Starting phenix.real_space_refine
on Thu Mar 13 17:15:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tq2_41499/03_2025/8tq2_41499_neut.cif"
  }
  resolution = 3.8
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4357 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3569      2.51       5
     N     931      2.21       5
     O     969      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5505
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 639
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 8, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 120
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "A"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2561
          Classifications: {'peptide': 313}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2185
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 261, 2178
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 12, 'TRANS': 248}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 261, 2178
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 12, 'TRANS': 248}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2226
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AVAL B 163 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL B 163 " occ=0.50
  Time building chain proxies: 7.05, per 1000 atoms: 1.28
  Number of scatterers: 5505
  At special positions: 0
  Unit cell: (81.3276, 101.659, 82.3977, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O     969      8.00
     N     931      7.00
     C    3569      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: 1.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      52.5% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'C' and resid 37 through 44
      removed outlier: 3.546A  pdb=" N   LYS C  42 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 84
    Processing helix  chain 'D' and resid 1619 through 1623
      removed outlier: 3.693A  pdb=" N   VAL D1622 " --> pdb=" O   ARG D1619 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY D1623 " --> pdb=" O   ASP D1620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1619 through 1623'
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 60 through 71
    Processing helix  chain 'A' and resid 104 through 111
    Processing helix  chain 'A' and resid 124 through 145
      removed outlier: 3.629A  pdb=" N   VAL A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 214 through 230
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.750A  pdb=" N   MET A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.714A  pdb=" N   HIS A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 316
      removed outlier: 3.949A  pdb=" N   HIS A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 332
      removed outlier: 3.600A  pdb=" N   ALA A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   MET A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 13
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 25 through 30
    Processing helix  chain 'B' and resid 33 through 55
    Processing helix  chain 'B' and resid 58 through 70
      removed outlier: 3.914A  pdb=" N   ILE B  62 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 75
    Processing helix  chain 'B' and resid 82 through 98
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 104 through 120
      removed outlier: 3.512A  pdb=" N   PHE B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 146
    Processing helix  chain 'B' and resid 155 through 167
    Processing helix  chain 'B' and resid 172 through 183
    Processing helix  chain 'B' and resid 184 through 186
      No H-bonds generated for 'chain 'B' and resid 184 through 186'
    Processing helix  chain 'B' and resid 187 through 192
    Processing helix  chain 'B' and resid 193 through 209
      removed outlier: 3.535A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
      removed outlier: 3.793A  pdb=" N   GLU B 219 " --> pdb=" O   GLN B 215 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU B 220 " --> pdb=" O   TRP B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 241
    Processing helix  chain 'B' and resid 242 through 244
      No H-bonds generated for 'chain 'B' and resid 242 through 244'
    Processing helix  chain 'B' and resid 245 through 256
      removed outlier: 3.619A  pdb=" N   GLU B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   ALA B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   THR B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29
      removed outlier: 6.584A  pdb=" N   LYS A  26 " --> pdb=" O   LYS A  37 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LYS A  37 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   VAL A  93 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   LYS A  92 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   LEU A  86 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TRP A  94 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   VAL A  84 " --> pdb=" O   TRP A  94 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   LEU A  96 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103
      removed outlier: 4.430A  pdb=" N   MET A 160 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ARG A 168 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148

    230 hydrogen bonds defined for protein.
    679 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: 1.48

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1743
        1.35 -     1.46: 1291
        1.46 -     1.58: 2552
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 5644
  Sorted by residual:
  bond pdb=" C   MET A 273 "
       pdb=" N   PRO A 274 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.03e-01
  bond pdb=" CB  GLU B  98 "
       pdb=" CG  GLU B  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.99e-01
  bond pdb=" CG  GLU B  98 "
       pdb=" CD  GLU B  98 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.59e-01
  bond pdb=" CA  ASP A 137 "
       pdb=" CB  ASP A 137 "
    ideal  model  delta    sigma   weight residual
    1.528  1.541 -0.013 1.59e-02 3.96e+03 6.43e-01
  bond pdb=" N   PRO B 193 "
       pdb=" CA  PRO B 193 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.31e-02 5.83e+03 6.20e-01
  ... (remaining 5639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 7458
        1.53 -     3.05: 125
        3.05 -     4.58: 32
        4.58 -     6.10: 7
        6.10 -     7.63: 3
  Bond angle restraints: 7625
  Sorted by residual:
  angle pdb=" CB  MET B 250 "
        pdb=" CG  MET B 250 "
        pdb=" SD  MET B 250 "
      ideal   model   delta    sigma   weight residual
     112.70  120.33   -7.63 3.00e+00 1.11e-01 6.47e+00
  angle pdb=" CB  MET B  86 "
        pdb=" CG  MET B  86 "
        pdb=" SD  MET B  86 "
      ideal   model   delta    sigma   weight residual
     112.70  120.32   -7.62 3.00e+00 1.11e-01 6.46e+00
  angle pdb=" CA  MET A 174 "
        pdb=" CB  MET A 174 "
        pdb=" CG  MET A 174 "
      ideal   model   delta    sigma   weight residual
     114.10  118.42   -4.32 2.00e+00 2.50e-01 4.67e+00
  angle pdb=" C   LEU A  69 "
        pdb=" N   LEU A  70 "
        pdb=" CA  LEU A  70 "
      ideal   model   delta    sigma   weight residual
     121.94  117.69    4.25 2.00e+00 2.50e-01 4.52e+00
  angle pdb=" C   LYS C  15 "
        pdb=" N   ARG C  16 "
        pdb=" CA  ARG C  16 "
      ideal   model   delta    sigma   weight residual
     120.58  123.32   -2.74 1.32e+00 5.74e-01 4.29e+00
  ... (remaining 7620 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 2991
       16.18 -    32.35: 337
       32.35 -    48.53: 71
       48.53 -    64.70: 10
       64.70 -    80.88: 7
  Dihedral angle restraints: 3416
    sinusoidal: 1431
      harmonic: 1985
  Sorted by residual:
  dihedral pdb=" CA  ASP B  20 "
           pdb=" CB  ASP B  20 "
           pdb=" CG  ASP B  20 "
           pdb=" OD1 ASP B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.65   51.65     1      2.00e+01 2.50e-03 9.11e+00
  dihedral pdb=" CG  ARG B  58 "
           pdb=" CD  ARG B  58 "
           pdb=" NE  ARG B  58 "
           pdb=" CZ  ARG B  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.55   40.45     2      1.50e+01 4.44e-03 8.98e+00
  dihedral pdb=" CB  GLU A 101 "
           pdb=" CG  GLU A 101 "
           pdb=" CD  GLU A 101 "
           pdb=" OE1 GLU A 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.88  -80.88     1      3.00e+01 1.11e-03 8.98e+00
  ... (remaining 3413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 481
       0.028 -    0.057: 204
       0.057 -    0.085: 90
       0.085 -    0.113: 47
       0.113 -    0.141: 5
  Chirality restraints: 827
  Sorted by residual:
  chirality pdb=" CA  VAL B 222 "
            pdb=" N   VAL B 222 "
            pdb=" C   VAL B 222 "
            pdb=" CB  VAL B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  LEU A  70 "
            pdb=" N   LEU A  70 "
            pdb=" C   LEU A  70 "
            pdb=" CB  LEU A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  VAL A 195 "
            pdb=" N   VAL A 195 "
            pdb=" C   VAL A 195 "
            pdb=" CB  VAL A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 824 not shown)

  Planarity restraints: 964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  25 "    0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO C  26 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C  26 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  26 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 340 "    0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO A 341 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  28 "    0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO C  29 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C  29 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  29 "    0.016 5.00e-02 4.00e+02
  ... (remaining 961 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1376
        2.80 -     3.33: 5197
        3.33 -     3.85: 8567
        3.85 -     4.38: 9625
        4.38 -     4.90: 16927
  Nonbonded interactions: 41692
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 203 "
            pdb=" NH2 ARG A 323 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   LYS B  70 "
            pdb=" N   PHE B  72 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   THR B 252 "
            pdb=" OG  SER B 255 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ILE A  59 "
            pdb=" NZ  LYS B  96 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 GLN C  27 "
            pdb=" O   HIS A 143 "
     model   vdw
     2.332 3.120
  ... (remaining 41687 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=0.00 max=1.00 mean=0.98
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:             4.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.040
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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      :  0.002   0.031   5644  Z= 0.145
  Angle     :  0.551   7.630   7625  Z= 0.276
  Chirality :  0.041   0.141    827
  Planarity :  0.004   0.041    964
  Dihedral  : 14.159  80.877   2124
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.33), residues: 655
  helix:  1.66 (0.31), residues: 311
  sheet:  1.88 (1.30), residues: 13
  loop : -0.75 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  38 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.007   0.001   TYR C  25 
 ARG   0.008   0.000   ARG A 209 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.631 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.5644 (mmp) cc_final: 0.4255 (tmm)
REVERT: A   61 MET cc_start: 0.7989 (mmm) cc_final: 0.7777 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1590
  time to fit residues: 20.3247
Evaluate side-chains
  67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
D1631 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.111208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.091122 restraints weight = 31673.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.095736 restraints weight = 15808.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.096367 restraints weight = 9437.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5644  Z= 0.262
  Angle     :  0.592  10.857   7625  Z= 0.296
  Chirality :  0.044   0.150    827
  Planarity :  0.004   0.033    964
  Dihedral  :  3.827  17.339    728
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.97 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.32), residues: 655
  helix:  1.42 (0.30), residues: 317
  sheet: -0.41 (0.94), residues: 25
  loop : -0.48 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  38 
 HIS   0.005   0.001   HIS A 310 
 PHE   0.010   0.001   PHE A 180 
 TYR   0.014   0.001   TYR B 184 
 ARG   0.003   0.000   ARG A 178 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.681 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6041 (mmp) cc_final: 0.4413 (tmm)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1405
  time to fit residues: 14.2833
Evaluate side-chains
  67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 22 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  40 ASN
D1631 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.111931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.090535 restraints weight = 26522.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.095171 restraints weight = 13547.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098580 restraints weight = 6599.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5644  Z= 0.176
  Angle     :  0.533   8.335   7625  Z= 0.263
  Chirality :  0.042   0.138    827
  Planarity :  0.004   0.033    964
  Dihedral  :  3.748  15.915    728
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 10.13 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.33), residues: 655
  helix:  1.47 (0.30), residues: 319
  sheet: -0.21 (0.95), residues: 25
  loop : -0.40 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.004   0.001   HIS D1631 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.008   0.001   TYR B 184 
 ARG   0.006   0.000   ARG C  16 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.687 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.5989 (mmp) cc_final: 0.4463 (tmm)
REVERT: B  138 CYS cc_start: 0.8974 (t) cc_final: 0.8771 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 73
  average time/residue: 0.1299
  time to fit residues: 13.7943
Evaluate side-chains
  68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
D1631 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.110790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.090350 restraints weight = 20387.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.093717 restraints weight = 10864.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.094959 restraints weight = 6665.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5644  Z= 0.206
  Angle     :  0.527   6.073   7625  Z= 0.266
  Chirality :  0.042   0.154    827
  Planarity :  0.004   0.045    964
  Dihedral  :  3.800  14.982    728
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.63 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.33), residues: 655
  helix:  1.32 (0.29), residues: 320
  sheet: -0.12 (0.95), residues: 25
  loop : -0.37 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.004   0.001   HIS D1631 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.010   0.001   TYR B 184 
 ARG   0.002   0.000   ARG A 323 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.650 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6184 (mmp) cc_final: 0.4520 (tmm)
REVERT: A   61 MET cc_start: 0.8071 (tpp) cc_final: 0.7443 (mmt)
REVERT: A  107 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9151 (mm)
REVERT: B  132 MET cc_start: 0.7644 (tpt) cc_final: 0.7299 (tpp)
  outliers start: 10
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1329
  time to fit residues: 14.4923
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   47 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0870
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
D1631 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.112522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.091811 restraints weight = 28187.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.096138 restraints weight = 12860.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098778 restraints weight = 7299.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5644  Z= 0.142
  Angle     :  0.511   9.350   7625  Z= 0.252
  Chirality :  0.041   0.143    827
  Planarity :  0.004   0.043    964
  Dihedral  :  3.670  14.575    728
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 12.96 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.33), residues: 655
  helix:  1.46 (0.30), residues: 320
  sheet:  0.12 (0.99), residues: 25
  loop : -0.28 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.005   0.001   HIS D1631 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.006   0.001   TYR B  76 
 ARG   0.001   0.000   ARG A 323 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.721 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6035 (mmp) cc_final: 0.4433 (ppp)
REVERT: A   61 MET cc_start: 0.8034 (tpp) cc_final: 0.7498 (mmt)
REVERT: A  107 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9143 (mm)
  outliers start: 4
  outliers final: 2
  residues processed: 75
  average time/residue: 0.1272
  time to fit residues: 13.8825
Evaluate side-chains
  69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  252 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0040
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
C  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.112912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.092568 restraints weight = 32825.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097493 restraints weight = 15281.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098414 restraints weight = 8692.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5644  Z= 0.147
  Angle     :  0.512   7.800   7625  Z= 0.250
  Chirality :  0.041   0.153    827
  Planarity :  0.004   0.036    964
  Dihedral  :  3.611  14.203    728
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.62 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.33), residues: 655
  helix:  1.47 (0.29), residues: 320
  sheet:  0.16 (1.01), residues: 25
  loop : -0.23 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.003   0.000   HIS A  88 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.007   0.001   TYR B  76 
 ARG   0.007   0.000   ARG C  16 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.647 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6148 (mmp) cc_final: 0.4454 (ppp)
REVERT: A   61 MET cc_start: 0.8039 (tpp) cc_final: 0.7517 (mmt)
REVERT: A  107 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9137 (mm)
REVERT: B  132 MET cc_start: 0.7606 (tpt) cc_final: 0.7290 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1247
  time to fit residues: 13.3643
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.111160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.089905 restraints weight = 27694.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.095030 restraints weight = 12492.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097591 restraints weight = 5881.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5644  Z= 0.201
  Angle     :  0.544   9.496   7625  Z= 0.267
  Chirality :  0.042   0.161    827
  Planarity :  0.004   0.044    964
  Dihedral  :  3.720  16.657    728
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.45 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.33), residues: 655
  helix:  1.39 (0.29), residues: 320
  sheet:  0.15 (1.01), residues: 25
  loop : -0.25 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.009   0.001   PHE B  44 
 TYR   0.009   0.001   TYR B 184 
 ARG   0.002   0.000   ARG A 178 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.681 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6030 (mmp) cc_final: 0.4432 (ppp)
REVERT: A   61 MET cc_start: 0.7995 (tpp) cc_final: 0.7434 (mmt)
REVERT: A  107 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9173 (mm)
REVERT: B  132 MET cc_start: 0.7629 (tpt) cc_final: 0.7249 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1228
  time to fit residues: 12.9387
Evaluate side-chains
  69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.110945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.090213 restraints weight = 31381.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.094568 restraints weight = 14358.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.096028 restraints weight = 8272.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5644  Z= 0.200
  Angle     :  0.552   9.372   7625  Z= 0.270
  Chirality :  0.042   0.166    827
  Planarity :  0.004   0.044    964
  Dihedral  :  3.782  15.978    728
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.95 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.33), residues: 655
  helix:  1.35 (0.29), residues: 320
  sheet:  0.14 (1.04), residues: 25
  loop : -0.23 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  38 
 HIS   0.002   0.001   HIS A  88 
 PHE   0.009   0.001   PHE B  44 
 TYR   0.009   0.001   TYR B 184 
 ARG   0.008   0.000   ARG C  16 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.617 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6316 (mmp) cc_final: 0.4514 (ppp)
REVERT: A   61 MET cc_start: 0.8059 (tpp) cc_final: 0.7502 (mmt)
REVERT: A  107 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9143 (mm)
REVERT: B  132 MET cc_start: 0.7682 (tpt) cc_final: 0.7328 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.1273
  time to fit residues: 13.2117
Evaluate side-chains
  72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue  190 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 17 optimal weight:    0.1980
   chunk 28 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.111982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.090820 restraints weight = 27803.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.096036 restraints weight = 12629.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099198 restraints weight = 5987.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5644  Z= 0.159
  Angle     :  0.545  10.009   7625  Z= 0.267
  Chirality :  0.042   0.162    827
  Planarity :  0.004   0.041    964
  Dihedral  :  3.714  16.473    728
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.78 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.33), residues: 655
  helix:  1.43 (0.29), residues: 320
  sheet:  0.19 (1.07), residues: 25
  loop : -0.20 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  38 
 HIS   0.002   0.000   HIS A  88 
 PHE   0.009   0.001   PHE B  44 
 TYR   0.007   0.001   TYR B  76 
 ARG   0.002   0.000   ARG C  16 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.701 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.6069 (mmp) cc_final: 0.4465 (ppp)
REVERT: A   61 MET cc_start: 0.8041 (tpp) cc_final: 0.7476 (mmt)
REVERT: A  107 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9167 (mm)
  outliers start: 9
  outliers final: 5
  residues processed: 71
  average time/residue: 0.1303
  time to fit residues: 13.5629
Evaluate side-chains
  69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue  190 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 12 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0070
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.111809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.091386 restraints weight = 17839.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.094658 restraints weight = 9110.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.096854 restraints weight = 5771.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5644  Z= 0.161
  Angle     :  0.535   9.923   7625  Z= 0.264
  Chirality :  0.041   0.150    827
  Planarity :  0.004   0.042    964
  Dihedral  :  3.742  20.073    728
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.11 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.33), residues: 655
  helix:  1.43 (0.29), residues: 320
  sheet:  0.18 (1.04), residues: 25
  loop : -0.19 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  38 
 HIS   0.002   0.000   HIS A  88 
 PHE   0.009   0.001   PHE B  44 
 TYR   0.007   0.001   TYR B  76 
 ARG   0.007   0.000   ARG C  16 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.656 
Fit side-chains
REVERT: D 1617 MET cc_start: 0.5966 (mmp) cc_final: 0.4460 (ppp)
REVERT: A   61 MET cc_start: 0.8056 (tpp) cc_final: 0.7511 (mmt)
REVERT: A  107 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9181 (mm)
REVERT: B  132 MET cc_start: 0.7541 (tpt) cc_final: 0.7209 (tpp)
REVERT: B  137 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7093 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1337
  time to fit residues: 13.6339
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue  139 GLU
Chi-restraints excluded: chain B residue  190 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0170
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.111227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.090456 restraints weight = 25766.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.095486 restraints weight = 11803.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.098025 restraints weight = 5822.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       87 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5644  Z= 0.184
  Angle     :  0.552   9.985   7625  Z= 0.274
  Chirality :  0.042   0.171    827
  Planarity :  0.004   0.042    964
  Dihedral  :  3.796  17.911    728
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.28 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.33), residues: 655
  helix:  1.35 (0.29), residues: 320
  sheet:  0.19 (1.04), residues: 25
  loop : -0.21 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  38 
 HIS   0.007   0.001   HIS A  88 
 PHE   0.010   0.001   PHE B 244 
 TYR   0.015   0.001   TYR B 141 
 ARG   0.001   0.000   ARG A 178 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1911.35 seconds
wall clock time: 33 minutes 50.18 seconds (2030.18 seconds total)