  0.609   6.913  10832  Z= 0.315
  Chirality :  0.045   0.172   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  7.032  81.659   1108
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.68 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.27), residues: 1002
  helix:  0.65 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.12 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 134 
 HIS   0.004   0.001   HIS A 157 
 PHE   0.013   0.001   PHE A 207 
 TYR   0.009   0.001   TYR A 481 
 ARG   0.001   0.000   ARG A 529 

*********************** 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
  96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7371 (mt0)
REVERT: A  148 MET cc_start: 0.6379 (mmm) cc_final: 0.6079 (mmm)
REVERT: A  168 MET cc_start: 0.7840 (mmm) cc_final: 0.7545 (mmm)
REVERT: A  434 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7722 (mp)
REVERT: A  480 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7090 (m-40)
REVERT: B  104 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7378 (mt0)
REVERT: B  148 MET cc_start: 0.6362 (mmm) cc_final: 0.6078 (mmm)
REVERT: B  168 MET cc_start: 0.7861 (mmm) cc_final: 0.7571 (mmm)
REVERT: B  434 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7729 (mp)
REVERT: B  480 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7091 (m-40)
  outliers start: 18
  outliers final: 12
  residues processed: 96
  average time/residue: 0.2982
  time to fit residues: 43.4274
Evaluate side-chains
  92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 1.624 
-------------------------------------------------------------------------------
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  206 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
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  206 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0870
   chunk 94 optimal weight:    0.7980
   chunk 85 optimal weight:    0.1980
   chunk 43 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.178515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.154064 restraints weight = 7396.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 1.36
r_work: 0.3752 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7936  Z= 0.220
  Angle     :  0.596   6.818  10832  Z= 0.307
  Chirality :  0.044   0.173   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  6.861  81.131   1108
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.27), residues: 1002
  helix:  0.82 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.08 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 534 
 HIS   0.004   0.001   HIS A 157 
 PHE   0.011   0.001   PHE B 207 
 TYR   0.009   0.001   TYR A 481 
 ARG   0.001   0.000   ARG A 529 

*********************** 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
  96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7365 (mt0)
REVERT: A  148 MET cc_start: 0.6304 (mmm) cc_final: 0.6066 (mmm)
REVERT: A  168 MET cc_start: 0.7777 (mmm) cc_final: 0.7514 (mmm)
REVERT: A  434 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: A  480 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7059 (m-40)
REVERT: B  104 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7381 (mt0)
REVERT: B  148 MET cc_start: 0.6293 (mmm) cc_final: 0.6065 (mmm)
REVERT: B  168 MET cc_start: 0.7817 (mmm) cc_final: 0.7554 (mmm)
REVERT: B  434 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: B  480 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7039 (m-40)
  outliers start: 22
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1583
  time to fit residues: 23.1676
Evaluate side-chains
  92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
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  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain B residue   63 PHE
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  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0050
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.173503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.150920 restraints weight = 7419.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.18
r_work: 0.3698 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7936  Z= 0.291
  Angle     :  0.638   7.089  10832  Z= 0.330
  Chirality :  0.047   0.232   1282
  Planarity :  0.006   0.053   1346
  Dihedral  :  7.106  80.789   1108
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.27), residues: 1002
  helix:  0.68 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.12 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 534 
 HIS   0.004   0.001   HIS B 157 
 PHE   0.017   0.001   PHE B 207 
 TYR   0.008   0.001   TYR A 481 
 ARG   0.002   0.000   ARG A 529 

********************** 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
  112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7370 (mt0)
REVERT: A  148 MET cc_start: 0.6287 (mmm) cc_final: 0.6069 (mmm)
REVERT: A  168 MET cc_start: 0.7906 (mmm) cc_final: 0.7657 (mmm)
REVERT: A  434 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7712 (mp)
REVERT: A  480 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7128 (m-40)
REVERT: B  104 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7384 (mt0)
REVERT: B  148 MET cc_start: 0.6268 (mmm) cc_final: 0.6056 (mmm)
REVERT: B  168 MET cc_start: 0.7922 (mmm) cc_final: 0.7678 (mmm)
REVERT: B  434 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: B  480 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7116 (m-40)
  outliers start: 22
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1486
  time to fit residues: 25.0828
Evaluate side-chains
  108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
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  206 VAL
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  480 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   63 PHE
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  206 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  480 ASN
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.170219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145440 restraints weight = 7445.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.35
r_work: 0.3679 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7936  Z= 0.335
  Angle     :  0.672   7.303  10832  Z= 0.347
  Chirality :  0.048   0.217   1282
  Planarity :  0.006   0.052   1346
  Dihedral  :  7.380  81.765   1108
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.68 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.27), residues: 1002
  helix:  0.52 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.20 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 534 
 HIS   0.004   0.001   HIS A 157 
 PHE   0.019   0.002   PHE B 207 
 TYR   0.008   0.001   TYR A 481 
 ARG   0.002   0.000   ARG A 463 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4636.28 seconds
wall clock time: 84 minutes 8.28 seconds (5048.28 seconds total)