Starting phenix.real_space_refine
on Tue Feb 11 03:59:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1z_36806/02_2025/8k1z_36806.cif"
  }
  resolution = 3.41
  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=  -0.001 sd=   0.074
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
     K       5      8.98       5
     S      32      5.16       5
     C    2706      2.51       5
     N     616      2.21       5
     O     700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4059
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 109
          Unusual residues: {'  K': 4, 'Y01': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 106
          Unusual residues: {'  K': 1, 'Y01': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.05, per 1000 atoms: 0.75
  Number of scatterers: 4059
  At special positions: 0
  Unit cell: (64.9, 73.7, 89.1, 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)
     K       5     19.00
     S      32     16.00
     O     700      8.00
     N     616      7.00
     C    2706      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: 1.05
  Conformation dependent library (CDL) restraints added in 433.5 milliseconds
  

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 53
      removed outlier: 5.621A  pdb=" N   ASP A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   HIS A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 3.707A  pdb=" N   ARG A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 79 through 92
    Processing helix  chain 'A' and resid 103 through 147
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 155 through 183
      removed outlier: 3.791A  pdb=" N   GLU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 198
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 217 through 241
      removed outlier: 3.511A  pdb=" N   ASN A 240 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 248
      removed outlier: 3.611A  pdb=" N   THR A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 53
      removed outlier: 5.619A  pdb=" N   ASP B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   HIS B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 70
      removed outlier: 3.680A  pdb=" N   ARG B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 79 through 92
    Processing helix  chain 'B' and resid 103 through 147
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 155 through 180
    Processing helix  chain 'B' and resid 185 through 198
    Processing helix  chain 'B' and resid 212 through 217
    Processing helix  chain 'B' and resid 217 through 248
      removed outlier: 4.307A  pdb=" N   ARG B 245 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)

    328 hydrogen bonds defined for protein.
    972 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 1.21 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: 673
        1.33 -     1.45: 1085
        1.45 -     1.57: 2350
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 4156
  Sorted by residual:
  bond pdb=" CA  MET A 156 "
       pdb=" C   MET A 156 "
    ideal  model  delta    sigma   weight residual
    1.524  1.481  0.043 1.26e-02 6.30e+03 1.17e+01
  bond pdb=" CA  GLU B 157 "
       pdb=" C   GLU B 157 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.038 1.29e-02 6.01e+03 8.55e+00
  bond pdb=" C   GLU B 157 "
       pdb=" N   ASN B 158 "
    ideal  model  delta    sigma   weight residual
    1.335  1.296  0.039 1.36e-02 5.41e+03 8.03e+00
  bond pdb=" N   MET A 156 "
       pdb=" CA  MET A 156 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.20e-02 6.94e+03 7.97e+00
  bond pdb=" C   MET A 156 "
       pdb=" N   GLU A 157 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.025 1.30e-02 5.92e+03 3.81e+00
  ... (remaining 4151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5483
        0.98 -     1.96: 114
        1.96 -     2.94: 24
        2.94 -     3.92: 12
        3.92 -     4.90: 11
  Bond angle restraints: 5644
  Sorted by residual:
  angle pdb=" N   VAL A 242 "
        pdb=" CA  VAL A 242 "
        pdb=" C   VAL A 242 "
      ideal   model   delta    sigma   weight residual
     113.71  109.72    3.99 9.50e-01 1.11e+00 1.76e+01
  angle pdb=" N   MET A 156 "
        pdb=" CA  MET A 156 "
        pdb=" C   MET A 156 "
      ideal   model   delta    sigma   weight residual
     111.14  107.73    3.41 1.08e+00 8.57e-01 9.95e+00
  angle pdb=" C   SER A 155 "
        pdb=" N   MET A 156 "
        pdb=" CA  MET A 156 "
      ideal   model   delta    sigma   weight residual
     120.44  116.32    4.12 1.36e+00 5.41e-01 9.20e+00
  angle pdb=" N   VAL A 243 "
        pdb=" CA  VAL A 243 "
        pdb=" C   VAL A 243 "
      ideal   model   delta    sigma   weight residual
     112.12  110.12    2.00 8.40e-01 1.42e+00 5.65e+00
  angle pdb=" C   LYS A   2 "
        pdb=" CA  LYS A   2 "
        pdb=" CB  LYS A   2 "
      ideal   model   delta    sigma   weight residual
     110.10  114.41   -4.31 1.90e+00 2.77e-01 5.13e+00
  ... (remaining 5639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2396
       16.09 -    32.18: 238
       32.18 -    48.27: 55
       48.27 -    64.36: 15
       64.36 -    80.44: 8
  Dihedral angle restraints: 2712
    sinusoidal: 1310
      harmonic: 1402
  Sorted by residual:
  dihedral pdb=" CG  ARG A   7 "
           pdb=" CD  ARG A   7 "
           pdb=" NE  ARG A   7 "
           pdb=" CZ  ARG A   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.50  -40.50     2      1.50e+01 4.44e-03 9.00e+00
  dihedral pdb=" CB  GLU B 130 "
           pdb=" CG  GLU B 130 "
           pdb=" CD  GLU B 130 "
           pdb=" OE1 GLU B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.79  -79.79     1      3.00e+01 1.11e-03 8.78e+00
  dihedral pdb=" CB  GLU A 130 "
           pdb=" CG  GLU A 130 "
           pdb=" CD  GLU A 130 "
           pdb=" OE1 GLU A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.69  -79.69     1      3.00e+01 1.11e-03 8.76e+00
  ... (remaining 2709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 450
       0.022 -    0.043: 72
       0.043 -    0.065: 86
       0.065 -    0.087: 27
       0.087 -    0.108: 15
  Chirality restraints: 650
  Sorted by residual:
  chirality pdb=" CA  VAL B  76 "
            pdb=" N   VAL B  76 "
            pdb=" C   VAL B  76 "
            pdb=" CB  VAL B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.94e-01
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.79e-01
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.54   -0.10 2.00e-01 2.50e+01 2.58e-01
  ... (remaining 647 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A   2 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   LYS A   2 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LYS A   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A   3 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 156 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   MET B 156 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET B 156 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU B 157 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 156 "    0.005 2.00e-02 2.50e+03   9.51e-03 9.05e-01
        pdb=" C   MET A 156 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   MET A 156 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A 157 "    0.006 2.00e-02 2.50e+03
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.82: 1154
        2.82 -     3.40: 4506
        3.40 -     3.98: 7281
        3.98 -     4.56: 10210
        4.56 -     5.14: 14419
  Nonbonded interactions: 37570
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 179 "
            pdb=" O   TRP B 184 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE1 GLN A 126 "
            pdb=" ND2 ASN A 240 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OD2 ASP B  58 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG  SER A 179 "
            pdb=" O   TRP A 184 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A  58 "
            pdb=" OH  TYR B  52 "
     model   vdw
     2.313 3.040
  ... (remaining 37565 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 248 or resid 301 through 304))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.700
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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   0.043   4156  Z= 0.119
  Angle     :  0.420   4.902   5644  Z= 0.247
  Chirality :  0.032   0.108    650
  Planarity :  0.002   0.019    664
  Dihedral  : 13.664  80.444   1816
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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:  5.04 (0.38), residues: 476
  helix:  3.84 (0.25), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.42 (0.71), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 184 
 HIS   0.001   0.000   HIS A  98 
 PHE   0.004   0.000   PHE B 109 
 TYR   0.007   0.001   TYR B  18 
 ARG   0.001   0.000   ARG B 131 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 PHE cc_start: 0.6915 (m-80) cc_final: 0.6458 (t80)
REVERT: A   42 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8046 (tppt)
REVERT: A   47 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7485 (ttp80)
REVERT: A  111 MET cc_start: 0.7869 (mtm) cc_final: 0.7653 (mtp)
REVERT: A  135 PHE cc_start: 0.7010 (t80) cc_final: 0.5929 (m-10)
REVERT: B   16 PHE cc_start: 0.6839 (m-80) cc_final: 0.6434 (t80)
REVERT: B   42 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8030 (tppt)
REVERT: B   47 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7448 (ttp80)
REVERT: B  111 MET cc_start: 0.7910 (mtm) cc_final: 0.7710 (mtp)
REVERT: B  135 PHE cc_start: 0.7018 (t80) cc_final: 0.5917 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2199
  time to fit residues: 27.2268
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.193178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.145726 restraints weight = 4211.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.34
r_work: 0.3185 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4156  Z= 0.270
  Angle     :  0.610   6.813   5644  Z= 0.320
  Chirality :  0.040   0.145    650
  Planarity :  0.004   0.043    664
  Dihedral  :  5.531  37.850    952
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.07 %
    Favored  : 88.97 %
  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:  4.98 (0.40), residues: 476
  helix:  3.72 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.54 (0.85), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.002   0.001   HIS B  72 
 PHE   0.014   0.002   PHE B 223 
 TYR   0.027   0.002   TYR A  85 
 ARG   0.006   0.001   ARG B 137 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 PHE cc_start: 0.7673 (m-80) cc_final: 0.6429 (t80)
REVERT: A   47 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7404 (ttp80)
REVERT: A  135 PHE cc_start: 0.7314 (t80) cc_final: 0.6132 (m-10)
REVERT: A  173 ILE cc_start: 0.8297 (mt) cc_final: 0.8079 (mt)
REVERT: A  215 GLN cc_start: 0.7469 (mt0) cc_final: 0.7252 (mt0)
REVERT: B   16 PHE cc_start: 0.7605 (m-80) cc_final: 0.6405 (t80)
REVERT: B   38 GLU cc_start: 0.8025 (tp30) cc_final: 0.7793 (tp30)
REVERT: B   42 LYS cc_start: 0.8272 (ttmm) cc_final: 0.8051 (tppt)
REVERT: B   47 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7441 (ttp80)
REVERT: B  135 PHE cc_start: 0.7291 (t80) cc_final: 0.6112 (m-10)
REVERT: B  173 ILE cc_start: 0.8440 (mt) cc_final: 0.8239 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 98
  average time/residue: 0.2104
  time to fit residues: 24.4536
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.190876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.142765 restraints weight = 4227.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.31
r_work: 0.3171 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4156  Z= 0.208
  Angle     :  0.543   6.623   5644  Z= 0.285
  Chirality :  0.036   0.157    650
  Planarity :  0.003   0.018    664
  Dihedral  :  5.024  36.822    952
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.46 %
    Favored  : 83.58 %
  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:  4.91 (0.39), residues: 476
  helix:  3.68 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.51 (0.85), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 184 
 HIS   0.002   0.000   HIS B  72 
 PHE   0.010   0.001   PHE B 246 
 TYR   0.015   0.001   TYR B  85 
 ARG   0.002   0.000   ARG B  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LYS cc_start: 0.8878 (tppt) cc_final: 0.8660 (tppt)
REVERT: A  135 PHE cc_start: 0.7400 (t80) cc_final: 0.6195 (m-10)
REVERT: A  173 ILE cc_start: 0.8485 (mt) cc_final: 0.8284 (mt)
REVERT: B   44 GLU cc_start: 0.8128 (tp30) cc_final: 0.7857 (tp30)
REVERT: B  135 PHE cc_start: 0.7318 (t80) cc_final: 0.6138 (m-10)
REVERT: B  173 ILE cc_start: 0.8506 (mt) cc_final: 0.8281 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 88
  average time/residue: 0.2358
  time to fit residues: 24.3239
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.1980
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.188838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.144195 restraints weight = 4259.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.36
r_work: 0.3131 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4156  Z= 0.192
  Angle     :  0.539   8.361   5644  Z= 0.277
  Chirality :  0.036   0.169    650
  Planarity :  0.003   0.015    664
  Dihedral  :  4.735  34.639    952
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.22 %
    Favored  : 83.09 %
  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:  4.76 (0.39), residues: 476
  helix:  3.62 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.19 (0.83), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.009   0.001   PHE B 223 
 TYR   0.014   0.001   TYR B  85 
 ARG   0.003   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.8042 (tp30) cc_final: 0.7765 (tp30)
REVERT: A   44 GLU cc_start: 0.7716 (tp30) cc_final: 0.7494 (tp30)
REVERT: A  135 PHE cc_start: 0.7391 (t80) cc_final: 0.6176 (m-10)
REVERT: A  173 ILE cc_start: 0.8591 (mt) cc_final: 0.8382 (mt)
REVERT: B   44 GLU cc_start: 0.7708 (tp30) cc_final: 0.7487 (tp30)
REVERT: B  135 PHE cc_start: 0.7383 (t80) cc_final: 0.6182 (m-10)
REVERT: B  173 ILE cc_start: 0.8601 (mt) cc_final: 0.8396 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2349
  time to fit residues: 24.8142
Evaluate side-chains
  92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.185324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.138516 restraints weight = 4362.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.21
r_work: 0.3022 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4156  Z= 0.224
  Angle     :  0.549   6.142   5644  Z= 0.288
  Chirality :  0.037   0.156    650
  Planarity :  0.003   0.015    664
  Dihedral  :  4.675  34.495    952
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.71 %
    Favored  : 81.86 %
  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:  4.62 (0.39), residues: 476
  helix:  3.55 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.05 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 184 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.009   0.001   PHE B 223 
 TYR   0.015   0.001   TYR B  85 
 ARG   0.002   0.000   ARG B  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8082 (tt)
REVERT: A   70 GLU cc_start: 0.7531 (pt0) cc_final: 0.7217 (pm20)
REVERT: A  168 MET cc_start: 0.8246 (mmm) cc_final: 0.7710 (mmt)
REVERT: A  173 ILE cc_start: 0.8578 (mt) cc_final: 0.8371 (mt)
REVERT: A  227 TYR cc_start: 0.8737 (t80) cc_final: 0.8144 (t80)
REVERT: B   29 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8093 (tt)
REVERT: B  135 PHE cc_start: 0.7438 (t80) cc_final: 0.6159 (m-10)
REVERT: B  173 ILE cc_start: 0.8602 (mt) cc_final: 0.8383 (mt)
REVERT: B  227 TYR cc_start: 0.8708 (t80) cc_final: 0.8138 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 104
  average time/residue: 0.2153
  time to fit residues: 26.6987
Evaluate side-chains
  104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0970
   chunk 44 optimal weight:    0.0770
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.187370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.140223 restraints weight = 4292.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.12
r_work: 0.3117 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4156  Z= 0.186
  Angle     :  0.569   8.660   5644  Z= 0.295
  Chirality :  0.036   0.146    650
  Planarity :  0.003   0.016    664
  Dihedral  :  4.674  37.167    952
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 15.93 %
    Favored  : 80.39 %
  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:  4.72 (0.39), residues: 476
  helix:  3.63 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.07 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 184 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.024   0.001   PHE B 112 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.002   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: A   38 GLU cc_start: 0.8167 (tp30) cc_final: 0.7904 (tp30)
REVERT: A  135 PHE cc_start: 0.6950 (t80) cc_final: 0.5821 (m-10)
REVERT: B   29 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8070 (tt)
REVERT: B  135 PHE cc_start: 0.7478 (t80) cc_final: 0.6175 (m-10)
REVERT: B  173 ILE cc_start: 0.8595 (mt) cc_final: 0.8372 (mt)
REVERT: B  227 TYR cc_start: 0.8703 (t80) cc_final: 0.8190 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 96
  average time/residue: 0.2232
  time to fit residues: 25.2257
Evaluate side-chains
  96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.184947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.140393 restraints weight = 4313.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.49
r_work: 0.3034 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4156  Z= 0.209
  Angle     :  0.549   6.793   5644  Z= 0.289
  Chirality :  0.036   0.159    650
  Planarity :  0.003   0.016    664
  Dihedral  :  4.694  38.694    952
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.67 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.68 (0.39), residues: 476
  helix:  3.61 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.15 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.017   0.001   PHE B 112 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8051 (tt)
REVERT: A   38 GLU cc_start: 0.8104 (tp30) cc_final: 0.7812 (tp30)
REVERT: A   70 GLU cc_start: 0.7460 (pt0) cc_final: 0.7123 (pm20)
REVERT: A  135 PHE cc_start: 0.7055 (t80) cc_final: 0.5740 (m-10)
REVERT: A  227 TYR cc_start: 0.8769 (t80) cc_final: 0.8223 (t80)
REVERT: B   29 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8116 (tt)
REVERT: B   70 GLU cc_start: 0.7670 (pt0) cc_final: 0.7065 (pm20)
REVERT: B  135 PHE cc_start: 0.7531 (t80) cc_final: 0.6199 (m-10)
REVERT: B  173 ILE cc_start: 0.8623 (mt) cc_final: 0.8409 (mt)
REVERT: B  227 TYR cc_start: 0.8762 (t80) cc_final: 0.8224 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 97
  average time/residue: 0.2121
  time to fit residues: 24.2510
Evaluate side-chains
  104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.184570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.138935 restraints weight = 4226.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.26
r_work: 0.3054 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.4683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4156  Z= 0.206
  Angle     :  0.564   9.749   5644  Z= 0.292
  Chirality :  0.036   0.153    650
  Planarity :  0.002   0.015    664
  Dihedral  :  4.668  39.415    952
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.18 %
    Favored  : 80.15 %
  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:  4.73 (0.39), residues: 476
  helix:  3.65 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.17 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.009   0.001   PHE A  16 
 TYR   0.012   0.001   TYR B  85 
 ARG   0.002   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8126 (tt)
REVERT: A  135 PHE cc_start: 0.7187 (t80) cc_final: 0.5890 (m-10)
REVERT: A  227 TYR cc_start: 0.8829 (t80) cc_final: 0.8297 (t80)
REVERT: B   29 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B  135 PHE cc_start: 0.7642 (t80) cc_final: 0.6319 (m-10)
REVERT: B  173 ILE cc_start: 0.8699 (mt) cc_final: 0.8476 (mt)
REVERT: B  227 TYR cc_start: 0.8825 (t80) cc_final: 0.8275 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 95
  average time/residue: 0.2144
  time to fit residues: 24.0977
Evaluate side-chains
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.184968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.138634 restraints weight = 4276.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.09
r_work: 0.3064 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4156  Z= 0.193
  Angle     :  0.563   9.296   5644  Z= 0.298
  Chirality :  0.036   0.160    650
  Planarity :  0.002   0.017    664
  Dihedral  :  4.654  40.373    952
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.65 %
    Favored  : 78.92 %
  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:  4.80 (0.39), residues: 476
  helix:  3.70 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.16 (0.81), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.009   0.001   PHE B 109 
 TYR   0.014   0.001   TYR A 113 
 ARG   0.002   0.000   ARG B  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8090 (tt)
REVERT: A   38 GLU cc_start: 0.8180 (tp30) cc_final: 0.7918 (tp30)
REVERT: A   42 LYS cc_start: 0.8957 (tppt) cc_final: 0.8730 (tppt)
REVERT: A  135 PHE cc_start: 0.7077 (t80) cc_final: 0.5797 (m-10)
REVERT: A  227 TYR cc_start: 0.8770 (t80) cc_final: 0.8143 (t80)
REVERT: B   29 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8064 (tt)
REVERT: B   70 GLU cc_start: 0.7718 (pt0) cc_final: 0.7230 (pm20)
REVERT: B  173 ILE cc_start: 0.8603 (mt) cc_final: 0.8393 (mt)
REVERT: B  227 TYR cc_start: 0.8758 (t80) cc_final: 0.8206 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 97
  average time/residue: 0.2132
  time to fit residues: 24.3672
Evaluate side-chains
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.3948

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.188503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.140732 restraints weight = 4235.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.28
r_work: 0.3119 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4156  Z= 0.184
  Angle     :  0.577  10.663   5644  Z= 0.308
  Chirality :  0.037   0.163    650
  Planarity :  0.002   0.016    664
  Dihedral  :  4.635  41.218    952
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.63 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.90 (0.39), residues: 476
  helix:  3.76 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.06 (0.81), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.009   0.001   PHE A 109 
 TYR   0.013   0.001   TYR B 113 
 ARG   0.002   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8069 (tt)
REVERT: A   38 GLU cc_start: 0.8192 (tp30) cc_final: 0.7909 (tp30)
REVERT: A   42 LYS cc_start: 0.8953 (tppt) cc_final: 0.8739 (tppt)
REVERT: A  135 PHE cc_start: 0.7018 (t80) cc_final: 0.5740 (m-10)
REVERT: A  227 TYR cc_start: 0.8766 (t80) cc_final: 0.8180 (t80)
REVERT: B   29 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8109 (tt)
REVERT: B   38 GLU cc_start: 0.8130 (tp30) cc_final: 0.7835 (tp30)
REVERT: B   70 GLU cc_start: 0.7740 (pt0) cc_final: 0.7149 (pm20)
REVERT: B  135 PHE cc_start: 0.6996 (t80) cc_final: 0.5776 (m-10)
REVERT: B  173 ILE cc_start: 0.8615 (mt) cc_final: 0.8401 (mt)
REVERT: B  227 TYR cc_start: 0.8756 (t80) cc_final: 0.8261 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2284
  time to fit residues: 25.0779
Evaluate side-chains
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0970
   chunk 32 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0370
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.3234

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.184303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.139421 restraints weight = 4267.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.13
r_work: 0.3078 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4156  Z= 0.180
  Angle     :  0.573  10.331   5644  Z= 0.304
  Chirality :  0.036   0.157    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.631  41.802    952
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.61 %
    Favored  : 77.70 %
  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:  4.98 (0.39), residues: 476
  helix:  3.82 (0.24), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.07 (0.82), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 184 
 HIS   0.000   0.000   HIS B 188 
 PHE   0.009   0.001   PHE B 109 
 TYR   0.012   0.001   TYR A  59 
 ARG   0.002   0.000   ARG B  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2084.01 seconds
wall clock time: 37 minutes 44.61 seconds (2264.61 seconds total)