Starting phenix.real_space_refine
on Thu Mar  6 03:20:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu5_21387/03_2025/6vu5_21387.cif"
  }
  resolution = 3.5
  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=   0.006
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
     P       2      5.49       5
     S      25      5.16       5
     C    2961      2.51       5
     N     815      2.21       5
     O     854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 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: 4657
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3454
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 14, 'TRANS': 426}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'TPO:plan-1': 1, 'ARG:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 53
    Chain: "A"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 135
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'TRANS': 26}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'UNK:plan-1': 27}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 1068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1068
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 130}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 3.32, per 1000 atoms: 0.71
  Number of scatterers: 4657
  At special positions: 0
  Unit cell: (109.06, 58.22, 83.64, 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      25     16.00
     P       2     15.00
     O     854      8.00
     N     815      7.00
     C    2961      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 565.6 milliseconds
  

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1168

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 2 sheets defined
      58.3% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
      removed outlier: 3.771A  pdb=" N   ASP A   8 " --> pdb=" O   ARG A   4 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A  12 " --> pdb=" O   ASP A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 29
      removed outlier: 4.285A  pdb=" N   ARG A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 39 through 57
      removed outlier: 3.740A  pdb=" N   GLN A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 6.287A  pdb=" N   SER A  78 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A  80 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 75 through 80'
    Processing helix  chain 'A' and resid 85 through 96
      removed outlier: 3.759A  pdb=" N   LEU A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 127
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 3.727A  pdb=" N   MET A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 150
      removed outlier: 4.474A  pdb=" N   GLU A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 174
      removed outlier: 3.643A  pdb=" N   GLN A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.592A  pdb=" N   LEU A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 232
    Processing helix  chain 'A' and resid 242 through 260
      removed outlier: 4.121A  pdb=" N   MET A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 280
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.676A  pdb=" N   LEU A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 320
    Processing helix  chain 'A' and resid 332 through 341
      removed outlier: 4.586A  pdb=" N   THR A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 356
    Processing helix  chain 'A' and resid 371 through 380
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 389 through 398
      removed outlier: 4.516A  pdb=" N   LEU A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 413 through 417
      removed outlier: 3.672A  pdb=" N   ALA A 416 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 417 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 413 through 417'
    Processing helix  chain 'A' and resid 474 through 483
    Processing helix  chain 'B' and resid 246 through 255
    Processing helix  chain 'B' and resid 255 through 260
      removed outlier: 3.817A  pdb=" N   ILE B 259 " --> pdb=" O   PHE B 255 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 255 through 260'
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 287 through 291
      removed outlier: 4.149A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 315
    Processing helix  chain 'B' and resid 338 through 354
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212
    Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 272
      removed outlier: 6.660A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   HIS B 327 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 271 " --> pdb=" O   HIS B 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    193 hydrogen bonds defined for protein.
    567 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: 1.04

  Time building geometry restraints manager: 1.33 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: 1329
        1.33 -     1.45: 735
        1.45 -     1.57: 2621
        1.57 -     1.69: 7
        1.69 -     1.81: 39
  Bond restraints: 4731
  Sorted by residual:
  bond pdb=" OG1 TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" O3P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" O2P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" O1P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.525  1.476  0.049 2.00e-02 2.50e+03 6.08e+00
  bond pdb=" CB  VAL A 275 "
       pdb=" CG1 VAL A 275 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.41e+00
  ... (remaining 4726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 6213
        2.50 -     4.99: 166
        4.99 -     7.49: 21
        7.49 -     9.99: 9
        9.99 -    12.49: 1
  Bond angle restraints: 6410
  Sorted by residual:
  angle pdb=" CB  TPO A 440 "
        pdb=" OG1 TPO A 440 "
        pdb=" P   TPO A 440 "
      ideal   model   delta    sigma   weight residual
     119.31  106.82   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" C   VAL B 223 "
        pdb=" N   THR B 224 "
        pdb=" CA  THR B 224 "
      ideal   model   delta    sigma   weight residual
     121.54  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" OG1 TPO A 440 "
        pdb=" P   TPO A 440 "
        pdb=" O1P TPO A 440 "
      ideal   model   delta    sigma   weight residual
     100.43  109.19   -8.76 3.00e+00 1.11e-01 8.52e+00
  angle pdb=" CA  LEU A 278 "
        pdb=" CB  LEU A 278 "
        pdb=" CG  LEU A 278 "
      ideal   model   delta    sigma   weight residual
     116.30  126.28   -9.98 3.50e+00 8.16e-02 8.14e+00
  angle pdb=" C   ILE B 337 "
        pdb=" N   ARG B 338 "
        pdb=" CA  ARG B 338 "
      ideal   model   delta    sigma   weight residual
     122.61  126.88   -4.27 1.56e+00 4.11e-01 7.51e+00
  ... (remaining 6405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 2527
       17.08 -    34.16: 277
       34.16 -    51.24: 61
       51.24 -    68.32: 10
       68.32 -    85.40: 3
  Dihedral angle restraints: 2878
    sinusoidal: 1100
      harmonic: 1778
  Sorted by residual:
  dihedral pdb=" CA  PRO A 358 "
           pdb=" C   PRO A 358 "
           pdb=" N   LEU A 359 "
           pdb=" CA  LEU A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.71  -29.29     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  LEU A 395 "
           pdb=" C   LEU A 395 "
           pdb=" N   PHE A 396 "
           pdb=" CA  PHE A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.40   25.60     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  LEU A 334 "
           pdb=" C   LEU A 334 "
           pdb=" N   SER A 335 "
           pdb=" CA  SER A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 2875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 712
       0.100 -    0.199: 47
       0.199 -    0.299: 2
       0.299 -    0.399: 0
       0.399 -    0.499: 1
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CB  ILE B 337 "
            pdb=" CA  ILE B 337 "
            pdb=" CG1 ILE B 337 "
            pdb=" CG2 ILE B 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.15    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  VAL A 355 "
            pdb=" CA  VAL A 355 "
            pdb=" CG1 VAL A 355 "
            pdb=" CG2 VAL A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 759 not shown)

  Planarity restraints: 818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 261 "    0.048 5.00e-02 4.00e+02   7.33e-02 8.59e+00
        pdb=" N   PRO B 262 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 262 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 262 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 156 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO A 157 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 331 "   -0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 332 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 815 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 839
        2.76 -     3.30: 4361
        3.30 -     3.83: 7693
        3.83 -     4.37: 8746
        4.37 -     4.90: 14932
  Nonbonded interactions: 36571
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 168 "
            pdb=" OG1 THR A 172 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   LEU A 227 "
            pdb=" OG1 THR A 231 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   PRO A 213 "
            pdb=" OG1 THR A 217 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   LEU A 281 "
            pdb=" NH2 ARG B 338 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" ND2 ASN B 266 "
            pdb=" O   SER B 268 "
     model   vdw
     2.372 3.120
  ... (remaining 36566 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.270
  Find NCS groups from input model:        0.040
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.109   4731  Z= 0.437
  Angle     :  0.990  12.485   6410  Z= 0.505
  Chirality :  0.056   0.499    762
  Planarity :  0.007   0.073    818
  Dihedral  : 15.263  85.402   1710
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -4.94 (0.26), residues: 556
  helix: -3.14 (0.20), residues: 331
  sheet: -1.07 (1.45), residues: 12
  loop : -3.43 (0.34), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 263 
 HIS   0.008   0.002   HIS A 158 
 PHE   0.029   0.002   PHE A 270 
 TYR   0.013   0.002   TYR B 235 
 ARG   0.004   0.001   ARG A  43 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7825 (mt) cc_final: 0.7516 (mt)
REVERT: A  150 LEU cc_start: 0.8718 (tp) cc_final: 0.8432 (tt)
REVERT: A  180 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6799 (mm110)
REVERT: A  257 CYS cc_start: 0.7732 (t) cc_final: 0.7320 (t)
REVERT: A  306 MET cc_start: 0.8405 (mmt) cc_final: 0.7749 (mmt)
REVERT: B  249 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6754 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1613
  time to fit residues: 25.6079
Evaluate side-chains
  79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0270
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6842

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
A 180 GLN
A 184 GLN
A 414 ASN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.172837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.141436 restraints weight = 6640.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.145633 restraints weight = 3991.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148485 restraints weight = 2869.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4731  Z= 0.208
  Angle     :  0.641   8.876   6410  Z= 0.320
  Chirality :  0.040   0.156    762
  Planarity :  0.005   0.045    818
  Dihedral  :  5.843  26.445    655
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.34 %
    Favored  : 80.88 %
  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: -3.52 (0.31), residues: 556
  helix: -1.94 (0.25), residues: 331
  sheet:  None (None), residues: 0
  loop : -2.83 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.019   0.002   HIS A  62 
 PHE   0.020   0.001   PHE A 270 
 TYR   0.008   0.001   TYR A 445 
 ARG   0.008   0.000   ARG A 345 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8668 (tp) cc_final: 0.8238 (tt)
REVERT: A  151 TYR cc_start: 0.6400 (m-10) cc_final: 0.5907 (m-10)
REVERT: A  306 MET cc_start: 0.8282 (mmt) cc_final: 0.7824 (mmt)
REVERT: B  249 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6763 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1557
  time to fit residues: 20.9043
Evaluate side-chains
  88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0030
   chunk 44 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.175358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.144093 restraints weight = 6627.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148347 restraints weight = 3939.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.151142 restraints weight = 2820.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4731  Z= 0.186
  Angle     :  0.609  10.026   6410  Z= 0.302
  Chirality :  0.039   0.165    762
  Planarity :  0.004   0.034    818
  Dihedral  :  5.351  26.998    655
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.86 %
    Favored  : 78.57 %
  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: -2.98 (0.33), residues: 556
  helix: -1.46 (0.27), residues: 337
  sheet:  0.01 (1.59), residues: 14
  loop : -2.88 (0.38), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 158 
 PHE   0.019   0.001   PHE A 270 
 TYR   0.015   0.001   TYR A 445 
 ARG   0.004   0.000   ARG A 345 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.8360 (tpt90) cc_final: 0.8066 (tpt90)
REVERT: A  150 LEU cc_start: 0.8621 (tp) cc_final: 0.8206 (tt)
REVERT: A  151 TYR cc_start: 0.6348 (m-10) cc_final: 0.5824 (m-10)
REVERT: B  249 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6701 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1692
  time to fit residues: 21.9825
Evaluate side-chains
  89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0770
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0010
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5346

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

Flipped N/Q/H residues before XYZ refinement:
A 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.177414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.146337 restraints weight = 6727.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.150656 restraints weight = 4002.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.153596 restraints weight = 2855.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4731  Z= 0.190
  Angle     :  0.663  10.214   6410  Z= 0.316
  Chirality :  0.040   0.186    762
  Planarity :  0.004   0.035    818
  Dihedral  :  5.121  26.745    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.33 %
    Favored  : 76.68 %
  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: -2.61 (0.33), residues: 556
  helix: -1.16 (0.27), residues: 335
  sheet: -0.19 (1.54), residues: 14
  loop : -2.71 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.015   0.001   TYR A  95 
 ARG   0.003   0.000   ARG A 345 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.8387 (tpt90) cc_final: 0.8149 (tpt90)
REVERT: A  150 LEU cc_start: 0.8562 (tp) cc_final: 0.8148 (tt)
REVERT: A  151 TYR cc_start: 0.6400 (m-10) cc_final: 0.5747 (m-10)
REVERT: A  380 MET cc_start: 0.8295 (ttm) cc_final: 0.8017 (ttt)
REVERT: B  227 MET cc_start: 0.3717 (ppp) cc_final: 0.1820 (mtm)
  outliers start: 19
  outliers final: 15
  residues processed: 94
  average time/residue: 0.1775
  time to fit residues: 21.1381
Evaluate side-chains
  89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.0010
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.178367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.149018 restraints weight = 6642.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.153061 restraints weight = 4018.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.155826 restraints weight = 2867.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4731  Z= 0.182
  Angle     :  0.628  11.859   6410  Z= 0.302
  Chirality :  0.039   0.142    762
  Planarity :  0.004   0.032    818
  Dihedral  :  4.948  27.162    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.75 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.40 (0.34), residues: 556
  helix: -0.94 (0.27), residues: 335
  sheet: -0.42 (1.49), residues: 14
  loop : -2.68 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 263 
 HIS   0.003   0.001   HIS A 158 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.019   0.001   TYR A  95 
 ARG   0.002   0.000   ARG A 345 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8629 (tp) cc_final: 0.8228 (tt)
REVERT: A  151 TYR cc_start: 0.6397 (m-10) cc_final: 0.5814 (m-10)
REVERT: B  227 MET cc_start: 0.3657 (ppp) cc_final: 0.1262 (mtm)
  outliers start: 20
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1845
  time to fit residues: 22.8141
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0370
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 3 optimal weight:    0.1980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.179999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.149194 restraints weight = 6865.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.153635 restraints weight = 4137.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.156506 restraints weight = 2964.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.174
  Angle     :  0.626  11.480   6410  Z= 0.300
  Chirality :  0.039   0.145    762
  Planarity :  0.004   0.032    818
  Dihedral  :  4.785  27.469    655
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.33 %
    Favored  : 76.26 %
  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: -2.11 (0.34), residues: 556
  helix: -0.66 (0.28), residues: 328
  sheet: -0.52 (1.45), residues: 14
  loop : -2.58 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.015   0.001   TYR A  95 
 ARG   0.007   0.000   ARG A  63 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8612 (tp) cc_final: 0.8308 (tt)
REVERT: A  151 TYR cc_start: 0.6373 (m-10) cc_final: 0.5686 (m-10)
REVERT: A  380 MET cc_start: 0.8199 (ttm) cc_final: 0.7977 (ttt)
  outliers start: 21
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1593
  time to fit residues: 20.0369
Evaluate side-chains
  94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    0.0060
   chunk 48 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 45 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 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 = 0.4231 r_free = 0.4231 target = 0.180346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.151341 restraints weight = 6680.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.155403 restraints weight = 4024.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.158139 restraints weight = 2879.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.178
  Angle     :  0.678  12.101   6410  Z= 0.316
  Chirality :  0.040   0.236    762
  Planarity :  0.004   0.034    818
  Dihedral  :  4.677  27.375    655
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.80 %
    Favored  : 75.63 %
  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: -2.06 (0.34), residues: 556
  helix: -0.61 (0.28), residues: 328
  sheet: -0.38 (1.44), residues: 14
  loop : -2.59 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.025   0.001   TYR A  95 
 ARG   0.006   0.000   ARG A  63 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A   10 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5404 (tp)
REVERT: A  150 LEU cc_start: 0.8652 (tp) cc_final: 0.8358 (tt)
REVERT: A  151 TYR cc_start: 0.6421 (m-10) cc_final: 0.5743 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1553
  time to fit residues: 18.1926
Evaluate side-chains
  94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 44 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.178819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.149332 restraints weight = 6650.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.153445 restraints weight = 3989.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.156207 restraints weight = 2850.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4731  Z= 0.201
  Angle     :  0.675  13.125   6410  Z= 0.318
  Chirality :  0.041   0.216    762
  Planarity :  0.003   0.032    818
  Dihedral  :  4.705  28.304    655
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.01 %
    Favored  : 74.79 %
  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: -2.00 (0.35), residues: 556
  helix: -0.58 (0.28), residues: 330
  sheet: -0.29 (1.40), residues: 14
  loop : -2.57 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.010   0.001   PHE A 163 
 TYR   0.017   0.001   TYR A  95 
 ARG   0.005   0.000   ARG A  63 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8653 (tp) cc_final: 0.8374 (tt)
REVERT: A  151 TYR cc_start: 0.6422 (m-10) cc_final: 0.5734 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 89
  average time/residue: 0.1631
  time to fit residues: 18.8832
Evaluate side-chains
  96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.170438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.138578 restraints weight = 6863.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142778 restraints weight = 4176.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.145550 restraints weight = 3012.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4731  Z= 0.356
  Angle     :  0.766  13.940   6410  Z= 0.364
  Chirality :  0.045   0.223    762
  Planarity :  0.004   0.031    818
  Dihedral  :  5.310  32.089    655
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.43 %
    Favored  : 75.00 %
  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: -2.34 (0.33), residues: 556
  helix: -0.89 (0.27), residues: 329
  sheet: -0.29 (1.59), residues: 12
  loop : -2.61 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 263 
 HIS   0.018   0.002   HIS A  62 
 PHE   0.016   0.002   PHE B 228 
 TYR   0.019   0.002   TYR A  95 
 ARG   0.005   0.000   ARG A  63 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8712 (tp) cc_final: 0.8296 (tt)
REVERT: A  151 TYR cc_start: 0.6599 (m-10) cc_final: 0.5958 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 87
  average time/residue: 0.1653
  time to fit residues: 18.5340
Evaluate side-chains
  89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0970
   chunk 5 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.0980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.173458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.141993 restraints weight = 6758.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.146127 restraints weight = 4090.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.148917 restraints weight = 2952.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4731  Z= 0.257
  Angle     :  0.730  13.731   6410  Z= 0.345
  Chirality :  0.043   0.237    762
  Planarity :  0.004   0.033    818
  Dihedral  :  5.132  30.219    655
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.27 %
    Favored  : 74.16 %
  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: -2.23 (0.34), residues: 556
  helix: -0.81 (0.28), residues: 326
  sheet: -0.29 (1.46), residues: 14
  loop : -2.55 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 263 
 HIS   0.015   0.001   HIS A  62 
 PHE   0.015   0.001   PHE A 163 
 TYR   0.020   0.002   TYR B 325 
 ARG   0.004   0.000   ARG A  63 

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

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

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1112 Ramachandran restraints generated.
    556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7010 (tpp) cc_final: 0.6781 (tpp)
REVERT: A   10 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5487 (tp)
REVERT: A  150 LEU cc_start: 0.8688 (tp) cc_final: 0.8285 (tt)
REVERT: A  151 TYR cc_start: 0.6446 (m-10) cc_final: 0.5769 (m-10)
REVERT: B  325 TYR cc_start: 0.6469 (m-80) cc_final: 0.6137 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1584
  time to fit residues: 18.1869
Evaluate side-chains
  91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  218 HIS
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0050
   overall best weight:    0.5994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.175800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.144751 restraints weight = 6750.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148941 restraints weight = 4055.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.151639 restraints weight = 2900.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4731  Z= 0.205
  Angle     :  0.712  13.995   6410  Z= 0.335
  Chirality :  0.041   0.227    762
  Planarity :  0.004   0.033    818
  Dihedral  :  4.887  28.587    655
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.48 %
    Favored  : 74.16 %
  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: -2.14 (0.34), residues: 556
  helix: -0.78 (0.28), residues: 328
  sheet: -0.38 (1.40), residues: 14
  loop : -2.43 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 263 
 HIS   0.014   0.001   HIS A  62 
 PHE   0.015   0.001   PHE A 163 
 TYR   0.017   0.002   TYR A  95 
 ARG   0.005   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1808.66 seconds
wall clock time: 32 minutes 2.10 seconds (1922.10 seconds total)