Starting phenix.real_space_refine
on Tue Feb 11 07:34:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu5_21387/02_2025/6vu5_21387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu5_21387/02_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_21387/02_2025/6vu5_21387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu5_21387/02_2025/6vu5_21387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu5_21387/02_2025/6vu5_21387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu5_21387/02_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-5592/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: 3.59, per 1000 atoms: 0.77
  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: 1.24
  Conformation dependent library (CDL) restraints added in 573.7 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: 0.46
  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: 1.16

  Time building geometry restraints manager: 1.43 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:             0.460
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.340
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.950
-------------------------------------------------------------------------------
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  : 0.457 
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: 0.1567
  time to fit residues: 24.4724
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  : 0.476 
-------------------------------------------------------------------------------
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 = 0.172833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.141470 restraints weight = 6638.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.145617 restraints weight = 3981.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148502 restraints weight = 2866.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
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   0.157    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  : 0.547 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8669 (tp) cc_final: 0.8238 (tt)
REVERT: A  151 TYR cc_start: 0.6399 (m-10) cc_final: 0.5906 (m-10)
REVERT: A  306 MET cc_start: 0.8283 (mmt) cc_final: 0.7824 (mmt)
REVERT: B  249 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6763 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1553
  time to fit residues: 20.7324
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  : 0.487 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0870
   overall best weight:    0.7360

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.173219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.141438 restraints weight = 6694.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.145665 restraints weight = 4025.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148504 restraints weight = 2908.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4731  Z= 0.204
  Angle     :  0.617   9.948   6410  Z= 0.307
  Chirality :  0.040   0.166    762
  Planarity :  0.004   0.033    818
  Dihedral  :  5.448  27.361    655
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.44 %
    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: -3.02 (0.33), residues: 556
  helix: -1.49 (0.27), residues: 337
  sheet:  0.01 (1.59), residues: 14
  loop : -2.90 (0.38), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   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
  109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8632 (tp) cc_final: 0.8215 (tt)
REVERT: A  151 TYR cc_start: 0.6421 (m-10) cc_final: 0.5880 (m-10)
REVERT: B  249 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6754 (tm-30)
  outliers start: 19
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1545
  time to fit residues: 19.6740
Evaluate side-chains
  90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  320 SER
Chi-restraints excluded: chain B residue  340 VAL
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:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4183 r_free = 0.4183 target = 0.175203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.144017 restraints weight = 6745.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.148282 restraints weight = 4057.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.151100 restraints weight = 2929.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4731  Z= 0.213
  Angle     :  0.678  10.020   6410  Z= 0.323
  Chirality :  0.041   0.207    762
  Planarity :  0.004   0.034    818
  Dihedral  :  5.293  27.458    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.33 %
    Favored  : 77.94 %
  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: -2.82 (0.33), residues: 556
  helix: -1.28 (0.27), residues: 338
  sheet: -1.13 (1.44), residues: 16
  loop : -2.84 (0.38), residues: 202

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 163 
 TYR   0.033   0.002   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
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8613 (tp) cc_final: 0.8208 (tt)
REVERT: A  151 TYR cc_start: 0.6379 (m-10) cc_final: 0.5766 (m-10)
REVERT: A  197 GLU cc_start: 0.7621 (tp30) cc_final: 0.7389 (tp30)
REVERT: A  380 MET cc_start: 0.8316 (ttm) cc_final: 0.8025 (ttt)
REVERT: B  227 MET cc_start: 0.3608 (ppp) cc_final: 0.1778 (mtm)
REVERT: B  249 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6700 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1652
  time to fit residues: 18.5563
Evaluate side-chains
  86 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
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  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  229 LEU
Chi-restraints excluded: chain B residue  270 ILE
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:    0.0570
   chunk 40 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.177856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.146415 restraints weight = 6802.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.150734 restraints weight = 4110.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.153680 restraints weight = 2965.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2556

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= 0.184
  Angle     :  0.626  12.395   6410  Z= 0.301
  Chirality :  0.039   0.141    762
  Planarity :  0.004   0.031    818
  Dihedral  :  5.028  27.481    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.96 %
    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: -2.46 (0.34), residues: 556
  helix: -0.96 (0.28), residues: 331
  sheet: -0.47 (1.46), residues: 14
  loop : -2.74 (0.38), residues: 211

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 163 
 TYR   0.012   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
  106 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.8392 (tpt90) cc_final: 0.8150 (tpt90)
REVERT: A  150 LEU cc_start: 0.8648 (tp) cc_final: 0.8245 (tt)
REVERT: A  151 TYR cc_start: 0.6335 (m-10) cc_final: 0.5683 (m-10)
REVERT: B  227 MET cc_start: 0.3676 (ppp) cc_final: 0.1289 (mtm)
  outliers start: 18
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1727
  time to fit residues: 21.2542
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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 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  359 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.179836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.150170 restraints weight = 6701.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.154358 restraints weight = 4012.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.157081 restraints weight = 2856.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2762

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= 0.183
  Angle     :  0.621  11.046   6410  Z= 0.301
  Chirality :  0.040   0.216    762
  Planarity :  0.004   0.032    818
  Dihedral  :  4.893  27.655    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.54 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.37 (0.34), residues: 556
  helix: -0.85 (0.28), residues: 336
  sheet: -0.48 (1.48), residues: 14
  loop : -2.79 (0.39), residues: 206

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   0.018   0.002   TYR A  95 
 ARG   0.002   0.000   ARG A 345 

*********************** 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
  105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.8342 (tpt90) cc_final: 0.8121 (tpt90)
REVERT: A  150 LEU cc_start: 0.8675 (tp) cc_final: 0.8408 (tt)
REVERT: A  151 TYR cc_start: 0.6357 (m-10) cc_final: 0.5711 (m-10)
  outliers start: 19
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1705
  time to fit residues: 20.8440
Evaluate side-chains
  93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
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  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  359 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 48 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0570
   chunk 54 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.3476

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.180449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.151202 restraints weight = 6729.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.155330 restraints weight = 4070.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.158106 restraints weight = 2909.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3065

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= 0.172
  Angle     :  0.666  12.569   6410  Z= 0.312
  Chirality :  0.040   0.188    762
  Planarity :  0.004   0.042    818
  Dihedral  :  4.685  25.125    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.59 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.04 (0.35), residues: 556
  helix: -0.62 (0.29), residues: 331
  sheet: -0.58 (1.47), residues: 14
  loop : -2.55 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 263 
 HIS   0.004   0.001   HIS A 158 
 PHE   0.010   0.001   PHE A 163 
 TYR   0.012   0.001   TYR A  95 
 ARG   0.015   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
  100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8647 (tp) cc_final: 0.8372 (tt)
REVERT: A  151 TYR cc_start: 0.6371 (m-10) cc_final: 0.5743 (m-10)
  outliers start: 14
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1642
  time to fit residues: 20.1351
Evaluate side-chains
  87 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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  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  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  359 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0030
   chunk 54 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.178319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.148370 restraints weight = 6725.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.152392 restraints weight = 4134.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154967 restraints weight = 2998.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.3116

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= 0.199
  Angle     :  0.655  11.113   6410  Z= 0.312
  Chirality :  0.040   0.173    762
  Planarity :  0.004   0.044    818
  Dihedral  :  4.688  26.682    655
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.59 %
    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: -2.13 (0.35), residues: 556
  helix: -0.65 (0.28), residues: 338
  sheet: -0.42 (1.46), residues: 14
  loop : -2.75 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 158 
 PHE   0.009   0.001   PHE A 163 
 TYR   0.018   0.001   TYR A  95 
 ARG   0.011   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
  98 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8661 (tp) cc_final: 0.8379 (tt)
REVERT: A  151 TYR cc_start: 0.6417 (m-10) cc_final: 0.5734 (m-10)
REVERT: A  302 MET cc_start: 0.7760 (ptt) cc_final: 0.7477 (ptt)
  outliers start: 22
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1581
  time to fit residues: 18.0133
Evaluate side-chains
  92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
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  290 LEU
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  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:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5640

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.178841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.147972 restraints weight = 6762.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.152312 restraints weight = 3982.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.155149 restraints weight = 2827.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.3218

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= 0.189
  Angle     :  0.663  12.680   6410  Z= 0.312
  Chirality :  0.040   0.164    762
  Planarity :  0.004   0.035    818
  Dihedral  :  4.659  27.088    655
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.96 %
    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: -2.04 (0.35), residues: 556
  helix: -0.61 (0.28), residues: 336
  sheet: -0.37 (1.46), residues: 14
  loop : -2.61 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.004   0.001   HIS A 273 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.020   0.001   TYR A  95 
 ARG   0.011   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
  100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8625 (tp) cc_final: 0.8325 (tt)
REVERT: A  151 TYR cc_start: 0.6451 (m-10) cc_final: 0.5720 (m-10)
  outliers start: 21
  outliers final: 20
  residues processed: 87
  average time/residue: 0.1558
  time to fit residues: 17.6425
Evaluate side-chains
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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   73 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  343 MET
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  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.177461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.146317 restraints weight = 6730.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.150523 restraints weight = 4029.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.153305 restraints weight = 2890.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3259

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= 0.212
  Angle     :  0.667  11.531   6410  Z= 0.321
  Chirality :  0.041   0.159    762
  Planarity :  0.004   0.037    818
  Dihedral  :  4.698  27.677    655
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.59 %
    Favored  : 75.42 %
  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: -2.09 (0.35), residues: 556
  helix: -0.68 (0.28), residues: 336
  sheet: -0.26 (1.46), residues: 14
  loop : -2.59 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.016   0.001   HIS A  62 
 PHE   0.009   0.001   PHE A 315 
 TYR   0.020   0.002   TYR B 261 
 ARG   0.009   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
  95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A  150 LEU cc_start: 0.8640 (tp) cc_final: 0.8333 (tt)
REVERT: A  151 TYR cc_start: 0.6463 (m-10) cc_final: 0.5765 (m-10)
  outliers start: 19
  outliers final: 19
  residues processed: 84
  average time/residue: 0.1699
  time to fit residues: 18.3620
Evaluate side-chains
  91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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   73 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  343 MET
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  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0670
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.179573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.148508 restraints weight = 6830.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.152628 restraints weight = 4170.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.155460 restraints weight = 3026.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3404

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= 0.196
  Angle     :  0.666  11.865   6410  Z= 0.319
  Chirality :  0.040   0.149    762
  Planarity :  0.004   0.036    818
  Dihedral  :  4.690  27.815    655
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.22 %
    Favored  : 74.58 %
  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: -2.07 (0.34), residues: 556
  helix: -0.68 (0.28), residues: 336
  sheet: -0.48 (1.43), residues: 14
  loop : -2.53 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 263 
 HIS   0.016   0.001   HIS A  62 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.019   0.001   TYR A  95 
 ARG   0.009   0.000   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1739.88 seconds
wall clock time: 31 minutes 52.42 seconds (1912.42 seconds total)