Starting phenix.real_space_refine
on Fri Aug 22 13:28:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ber_16009/08_2025/8ber_16009.map"
  }
  resolution = 4.0
  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=   0.079 sd=   0.328
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: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2157      2.51       5
     N     546      2.21       5
     O     588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 3309
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1103
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 11, 'TRANS': 126}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1103
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 11, 'TRANS': 126}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1103
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 11, 'TRANS': 126}
          Chain breaks: 1
  Time building chain proxies: 1.23, per 1000 atoms: 0.37
  Number of scatterers: 3309
  At special positions: 0
  Unit cell: (94.095, 70.848, 81.918, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     588      8.00
     N     546      7.00
     C    2157      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS B  59 " 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: 0.34
  Conformation dependent library (CDL) restraints added in 155.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      78.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 8
    Processing helix  chain 'A' and resid 10 through 15
    Processing helix  chain 'A' and resid 16 through 17
      No H-bonds generated for 'chain 'A' and resid 16 through 17'
    Processing helix  chain 'A' and resid 18 through 22
    Processing helix  chain 'A' and resid 24 through 41
      removed outlier: 3.882A  pdb=" N   ARG A  37 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   GLU A  38 " --> pdb=" O   ALA A  34 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   ALA A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 73
      removed outlier: 3.664A  pdb=" N   THR A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 232 through 250
      removed outlier: 3.573A  pdb=" N   LYS A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
    Processing helix  chain 'B' and resid 10 through 16
    Processing helix  chain 'B' and resid 17 through 22
      removed outlier: 6.190A  pdb=" N   ASP B  20 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 36
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 47 through 73
    Processing helix  chain 'B' and resid 222 through 232
      removed outlier: 3.790A  pdb=" N   VAL B 226 " --> pdb=" O   ARG B 222 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 251
    Processing helix  chain 'B' and resid 251 through 268
      removed outlier: 4.230A  pdb=" N   THR B 268 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 15
    Processing helix  chain 'C' and resid 16 through 17
      No H-bonds generated for 'chain 'C' and resid 16 through 17'
    Processing helix  chain 'C' and resid 18 through 22
    Processing helix  chain 'C' and resid 24 through 42
      removed outlier: 3.925A  pdb=" N   ARG C  37 " --> pdb=" O   SER C  33 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLU C  38 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   ALA C  39 " --> pdb=" O   LEU C  35 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER C  42 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 73
    Processing helix  chain 'C' and resid 224 through 251
      removed outlier: 5.207A  pdb=" N   LEU C 235 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LYS C 236 " --> pdb=" O   ASN C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 268

    221 hydrogen bonds defined for protein.
    639 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: 0.45

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1029
        1.34 -     1.46: 694
        1.46 -     1.57: 1661
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 3411
  Sorted by residual:
  bond pdb=" CA  ILE A 279 "
       pdb=" CB  ILE A 279 "
    ideal  model  delta    sigma   weight residual
    1.527  1.547 -0.021 1.31e-02 5.83e+03 2.45e+00
  bond pdb=" CG  MET C  64 "
       pdb=" SD  MET C  64 "
    ideal  model  delta    sigma   weight residual
    1.803  1.772  0.031 2.50e-02 1.60e+03 1.54e+00
  bond pdb=" CD  GLU A 257 "
       pdb=" OE1 GLU A 257 "
    ideal  model  delta    sigma   weight residual
    1.249  1.226  0.023 1.90e-02 2.77e+03 1.45e+00
  bond pdb=" CG  GLU A 257 "
       pdb=" CD  GLU A 257 "
    ideal  model  delta    sigma   weight residual
    1.516  1.487  0.029 2.50e-02 1.60e+03 1.32e+00
  bond pdb=" CG  GLU C 257 "
       pdb=" CD  GLU C 257 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.23e+00
  ... (remaining 3406 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 4591
        2.16 -     4.32: 63
        4.32 -     6.48: 7
        6.48 -     8.64: 0
        8.64 -    10.79: 1
  Bond angle restraints: 4662
  Sorted by residual:
  angle pdb=" C   TYR A 272 "
        pdb=" N   ARG A 273 "
        pdb=" CA  ARG A 273 "
      ideal   model   delta    sigma   weight residual
     120.49  131.28  -10.79 1.42e+00 4.96e-01 5.78e+01
  angle pdb=" N   GLU C 257 "
        pdb=" CA  GLU C 257 "
        pdb=" CB  GLU C 257 "
      ideal   model   delta    sigma   weight residual
     110.28  116.61   -6.33 1.55e+00 4.16e-01 1.67e+01
  angle pdb=" N   GLU A 257 "
        pdb=" CA  GLU A 257 "
        pdb=" CB  GLU A 257 "
      ideal   model   delta    sigma   weight residual
     110.28  116.25   -5.97 1.55e+00 4.16e-01 1.49e+01
  angle pdb=" C   ILE C 256 "
        pdb=" N   GLU C 257 "
        pdb=" CA  GLU C 257 "
      ideal   model   delta    sigma   weight residual
     120.31  115.08    5.23 1.52e+00 4.33e-01 1.18e+01
  angle pdb=" C   ASN C 232 "
        pdb=" N   MET C 233 "
        pdb=" CA  MET C 233 "
      ideal   model   delta    sigma   weight residual
     122.23  117.61    4.62 1.57e+00 4.06e-01 8.64e+00
  ... (remaining 4657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.96: 1709
       11.96 -    23.92: 200
       23.92 -    35.88: 62
       35.88 -    47.85: 22
       47.85 -    59.81: 8
  Dihedral angle restraints: 2001
    sinusoidal: 792
      harmonic: 1209
  Sorted by residual:
  dihedral pdb=" CA  ILE B 266 "
           pdb=" C   ILE B 266 "
           pdb=" N   ARG B 267 "
           pdb=" CA  ARG B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.34  -21.66     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS B  59 "
           pdb=" CB  CYS B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.36  -30.36     1      1.00e+01 1.00e-02 1.32e+01
  dihedral pdb=" CA  ARG B 267 "
           pdb=" C   ARG B 267 "
           pdb=" N   THR B 268 "
           pdb=" CA  THR B 268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 1998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 452
       0.056 -    0.112: 66
       0.112 -    0.168: 4
       0.168 -    0.224: 1
       0.224 -    0.280: 2
  Chirality restraints: 525
  Sorted by residual:
  chirality pdb=" CB  ILE A 279 "
            pdb=" CA  ILE A 279 "
            pdb=" CG1 ILE A 279 "
            pdb=" CG2 ILE A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CB  ILE C 279 "
            pdb=" CA  ILE C 279 "
            pdb=" CG1 ILE C 279 "
            pdb=" CG2 ILE C 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CB  THR C 282 "
            pdb=" CA  THR C 282 "
            pdb=" OG1 THR C 282 "
            pdb=" CG2 THR C 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 522 not shown)

  Planarity restraints: 585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 230 "   -0.014 2.00e-02 2.50e+03   2.71e-02 7.36e+00
        pdb=" C   ASN C 230 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ASN C 230 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR C 231 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 269 "   -0.028 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO B 270 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 273 "   -0.019 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO C 274 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 274 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 274 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 582 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 480
        2.75 -     3.29: 3664
        3.29 -     3.83: 5909
        3.83 -     4.36: 6389
        4.36 -     4.90: 10758
  Nonbonded interactions: 27200
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 228 "
            pdb=" ND2 ASN C 232 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O   VAL A  11 "
            pdb=" OG  SER A  15 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASN C 230 "
            pdb=" N   THR C 231 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OE2 GLU A   6 "
            pdb=" NH1 ARG B  54 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   VAL A 229 "
            pdb=" N   GLY A 234 "
     model   vdw
     2.284 3.120
  ... (remaining 27195 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'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.610
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.900
  Find NCS groups from input model:        0.040
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
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      :  0.003   0.031   3412  Z= 0.145
  Angle     :  0.613  10.795   4664  Z= 0.352
  Chirality :  0.041   0.280    525
  Planarity :  0.004   0.042    585
  Dihedral  : 12.678  59.807   1212
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.47 (0.44), residues: 402
  helix:  1.88 (0.31), residues: 294
  sheet:  None (None), residues: 0
  loop :  1.18 (0.68), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  54 
 TYR   0.006   0.001   TYR A 272 
 PHE   0.013   0.001   PHE B 237 
 TRP   0.017   0.001   TRP C  60 
 HIS   0.002   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3411)
  covalent geometry    : angle       0.61259 ( 4662)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       0.42843 (    2)
  hydrogen bonds       : bond        0.12766 (  221)
  hydrogen bonds       : angle       5.87873 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   64 MET cc_start: 0.9413 (mmp) cc_final: 0.9127 (mmt)
REVERT: A  233 MET cc_start: 0.9353 (mpp) cc_final: 0.9003 (mpp)
REVERT: B   64 MET cc_start: 0.9228 (mmp) cc_final: 0.8838 (mmt)
REVERT: B  233 MET cc_start: 0.9501 (pmm) cc_final: 0.9161 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0593
  time to fit residues: 1.6726
Evaluate side-chains
  11 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:   30.0000
   chunk 2 optimal weight:   30.0000
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:   30.0000
   chunk 22 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.3139 r_free = 0.3139 target = 0.030298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.027331 restraints weight = 58745.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.027889 restraints weight = 35580.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.028275 restraints weight = 24568.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.028550 restraints weight = 18371.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.028759 restraints weight = 14551.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3412  Z= 0.179
  Angle     :  0.626   6.944   4664  Z= 0.340
  Chirality :  0.043   0.288    525
  Planarity :  0.005   0.041    585
  Dihedral  :  4.633  21.932    447
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.55 (0.43), residues: 402
  helix:  1.98 (0.30), residues: 297
  sheet:  None (None), residues: 0
  loop :  1.04 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  54 
 TYR   0.008   0.001   TYR C 272 
 PHE   0.017   0.001   PHE B 237 
 TRP   0.012   0.001   TRP B  69 
 HIS   0.003   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3411)
  covalent geometry    : angle       0.62631 ( 4662)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.29860 (    2)
  hydrogen bonds       : bond        0.04286 (  221)
  hydrogen bonds       : angle       5.17237 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   64 MET cc_start: 0.9197 (mmp) cc_final: 0.8792 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0567
  time to fit residues: 1.0548
Evaluate side-chains
  12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 34 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    3.7586

-------------------------------------------------------------------------------
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 = 0.3141 r_free = 0.3141 target = 0.030323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.027331 restraints weight = 57739.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.027897 restraints weight = 35233.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.028273 restraints weight = 24291.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.028552 restraints weight = 18221.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.028746 restraints weight = 14475.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3412  Z= 0.130
  Angle     :  0.608   8.723   4664  Z= 0.316
  Chirality :  0.040   0.241    525
  Planarity :  0.004   0.044    585
  Dihedral  :  4.603  21.759    447
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.65 %
    Favored  : 91.80 %
  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:  2.56 (0.43), residues: 402
  helix:  1.95 (0.30), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.14 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  54 
 TYR   0.011   0.001   TYR B 228 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.009   0.001   TRP B 265 
 HIS   0.002   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3411)
  covalent geometry    : angle       0.60786 ( 4662)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       0.41416 (    2)
  hydrogen bonds       : bond        0.03985 (  221)
  hydrogen bonds       : angle       4.90589 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9221 (mmp) cc_final: 0.8786 (mmt)
REVERT: C  253 GLU cc_start: 0.9321 (pm20) cc_final: 0.9014 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0439
  time to fit residues: 0.9508
Evaluate side-chains
  13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:   30.0000
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 18 optimal weight:   30.0000
   chunk 13 optimal weight:   30.0000
   overall best weight:    4.9188

-------------------------------------------------------------------------------
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 = 0.3131 r_free = 0.3131 target = 0.030259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.027267 restraints weight = 57456.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.027812 restraints weight = 35249.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.028193 restraints weight = 24429.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.028459 restraints weight = 18389.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.028666 restraints weight = 14700.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3412  Z= 0.139
  Angle     :  0.630   9.736   4664  Z= 0.328
  Chirality :  0.040   0.226    525
  Planarity :  0.004   0.042    585
  Dihedral  :  4.575  21.544    447
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 10.11 %
    Favored  : 89.34 %
  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:  2.56 (0.43), residues: 402
  helix:  1.94 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.18 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  54 
 TYR   0.012   0.001   TYR B 228 
 PHE   0.008   0.001   PHE B 237 
 TRP   0.010   0.001   TRP B  69 
 HIS   0.002   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3411)
  covalent geometry    : angle       0.62958 ( 4662)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.48918 (    2)
  hydrogen bonds       : bond        0.03850 (  221)
  hydrogen bonds       : angle       4.83608 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9206 (mmp) cc_final: 0.8817 (mmt)
REVERT: C  253 GLU cc_start: 0.9307 (pm20) cc_final: 0.9044 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0483
  time to fit residues: 1.0421
Evaluate side-chains
  13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:   30.0000
   chunk 30 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:   50.0000
   chunk 21 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:   40.0000
   chunk 2 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3119 r_free = 0.3119 target = 0.030089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.027159 restraints weight = 57899.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.027711 restraints weight = 34763.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.028081 restraints weight = 23771.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.028356 restraints weight = 17785.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.028546 restraints weight = 14080.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3412  Z= 0.165
  Angle     :  0.640  10.090   4664  Z= 0.330
  Chirality :  0.040   0.228    525
  Planarity :  0.004   0.042    585
  Dihedral  :  4.589  21.839    447
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.66 %
    Favored  : 88.52 %
  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:  2.61 (0.44), residues: 402
  helix:  1.99 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.15 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  54 
 TYR   0.011   0.001   TYR B 228 
 PHE   0.009   0.001   PHE C 237 
 TRP   0.010   0.001   TRP B  69 
 HIS   0.003   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3411)
  covalent geometry    : angle       0.64039 ( 4662)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.36610 (    2)
  hydrogen bonds       : bond        0.03740 (  221)
  hydrogen bonds       : angle       4.79193 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9258 (mmp) cc_final: 0.8848 (mmt)
REVERT: C  253 GLU cc_start: 0.9332 (pm20) cc_final: 0.9073 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 15
  average time/residue: 0.0568
  time to fit residues: 1.2780
Evaluate side-chains
  13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 1 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 6 optimal weight:   30.0000
   chunk 27 optimal weight:    9.9990
   overall best weight:    4.2786

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.030264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.027349 restraints weight = 57876.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.027894 restraints weight = 34860.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.028273 restraints weight = 23890.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.028537 restraints weight = 17867.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.028731 restraints weight = 14270.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3412  Z= 0.126
  Angle     :  0.600   9.629   4664  Z= 0.311
  Chirality :  0.039   0.206    525
  Planarity :  0.004   0.040    585
  Dihedral  :  4.523  21.692    447
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.02 %
    Favored  : 87.43 %
  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:  2.72 (0.44), residues: 402
  helix:  2.07 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.21 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  54 
 TYR   0.014   0.001   TYR B 228 
 PHE   0.007   0.001   PHE C  16 
 TRP   0.009   0.001   TRP B  69 
 HIS   0.002   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3411)
  covalent geometry    : angle       0.59992 ( 4662)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.37375 (    2)
  hydrogen bonds       : bond        0.03587 (  221)
  hydrogen bonds       : angle       4.64831 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9262 (mmp) cc_final: 0.8858 (mmt)
REVERT: C   64 MET cc_start: 0.9019 (mmm) cc_final: 0.8776 (mmm)
REVERT: C  253 GLU cc_start: 0.9299 (pm20) cc_final: 0.9065 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0587
  time to fit residues: 1.2220
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:   30.0000
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.030014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.027078 restraints weight = 59131.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.027634 restraints weight = 35004.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.028023 restraints weight = 23812.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.028286 restraints weight = 17630.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.028492 restraints weight = 14016.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3412  Z= 0.167
  Angle     :  0.609   8.154   4664  Z= 0.319
  Chirality :  0.039   0.218    525
  Planarity :  0.004   0.040    585
  Dihedral  :  4.529  21.758    447
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.57 %
    Favored  : 86.89 %
  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:  2.76 (0.44), residues: 402
  helix:  2.11 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.19 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  54 
 TYR   0.011   0.001   TYR B 228 
 PHE   0.008   0.001   PHE A  21 
 TRP   0.011   0.001   TRP B  69 
 HIS   0.003   0.001   HIS B  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3411)
  covalent geometry    : angle       0.60865 ( 4662)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.36535 (    2)
  hydrogen bonds       : bond        0.03508 (  221)
  hydrogen bonds       : angle       4.62166 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9297 (mmp) cc_final: 0.8873 (mmt)
REVERT: C   64 MET cc_start: 0.9046 (mmm) cc_final: 0.8826 (mmm)
REVERT: C  253 GLU cc_start: 0.9365 (pm20) cc_final: 0.9115 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0561
  time to fit residues: 1.1653
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:   50.0000
   chunk 2 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   overall best weight:    4.7788

-------------------------------------------------------------------------------
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 = 0.3122 r_free = 0.3122 target = 0.030102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.026980 restraints weight = 59737.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.027598 restraints weight = 34119.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.028021 restraints weight = 22603.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.028312 restraints weight = 16468.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.028538 restraints weight = 12887.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3412  Z= 0.130
  Angle     :  0.585   8.982   4664  Z= 0.306
  Chirality :  0.039   0.202    525
  Planarity :  0.004   0.040    585
  Dihedral  :  4.478  21.765    447
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 13.11 %
    Favored  : 86.34 %
  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:  2.80 (0.44), residues: 402
  helix:  2.13 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.22 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.012   0.001   TYR B 228 
 PHE   0.007   0.001   PHE C  16 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.002   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3411)
  covalent geometry    : angle       0.58492 ( 4662)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.32746 (    2)
  hydrogen bonds       : bond        0.03494 (  221)
  hydrogen bonds       : angle       4.53570 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9328 (mmp) cc_final: 0.8884 (mmt)
REVERT: C   64 MET cc_start: 0.9039 (mmm) cc_final: 0.8825 (mmm)
REVERT: C  253 GLU cc_start: 0.9351 (pm20) cc_final: 0.9110 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0564
  time to fit residues: 1.1758
Evaluate side-chains
  14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   chunk 17 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    9.1990

-------------------------------------------------------------------------------
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 = 0.3110 r_free = 0.3110 target = 0.029803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.026843 restraints weight = 58947.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.027399 restraints weight = 35385.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.027782 restraints weight = 24232.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.028056 restraints weight = 18097.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.028256 restraints weight = 14403.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3412  Z= 0.208
  Angle     :  0.636   9.076   4664  Z= 0.335
  Chirality :  0.040   0.225    525
  Planarity :  0.005   0.040    585
  Dihedral  :  4.667  22.587    447
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 13.66 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.69 (0.44), residues: 402
  helix:  2.08 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.09 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 267 
 TYR   0.013   0.002   TYR A 272 
 PHE   0.009   0.001   PHE C 237 
 TRP   0.013   0.002   TRP A  60 
 HIS   0.003   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 3411)
  covalent geometry    : angle       0.63622 ( 4662)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.30161 (    2)
  hydrogen bonds       : bond        0.03615 (  221)
  hydrogen bonds       : angle       4.67440 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9350 (mmp) cc_final: 0.8919 (mmt)
  outliers start: 2
  outliers final: 2
  residues processed: 12
  average time/residue: 0.0605
  time to fit residues: 1.1048
Evaluate side-chains
  12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0170
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   overall best weight:    3.7624

-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.029988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.027032 restraints weight = 57712.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.027590 restraints weight = 34567.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.027964 restraints weight = 23664.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.028239 restraints weight = 17742.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.028426 restraints weight = 14080.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3412  Z= 0.121
  Angle     :  0.585   8.884   4664  Z= 0.308
  Chirality :  0.039   0.198    525
  Planarity :  0.004   0.040    585
  Dihedral  :  4.528  22.146    447
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.93 %
    Favored  : 85.25 %
  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:  2.75 (0.44), residues: 402
  helix:  2.10 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.20 (0.68), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.010   0.001   TYR B 228 
 PHE   0.008   0.001   PHE C  16 
 TRP   0.012   0.002   TRP A  60 
 HIS   0.002   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3411)
  covalent geometry    : angle       0.58513 ( 4662)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.25228 (    2)
  hydrogen bonds       : bond        0.03500 (  221)
  hydrogen bonds       : angle       4.52368 (  639)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 MET cc_start: 0.9369 (mmp) cc_final: 0.8928 (mmt)
REVERT: C  253 GLU cc_start: 0.9342 (pm20) cc_final: 0.9111 (pm20)
  outliers start: 3
  outliers final: 3
  residues processed: 15
  average time/residue: 0.0566
  time to fit residues: 1.3034
Evaluate side-chains
  15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue  257 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3111 r_free = 0.3111 target = 0.029877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.026879 restraints weight = 59257.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.027442 restraints weight = 35643.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.027827 restraints weight = 24444.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.028095 restraints weight = 18229.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.028309 restraints weight = 14554.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3412  Z= 0.166
  Angle     :  0.618   9.366   4664  Z= 0.323
  Chirality :  0.039   0.212    525
  Planarity :  0.004   0.040    585
  Dihedral  :  4.546  21.993    447
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 14.48 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.72 (0.44), residues: 402
  helix:  2.08 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop :  1.18 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.011   0.002   TYR A 272 
 PHE   0.009   0.001   PHE C 237 
 TRP   0.014   0.002   TRP A  60 
 HIS   0.002   0.001   HIS C  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3411)
  covalent geometry    : angle       0.61849 ( 4662)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.32498 (    2)
  hydrogen bonds       : bond        0.03497 (  221)
  hydrogen bonds       : angle       4.58405 (  639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 711.96 seconds
wall clock time: 13 minutes 3.25 seconds (783.25 seconds total)