Starting phenix.real_space_refine
on Fri Aug 22 14:52:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iep_35389/08_2025/8iep_35389.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    2939      2.51       5
     N     695      2.21       5
     O     759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4431
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2155
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 269}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2172
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "D"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 1.17, per 1000 atoms: 0.26
  Number of scatterers: 4431
  At special positions: 0
  Unit cell: (76.95, 85.86, 102.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       2     15.00
     O     759      8.00
     N     695      7.00
     C    2939      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 191 " - pdb=" SG  CYS C 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 191 " - pdb=" SG  CYS D 216 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 100.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1038

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 1 sheets defined
      79.0% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'C' and resid 46 through 74
    Processing helix  chain 'C' and resid 77 through 82
    Processing helix  chain 'C' and resid 84 through 105
      removed outlier: 3.671A  pdb=" N   ILE C  89 " --> pdb=" O   PRO C  85 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL C  90 " --> pdb=" O   ASN C  86 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR C  91 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 150
      Proline residue:  C 137  - end of helix
    Processing helix  chain 'C' and resid 161 through 187
      removed outlier: 3.599A  pdb=" N   LEU C 165 " --> pdb=" O   LYS C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 246
      removed outlier: 4.089A  pdb=" N   TRP C 224 " --> pdb=" O   TYR C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 281
    Processing helix  chain 'C' and resid 284 through 332
      Proline residue:  C 310  - end of helix
    Processing helix  chain 'D' and resid 46 through 74
    Processing helix  chain 'D' and resid 77 through 83
    Processing helix  chain 'D' and resid 84 through 105
      removed outlier: 3.595A  pdb=" N   VAL D  90 " --> pdb=" O   ASN D  86 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR D 103 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 149
      Proline residue:  D 137  - end of helix
    Processing helix  chain 'D' and resid 162 through 187
      removed outlier: 3.558A  pdb=" N   ASP D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 246
      removed outlier: 3.539A  pdb=" N   TRP D 224 " --> pdb=" O   TYR D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 281
    Processing helix  chain 'D' and resid 284 through 332
      Proline residue:  D 310  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 206 through 216
      removed outlier: 3.604A  pdb=" N   PHE C 215 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU C 195 " --> pdb=" O   MET D 199 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1152 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: 0.55

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 637
        1.31 -     1.44: 1216
        1.44 -     1.56: 2604
        1.56 -     1.69: 12
        1.69 -     1.81: 52
  Bond restraints: 4521
  Sorted by residual:
  bond pdb=" C39 PC1 C 601 "
       pdb=" C3A PC1 C 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.327  0.197 2.00e-02 2.50e+03 9.72e+01
  bond pdb=" C39 PC1 D 601 "
       pdb=" C3A PC1 D 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.327  0.197 2.00e-02 2.50e+03 9.69e+01
  bond pdb=" C31 PC1 D 601 "
       pdb=" O31 PC1 D 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.427 -0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" C31 PC1 C 601 "
       pdb=" O31 PC1 C 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.425 -0.095 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C21 PC1 D 601 "
       pdb=" O21 PC1 D 601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.383 -0.052 2.00e-02 2.50e+03 6.68e+00
  ... (remaining 4516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 6055
        2.81 -     5.62: 64
        5.62 -     8.43: 10
        8.43 -    11.24: 0
       11.24 -    14.05: 2
  Bond angle restraints: 6131
  Sorted by residual:
  angle pdb=" O12 PC1 C 601 "
        pdb=" P   PC1 C 601 "
        pdb=" O14 PC1 C 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.62   14.05 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" O12 PC1 D 601 "
        pdb=" P   PC1 D 601 "
        pdb=" O14 PC1 D 601 "
      ideal   model   delta    sigma   weight residual
     123.67  109.68   13.99 3.00e+00 1.11e-01 2.18e+01
  angle pdb=" CB  TRP D 229 "
        pdb=" CG  TRP D 229 "
        pdb=" CD2 TRP D 229 "
      ideal   model   delta    sigma   weight residual
     126.80  131.54   -4.74 1.40e+00 5.10e-01 1.14e+01
  angle pdb=" CB  TRP C 229 "
        pdb=" CG  TRP C 229 "
        pdb=" CD2 TRP C 229 "
      ideal   model   delta    sigma   weight residual
     126.80  131.38   -4.58 1.40e+00 5.10e-01 1.07e+01
  angle pdb=" CB  TRP D 229 "
        pdb=" CG  TRP D 229 "
        pdb=" CD1 TRP D 229 "
      ideal   model   delta    sigma   weight residual
     126.90  122.53    4.37 1.50e+00 4.44e-01 8.47e+00
  ... (remaining 6126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 2430
       17.93 -    35.87: 193
       35.87 -    53.80: 39
       53.80 -    71.74: 4
       71.74 -    89.67: 7
  Dihedral angle restraints: 2673
    sinusoidal: 1068
      harmonic: 1605
  Sorted by residual:
  dihedral pdb=" CA  ILE D 228 "
           pdb=" C   ILE D 228 "
           pdb=" N   TRP D 229 "
           pdb=" CA  TRP D 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.79   21.21     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ILE D 307 "
           pdb=" C   ILE D 307 "
           pdb=" N   PHE D 308 "
           pdb=" CA  PHE D 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ILE C 307 "
           pdb=" C   ILE C 307 "
           pdb=" N   PHE C 308 "
           pdb=" CA  PHE C 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.45  -18.55     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 2670 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 585
       0.044 -    0.088: 132
       0.088 -    0.132: 32
       0.132 -    0.176: 1
       0.176 -    0.219: 2
  Chirality restraints: 752
  Sorted by residual:
  chirality pdb=" CA  TRP C 229 "
            pdb=" N   TRP C 229 "
            pdb=" C   TRP C 229 "
            pdb=" CB  TRP C 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  TRP D 229 "
            pdb=" N   TRP D 229 "
            pdb=" C   TRP D 229 "
            pdb=" CB  TRP D 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.77e-01
  chirality pdb=" CB  ILE D 225 "
            pdb=" CA  ILE D 225 "
            pdb=" CG1 ILE D 225 "
            pdb=" CG2 ILE D 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 749 not shown)

  Planarity restraints: 712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 229 "    0.026 2.00e-02 2.50e+03   2.85e-02 2.03e+01
        pdb=" CG  TRP D 229 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 229 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 229 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 229 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 229 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 229 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 229 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 229 "   -0.024 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP C 229 "    0.070 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 229 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 229 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 229 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 229 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 229 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 229 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 252 "   -0.051 5.00e-02 4.00e+02   7.65e-02 9.37e+00
        pdb=" N   PRO D 253 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO D 253 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO D 253 "   -0.043 5.00e-02 4.00e+02
  ... (remaining 709 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 96
        2.71 -     3.26: 4336
        3.26 -     3.80: 7128
        3.80 -     4.35: 8488
        4.35 -     4.90: 15329
  Nonbonded interactions: 35377
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  58 "
            pdb=" OH  TYR C 103 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   TYR D 146 "
            pdb=" OG1 THR D 150 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OG1 THR C 202 "
            pdb=" OD1 ASP C 205 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER D  95 "
            pdb=" OD1 ASN D 304 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   TYR C 146 "
            pdb=" OG1 THR C 150 "
     model   vdw
     2.284 3.040
  ... (remaining 35372 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 'C' and (resid 44 through 152 or resid 161 through 601))
  selection = (chain 'D' and (resid 44 through 110 or resid 115 through 151 or (resid 152 thro \ 
ugh 161 and (name N or name CA or name C or name O or name CB )) or resid 162 th \ 
rough 601))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.210
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.050
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:6.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.197   4523  Z= 0.352
  Angle     :  0.785  14.045   6135  Z= 0.379
  Chirality :  0.040   0.219    752
  Planarity :  0.006   0.077    712
  Dihedral  : 14.244  89.673   1629
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.35), residues: 545
  helix:  2.79 (0.23), residues: 425
  sheet:  1.91 (0.98), residues: 34
  loop : -2.26 (0.60), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.009   0.001   TYR C 280 
 PHE   0.007   0.001   PHE D  67 
 TRP   0.078   0.003   TRP D 229 
 HIS   0.002   0.000   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 ( 4521)
  covalent geometry    : angle       0.78477 ( 6131)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       0.35660 (    4)
  hydrogen bonds       : bond        0.13165 (  385)
  hydrogen bonds       : angle       5.27970 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.099 
Fit side-chains
REVERT: C   82 MET cc_start: 0.7989 (ptt) cc_final: 0.7728 (ptp)
REVERT: C  115 SER cc_start: 0.8315 (m) cc_final: 0.8095 (t)
REVERT: C  149 PHE cc_start: 0.6381 (t80) cc_final: 0.6156 (t80)
REVERT: C  199 MET cc_start: 0.6610 (ttt) cc_final: 0.6288 (ttt)
REVERT: D  199 MET cc_start: 0.6786 (mtp) cc_final: 0.6538 (mtp)
REVERT: D  235 LEU cc_start: 0.7958 (mm) cc_final: 0.7755 (tp)
REVERT: D  283 SER cc_start: 0.8188 (m) cc_final: 0.7929 (p)
REVERT: D  318 PHE cc_start: 0.6959 (t80) cc_final: 0.6728 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.2405
  time to fit residues: 22.7815
Evaluate side-chains
  72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 50 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0000
   overall best weight:    0.1982

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN
D 282 HIS
D 304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.131828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.113892 restraints weight = 5810.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.75
r_work: 0.3436 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4523  Z= 0.137
  Angle     :  0.508   7.173   6135  Z= 0.272
  Chirality :  0.038   0.186    752
  Planarity :  0.005   0.069    712
  Dihedral  : 11.068  80.245    676
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.94 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.69 (0.34), residues: 545
  helix:  3.16 (0.22), residues: 427
  sheet:  2.44 (0.97), residues: 34
  loop : -1.84 (0.63), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 279 
 TYR   0.011   0.001   TYR D 103 
 PHE   0.008   0.001   PHE C 275 
 TRP   0.016   0.001   TRP D 229 
 HIS   0.001   0.000   HIS C 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4521)
  covalent geometry    : angle       0.50739 ( 6131)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       0.67621 (    4)
  hydrogen bonds       : bond        0.04549 (  385)
  hydrogen bonds       : angle       4.18547 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.177 
Fit side-chains
REVERT: D  279 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8492 (ttm170)
  outliers start: 10
  outliers final: 2
  residues processed: 72
  average time/residue: 0.2628
  time to fit residues: 20.3406
Evaluate side-chains
  67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  195 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
D 282 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.129965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.112266 restraints weight = 5775.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.71
r_work: 0.3418 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4523  Z= 0.203
  Angle     :  0.561   7.927   6135  Z= 0.297
  Chirality :  0.042   0.210    752
  Planarity :  0.006   0.065    712
  Dihedral  : 11.215  82.847    676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  7.13 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.85 (0.34), residues: 545
  helix:  3.22 (0.22), residues: 430
  sheet:  2.40 (0.95), residues: 34
  loop : -1.61 (0.68), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.012   0.001   TYR D 103 
 PHE   0.016   0.002   PHE D 318 
 TRP   0.011   0.001   TRP C 183 
 HIS   0.002   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 4521)
  covalent geometry    : angle       0.56152 ( 6131)
  SS BOND              : bond        0.00330 (    2)
  SS BOND              : angle       0.47185 (    4)
  hydrogen bonds       : bond        0.05052 (  385)
  hydrogen bonds       : angle       4.13028 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.154 
Fit side-chains
REVERT: C  107 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7487 (mt)
REVERT: D  279 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8452 (ttt90)
  outliers start: 13
  outliers final: 6
  residues processed: 72
  average time/residue: 0.2250
  time to fit residues: 17.4604
Evaluate side-chains
  71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  328 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 18 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0770
   overall best weight:    0.3138

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

Flipped N/Q/H residues before XYZ refinement:
D 256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.112922 restraints weight = 5699.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.71
r_work: 0.3434 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4523  Z= 0.149
  Angle     :  0.504   7.132   6135  Z= 0.269
  Chirality :  0.039   0.185    752
  Planarity :  0.005   0.066    712
  Dihedral  : 10.955  85.355    676
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  9.57 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.09 (0.34), residues: 545
  helix:  3.39 (0.22), residues: 428
  sheet:  2.77 (0.92), residues: 34
  loop : -1.55 (0.67), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 279 
 TYR   0.011   0.001   TYR D 103 
 PHE   0.011   0.001   PHE D 318 
 TRP   0.007   0.001   TRP C 284 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4521)
  covalent geometry    : angle       0.50369 ( 6131)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.36924 (    4)
  hydrogen bonds       : bond        0.04513 (  385)
  hydrogen bonds       : angle       4.00580 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.159 
Fit side-chains
REVERT: C  107 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7471 (mt)
REVERT: C  149 PHE cc_start: 0.7226 (t80) cc_final: 0.6868 (t80)
REVERT: C  319 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6820 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 69
  average time/residue: 0.2642
  time to fit residues: 19.4580
Evaluate side-chains
  70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain C residue  319 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  328 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0870
   chunk 3 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0670
   chunk 32 optimal weight:    0.1980
   chunk 23 optimal weight:    0.1980
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.1296

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN
C 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.131844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114543 restraints weight = 5766.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.72
r_work: 0.3440 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4523  Z= 0.112
  Angle     :  0.468   6.859   6135  Z= 0.249
  Chirality :  0.037   0.184    752
  Planarity :  0.005   0.068    712
  Dihedral  : 10.618  83.158    676
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.59 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.33 (0.34), residues: 545
  helix:  3.52 (0.22), residues: 429
  sheet:  2.90 (0.91), residues: 34
  loop : -1.31 (0.69), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 279 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.007   0.001   PHE C 275 
 TRP   0.006   0.001   TRP D 315 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4521)
  covalent geometry    : angle       0.46761 ( 6131)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.26922 (    4)
  hydrogen bonds       : bond        0.04043 (  385)
  hydrogen bonds       : angle       3.86898 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.102 
Fit side-chains
REVERT: C  149 PHE cc_start: 0.7228 (t80) cc_final: 0.6863 (t80)
REVERT: D  279 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8321 (ttm170)
  outliers start: 11
  outliers final: 3
  residues processed: 74
  average time/residue: 0.2713
  time to fit residues: 21.3245
Evaluate side-chains
  67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.128987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.111513 restraints weight = 5876.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.72
r_work: 0.3394 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4523  Z= 0.220
  Angle     :  0.569   7.494   6135  Z= 0.299
  Chirality :  0.043   0.207    752
  Planarity :  0.006   0.071    712
  Dihedral  : 11.432  86.707    676
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.22 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.02 (0.34), residues: 545
  helix:  3.27 (0.22), residues: 432
  sheet:  2.76 (0.88), residues: 34
  loop : -1.43 (0.69), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.012   0.001   TYR C 146 
 PHE   0.017   0.002   PHE D 318 
 TRP   0.009   0.001   TRP C 284 
 HIS   0.001   0.000   HIS C 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 4521)
  covalent geometry    : angle       0.56877 ( 6131)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       0.46918 (    4)
  hydrogen bonds       : bond        0.04940 (  385)
  hydrogen bonds       : angle       4.05096 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.165 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.8146 (m-80) cc_final: 0.7619 (m-80)
REVERT: C  149 PHE cc_start: 0.7288 (t80) cc_final: 0.6945 (t80)
REVERT: C  174 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.2511
  time to fit residues: 19.3693
Evaluate side-chains
  71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  328 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.129058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.111734 restraints weight = 5818.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.71
r_work: 0.3400 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4523  Z= 0.201
  Angle     :  0.566   9.314   6135  Z= 0.295
  Chirality :  0.042   0.207    752
  Planarity :  0.006   0.070    712
  Dihedral  : 11.583  88.895    676
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.24 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.96 (0.34), residues: 545
  helix:  3.25 (0.22), residues: 431
  sheet:  2.74 (0.87), residues: 34
  loop : -1.54 (0.68), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 279 
 TYR   0.010   0.001   TYR C 280 
 PHE   0.017   0.002   PHE C 275 
 TRP   0.008   0.001   TRP C 284 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 4521)
  covalent geometry    : angle       0.56639 ( 6131)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       0.33326 (    4)
  hydrogen bonds       : bond        0.04753 (  385)
  hydrogen bonds       : angle       4.03923 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.175 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.8141 (m-80) cc_final: 0.7604 (m-80)
REVERT: C  149 PHE cc_start: 0.7297 (t80) cc_final: 0.6956 (t80)
REVERT: C  174 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7493 (ttp)
REVERT: C  328 MET cc_start: 0.7519 (mmp) cc_final: 0.7289 (mmp)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2929
  time to fit residues: 21.6959
Evaluate side-chains
  71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  328 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 31 optimal weight:    0.3980
   chunk 27 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0770
   overall best weight:    0.2538

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.130598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.113355 restraints weight = 5778.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.70
r_work: 0.3426 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4523  Z= 0.136
  Angle     :  0.526   8.103   6135  Z= 0.273
  Chirality :  0.040   0.207    752
  Planarity :  0.005   0.068    712
  Dihedral  : 11.449  89.684    676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.24 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.20 (0.34), residues: 545
  helix:  3.43 (0.22), residues: 430
  sheet:  2.80 (0.88), residues: 34
  loop : -1.41 (0.68), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 279 
 TYR   0.009   0.001   TYR D 103 
 PHE   0.013   0.001   PHE C 275 
 TRP   0.007   0.001   TRP D 315 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4521)
  covalent geometry    : angle       0.52600 ( 6131)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.26025 (    4)
  hydrogen bonds       : bond        0.04294 (  385)
  hydrogen bonds       : angle       3.91994 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.169 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.8114 (m-80) cc_final: 0.7604 (m-80)
REVERT: C  149 PHE cc_start: 0.7292 (t80) cc_final: 0.6946 (t80)
REVERT: C  174 MET cc_start: 0.7618 (ttp) cc_final: 0.7388 (ttp)
REVERT: C  319 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: C  328 MET cc_start: 0.7498 (mmp) cc_final: 0.7206 (mmp)
  outliers start: 9
  outliers final: 6
  residues processed: 70
  average time/residue: 0.2948
  time to fit residues: 21.9912
Evaluate side-chains
  71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain C residue  319 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.129221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.112036 restraints weight = 5783.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.70
r_work: 0.3405 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4523  Z= 0.184
  Angle     :  0.573  11.800   6135  Z= 0.293
  Chirality :  0.042   0.211    752
  Planarity :  0.005   0.069    712
  Dihedral  : 11.567  86.845    676
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.03 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.05 (0.34), residues: 545
  helix:  3.31 (0.22), residues: 431
  sheet:  2.70 (0.86), residues: 34
  loop : -1.40 (0.68), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.010   0.001   TYR D 103 
 PHE   0.016   0.002   PHE C 275 
 TRP   0.008   0.001   TRP C 284 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 4521)
  covalent geometry    : angle       0.57347 ( 6131)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       0.38169 (    4)
  hydrogen bonds       : bond        0.04620 (  385)
  hydrogen bonds       : angle       3.99283 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.144 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.8120 (m-80) cc_final: 0.7613 (m-80)
REVERT: C  149 PHE cc_start: 0.7308 (t80) cc_final: 0.6972 (t80)
REVERT: C  174 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7450 (ttp)
REVERT: C  319 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6969 (mp0)
REVERT: C  326 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6813 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 0.3074
  time to fit residues: 22.2176
Evaluate side-chains
  71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain C residue  319 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   chunk 50 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.128375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.111294 restraints weight = 5748.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.68
r_work: 0.3395 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4523  Z= 0.215
  Angle     :  0.616  15.067   6135  Z= 0.311
  Chirality :  0.044   0.218    752
  Planarity :  0.006   0.071    712
  Dihedral  : 11.796  78.408    676
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.85 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.90 (0.34), residues: 545
  helix:  3.21 (0.22), residues: 431
  sheet:  2.66 (0.85), residues: 34
  loop : -1.51 (0.68), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.011   0.001   TYR C 146 
 PHE   0.018   0.002   PHE C 275 
 TRP   0.009   0.001   TRP D  54 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 4521)
  covalent geometry    : angle       0.61657 ( 6131)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       0.40287 (    4)
  hydrogen bonds       : bond        0.04857 (  385)
  hydrogen bonds       : angle       4.06358 ( 1152)

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

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

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1090 Ramachandran restraints generated.
    545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.113 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.8124 (m-80) cc_final: 0.7601 (m-80)
REVERT: C  149 PHE cc_start: 0.7325 (t80) cc_final: 0.7001 (t80)
REVERT: C  174 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7513 (ttp)
REVERT: C  182 THR cc_start: 0.8260 (t) cc_final: 0.8048 (m)
REVERT: C  319 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6940 (mp0)
REVERT: C  326 ARG cc_start: 0.7208 (mmm-85) cc_final: 0.6857 (mmm-85)
  outliers start: 8
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2943
  time to fit residues: 20.2241
Evaluate side-chains
  69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  282 HIS
Chi-restraints excluded: chain C residue  319 GLU
Chi-restraints excluded: chain D residue  127 LEU
Chi-restraints excluded: chain D residue  174 MET
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 5 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 49 optimal weight:    0.7980
   chunk 23 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.129377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.112222 restraints weight = 5805.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.70
r_work: 0.3413 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4523  Z= 0.153
  Angle     :  0.534   8.260   6135  Z= 0.280
  Chirality :  0.040   0.211    752
  Planarity :  0.005   0.068    712
  Dihedral  : 11.416  73.026    676
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.26 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.03 (0.34), residues: 545
  helix:  3.30 (0.22), residues: 431
  sheet:  2.61 (0.86), residues: 34
  loop : -1.41 (0.68), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.010   0.001   TYR D 103 
 PHE   0.015   0.001   PHE C 275 
 TRP   0.007   0.001   TRP D 315 
 HIS   0.001   0.000   HIS C 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4521)
  covalent geometry    : angle       0.53441 ( 6131)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.27651 (    4)
  hydrogen bonds       : bond        0.04458 (  385)
  hydrogen bonds       : angle       3.94215 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1611.98 seconds
wall clock time: 28 minutes 11.42 seconds (1691.42 seconds total)