Starting phenix.real_space_refine
on Wed Sep 17 05:16:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2025/9u48_63834.map"
  }
  resolution = 2.99
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1301 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      49      5.49       5
     S      21      5.16       5
     C    2206      2.51       5
     N     666      2.21       5
     O     848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3790
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2712
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 320}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1051
          Classifications: {'RNA': 49}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 10, 'rna3p': 38}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" P     C B  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" C6    C B  36 " occ=0.50
    residue:
      pdb=" P     U B  82 " occ=0.50
      ... (18 atoms not shown)
      pdb=" C6    U B  82 " occ=0.50
    residue:
      pdb=" P     G B  83 " occ=0.50
      ... (21 atoms not shown)
      pdb=" C4    G B  83 " occ=0.50
  Time building chain proxies: 0.91, per 1000 atoms: 0.24
  Number of scatterers: 3790
  At special positions: 0
  Unit cell: (59.76, 69.72, 90.47, 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      21     16.00
     P      49     15.00
     O     848      8.00
     N     666      7.00
     C    2206      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 105.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  638

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 0 sheets defined
      37.3% alpha, 0.0% beta
      13 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 79
    Processing helix  chain 'A' and resid 102 through 111
      removed outlier: 3.697A  pdb=" N   MET A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR A 111 " --> pdb=" O   GLY A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 175 through 181
    Processing helix  chain 'A' and resid 202 through 215
      removed outlier: 3.769A  pdb=" N   LYS A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 243
      Proline residue:  A 234  - end of helix
    Processing helix  chain 'A' and resid 274 through 277
      No H-bonds generated for 'chain 'A' and resid 274 through 277'
    Processing helix  chain 'A' and resid 285 through 287
      No H-bonds generated for 'chain 'A' and resid 285 through 287'
    Processing helix  chain 'A' and resid 300 through 317
      removed outlier: 6.744A  pdb=" N   ASP A 307 " --> pdb=" O   CYS A 303 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   ASP A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASN A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 346
    Processing helix  chain 'A' and resid 379 through 397
      removed outlier: 3.617A  pdb=" N   ASN A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    216 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      52 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1019
        1.34 -     1.46: 1028
        1.46 -     1.57: 1801
        1.57 -     1.69: 97
        1.69 -     1.81: 32
  Bond restraints: 3977
  Sorted by residual:
  bond pdb=" C   TYR A  70 "
       pdb=" N   ILE A  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.267  0.068 1.26e-02 6.30e+03 2.88e+01
  bond pdb=" O3'   G B  43 "
       pdb=" P     A B  44 "
    ideal  model  delta    sigma   weight residual
    1.607  1.651 -0.044 1.50e-02 4.44e+03 8.49e+00
  bond pdb=" O3'   A B  35 "
       pdb=" P     C B  36 "
    ideal  model  delta    sigma   weight residual
    1.607  1.651 -0.044 1.50e-02 4.44e+03 8.46e+00
  bond pdb=" N   THR A  81 "
       pdb=" CA  THR A  81 "
    ideal  model  delta    sigma   weight residual
    1.458  1.481 -0.023 1.00e-02 1.00e+04 5.12e+00
  bond pdb=" O3'   G B  40 "
       pdb=" P     A B  41 "
    ideal  model  delta    sigma   weight residual
    1.607  1.639 -0.032 1.50e-02 4.44e+03 4.43e+00
  ... (remaining 3972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 5402
        1.77 -     3.54: 177
        3.54 -     5.32: 21
        5.32 -     7.09: 7
        7.09 -     8.86: 2
  Bond angle restraints: 5609
  Sorted by residual:
  angle pdb=" O3'   A B  35 "
        pdb=" C3'   A B  35 "
        pdb=" C2'   A B  35 "
      ideal   model   delta    sigma   weight residual
     109.50  118.36   -8.86 1.50e+00 4.44e-01 3.49e+01
  angle pdb=" O3'   G B  43 "
        pdb=" C3'   G B  43 "
        pdb=" C2'   G B  43 "
      ideal   model   delta    sigma   weight residual
     113.70  107.14    6.56 1.50e+00 4.44e-01 1.92e+01
  angle pdb=" C4'   G B  43 "
        pdb=" C3'   G B  43 "
        pdb=" O3'   G B  43 "
      ideal   model   delta    sigma   weight residual
     113.00  119.17   -6.17 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" C4'   A B  35 "
        pdb=" C3'   A B  35 "
        pdb=" O3'   A B  35 "
      ideal   model   delta    sigma   weight residual
     109.40  114.88   -5.48 1.50e+00 4.44e-01 1.34e+01
  angle pdb=" CA  PRO A  65 "
        pdb=" C   PRO A  65 "
        pdb=" O   PRO A  65 "
      ideal   model   delta    sigma   weight residual
     118.29  121.61   -3.32 9.60e-01 1.09e+00 1.20e+01
  ... (remaining 5604 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.44: 2282
       33.44 -    66.87: 164
       66.87 -   100.31: 24
      100.31 -   133.75: 1
      133.75 -   167.18: 1
  Dihedral angle restraints: 2472
    sinusoidal: 1488
      harmonic: 984
  Sorted by residual:
  dihedral pdb=" C5'   A B  35 "
           pdb=" C4'   A B  35 "
           pdb=" C3'   A B  35 "
           pdb=" O3'   A B  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   96.14   50.86     1      8.00e+00 1.56e-02 5.53e+01
  dihedral pdb=" O4'   A B  35 "
           pdb=" C4'   A B  35 "
           pdb=" C3'   A B  35 "
           pdb=" C2'   A B  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -10.65   34.65     1      8.00e+00 1.56e-02 2.66e+01
  dihedral pdb=" C3'   A B  35 "
           pdb=" C4'   A B  35 "
           pdb=" O4'   A B  35 "
           pdb=" C1'   A B  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   27.76  -29.76     1      8.00e+00 1.56e-02 1.98e+01
  ... (remaining 2469 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 622
       0.106 -    0.213: 29
       0.213 -    0.319: 0
       0.319 -    0.425: 0
       0.425 -    0.531: 1
  Chirality restraints: 652
  Sorted by residual:
  chirality pdb=" C3'   A B  35 "
            pdb=" C4'   A B  35 "
            pdb=" O3'   A B  35 "
            pdb=" C2'   A B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.21   -0.53 2.00e-01 2.50e+01 7.06e+00
  chirality pdb=" CA  SAM A 401 "
            pdb=" N   SAM A 401 "
            pdb=" C   SAM A 401 "
            pdb=" CB  SAM A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.64   -0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" CA  PRO A 300 "
            pdb=" N   PRO A 300 "
            pdb=" C   PRO A 300 "
            pdb=" CB  PRO A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.65e-01
  ... (remaining 649 not shown)

  Planarity restraints: 527
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  70 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   TYR A  70 "    0.037 2.00e-02 2.50e+03
        pdb=" O   TYR A  70 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A  71 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  43 "    0.026 2.00e-02 2.50e+03   1.21e-02 4.37e+00
        pdb=" N9    G B  43 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    G B  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G B  43 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B  43 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G B  43 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G B  43 "    0.014 2.00e-02 2.50e+03
        pdb=" N1    G B  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  43 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G B  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  43 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 233 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO A 234 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "    0.029 5.00e-02 4.00e+02
  ... (remaining 524 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 483
        2.74 -     3.28: 3642
        3.28 -     3.82: 6851
        3.82 -     4.36: 8037
        4.36 -     4.90: 12493
  Nonbonded interactions: 31506
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 211 "
            pdb=" NZ  LYS A 215 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OH  TYR A 172 "
            pdb=" O2'   C B  36 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" NE  ARG A  89 "
            pdb=" OD2 ASP A 114 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   ARG A 217 "
            pdb=" OH  TYR A 223 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NZ  LYS A 257 "
            pdb=" OP2   A B  39 "
     model   vdw
     2.295 3.120
  ... (remaining 31501 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:7.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
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      :  0.006   0.068   3977  Z= 0.294
  Angle     :  0.753   8.861   5609  Z= 0.428
  Chirality :  0.051   0.531    652
  Planarity :  0.005   0.052    527
  Dihedral  : 20.562 167.183   1834
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  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: -1.25 (0.48), residues: 331
  helix:  0.56 (0.50), residues: 122
  sheet: -1.43 (0.59), residues: 75
  loop : -1.70 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 260 
 TYR   0.017   0.002   TYR A  70 
 PHE   0.025   0.002   PHE A 125 
 TRP   0.014   0.002   TRP A 265 
 HIS   0.002   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 3977)
  covalent geometry    : angle       0.75341 ( 5609)
  hydrogen bonds       : bond        0.09284 (  104)
  hydrogen bonds       : angle       5.40376 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ILE cc_start: 0.7660 (mt) cc_final: 0.7431 (mt)
REVERT: A  297 THR cc_start: 0.7429 (t) cc_final: 0.7193 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.7150
  time to fit residues: 44.6046
Evaluate side-chains
  56 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0470
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.3078

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.184589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.156620 restraints weight = 5217.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 2.18
r_work: 0.3874 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3977  Z= 0.152
  Angle     :  0.609   6.173   5609  Z= 0.309
  Chirality :  0.040   0.153    652
  Planarity :  0.004   0.047    527
  Dihedral  : 21.844 123.646   1139
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.78 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.08 (0.48), residues: 331
  helix:  0.75 (0.49), residues: 126
  sheet: -1.45 (0.59), residues: 77
  loop : -1.65 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  72 
 TYR   0.011   0.002   TYR A 111 
 PHE   0.019   0.002   PHE A 178 
 TRP   0.008   0.001   TRP A 265 
 HIS   0.002   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3977)
  covalent geometry    : angle       0.60930 ( 5609)
  hydrogen bonds       : bond        0.04963 (  104)
  hydrogen bonds       : angle       4.13914 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ILE cc_start: 0.7808 (mt) cc_final: 0.7575 (mt)
REVERT: A  270 MET cc_start: 0.7589 (mmp) cc_final: 0.7223 (mpp)
REVERT: A  285 SER cc_start: 0.8636 (t) cc_final: 0.8245 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 56
  average time/residue: 0.7835
  time to fit residues: 44.8989
Evaluate side-chains
  57 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  303 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.4308 r_free = 0.4308 target = 0.183553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.155755 restraints weight = 5097.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 2.18
r_work: 0.3847 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3853 r_free = 0.3853    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3977  Z= 0.150
  Angle     :  0.559   6.845   5609  Z= 0.284
  Chirality :  0.038   0.142    652
  Planarity :  0.004   0.045    527
  Dihedral  : 21.256 104.108   1139
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.69 %
    Favored  : 81.70 %
  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: -0.90 (0.49), residues: 331
  helix:  0.78 (0.49), residues: 126
  sheet: -1.20 (0.60), residues: 77
  loop : -1.53 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  72 
 TYR   0.008   0.001   TYR A 248 
 PHE   0.021   0.002   PHE A 178 
 TRP   0.008   0.001   TRP A 265 
 HIS   0.001   0.000   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3977)
  covalent geometry    : angle       0.55929 ( 5609)
  hydrogen bonds       : bond        0.04986 (  104)
  hydrogen bonds       : angle       3.99473 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.7572 (mmp) cc_final: 0.7265 (mpp)
REVERT: A  285 SER cc_start: 0.8677 (t) cc_final: 0.8336 (m)
REVERT: A  286 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7831 (ttpp)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.6921
  time to fit residues: 40.4939
Evaluate side-chains
  59 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  303 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    0.0070
   chunk 10 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.3998

-------------------------------------------------------------------------------
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 = 0.4295 r_free = 0.4295 target = 0.182565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.155745 restraints weight = 5088.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 2.02
r_work: 0.3883 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3886 r_free = 0.3886    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3977  Z= 0.158
  Angle     :  0.569   8.367   5609  Z= 0.286
  Chirality :  0.038   0.135    652
  Planarity :  0.004   0.044    527
  Dihedral  : 21.099 103.252   1139
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.32 %
    Favored  : 79.08 %
  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: -0.86 (0.48), residues: 331
  helix:  0.85 (0.49), residues: 126
  sheet: -1.23 (0.58), residues: 77
  loop : -1.50 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  72 
 TYR   0.008   0.001   TYR A 223 
 PHE   0.018   0.002   PHE A 178 
 TRP   0.007   0.001   TRP A 265 
 HIS   0.001   0.000   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3977)
  covalent geometry    : angle       0.56947 ( 5609)
  hydrogen bonds       : bond        0.04950 (  104)
  hydrogen bonds       : angle       4.01373 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6131 (mm-30)
REVERT: A  239 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7340 (mtpt)
REVERT: A  270 MET cc_start: 0.7636 (mmp) cc_final: 0.7313 (mpp)
REVERT: A  285 SER cc_start: 0.8629 (t) cc_final: 0.8260 (m)
REVERT: A  286 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7770 (ttpp)
REVERT: A  312 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6924 (mmtt)
REVERT: A  323 LYS cc_start: 0.7507 (tptt) cc_final: 0.7006 (tptt)
  outliers start: 11
  outliers final: 7
  residues processed: 61
  average time/residue: 0.6842
  time to fit residues: 42.7807
Evaluate side-chains
  66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  239 LYS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  332 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 7 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0060
   chunk 10 optimal weight:    0.1980
   chunk 25 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.1734

-------------------------------------------------------------------------------
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 = 0.4333 r_free = 0.4333 target = 0.186415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.160109 restraints weight = 5104.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 1.96
r_work: 0.3926 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3977  Z= 0.105
  Angle     :  0.515   8.021   5609  Z= 0.260
  Chirality :  0.036   0.128    652
  Planarity :  0.004   0.042    527
  Dihedral  : 20.930 100.207   1139
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.93 %
    Favored  : 77.45 %
  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: -0.67 (0.48), residues: 331
  helix:  1.00 (0.49), residues: 126
  sheet: -1.10 (0.60), residues: 77
  loop : -1.41 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  72 
 TYR   0.008   0.001   TYR A 113 
 PHE   0.015   0.001   PHE A 178 
 TRP   0.005   0.001   TRP A 265 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3977)
  covalent geometry    : angle       0.51522 ( 5609)
  hydrogen bonds       : bond        0.04386 (  104)
  hydrogen bonds       : angle       3.79450 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 SER cc_start: 0.6768 (OUTLIER) cc_final: 0.6502 (m)
REVERT: A  239 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7313 (mtpt)
REVERT: A  270 MET cc_start: 0.7510 (mmp) cc_final: 0.7221 (mpp)
REVERT: A  285 SER cc_start: 0.8649 (t) cc_final: 0.8291 (m)
REVERT: A  286 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7795 (ttpp)
REVERT: A  312 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6984 (mmtt)
  outliers start: 8
  outliers final: 4
  residues processed: 57
  average time/residue: 0.7150
  time to fit residues: 41.8102
Evaluate side-chains
  59 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  239 LYS
Chi-restraints excluded: chain A residue  358 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4293 r_free = 0.4293 target = 0.183080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.155139 restraints weight = 5152.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.09
r_work: 0.3861 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3862 r_free = 0.3862    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3862 r_free = 0.3862    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3977  Z= 0.194
  Angle     :  0.563   7.551   5609  Z= 0.289
  Chirality :  0.039   0.155    652
  Planarity :  0.004   0.045    527
  Dihedral  : 20.815 103.397   1139
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.26 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.75 (0.48), residues: 331
  helix:  0.91 (0.49), residues: 126
  sheet: -1.27 (0.57), residues: 79
  loop : -1.31 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 109 
 TYR   0.010   0.001   TYR A 248 
 PHE   0.019   0.002   PHE A 125 
 TRP   0.006   0.002   TRP A 373 
 HIS   0.002   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3977)
  covalent geometry    : angle       0.56271 ( 5609)
  hydrogen bonds       : bond        0.05272 (  104)
  hydrogen bonds       : angle       3.97770 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7996 (mm)
REVERT: A  137 MET cc_start: 0.8034 (mpt) cc_final: 0.7781 (mpt)
REVERT: A  138 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6194 (mm-30)
REVERT: A  239 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7359 (mtpt)
REVERT: A  270 MET cc_start: 0.7640 (mmp) cc_final: 0.7304 (mpp)
REVERT: A  285 SER cc_start: 0.8616 (t) cc_final: 0.8242 (m)
REVERT: A  286 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7829 (ttmm)
REVERT: A  312 LYS cc_start: 0.7327 (mmtt) cc_final: 0.7039 (mmtt)
  outliers start: 10
  outliers final: 3
  residues processed: 61
  average time/residue: 0.6611
  time to fit residues: 41.3559
Evaluate side-chains
  62 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  239 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0970
   chunk 6 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0980
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.2378

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.186005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.159468 restraints weight = 5189.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 1.99
r_work: 0.3915 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3977  Z= 0.117
  Angle     :  0.520   8.533   5609  Z= 0.262
  Chirality :  0.036   0.142    652
  Planarity :  0.004   0.042    527
  Dihedral  : 20.736 100.213   1139
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.55 %
    Favored  : 74.84 %
  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: -0.62 (0.48), residues: 331
  helix:  0.99 (0.49), residues: 126
  sheet: -1.13 (0.60), residues: 77
  loop : -1.28 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.007   0.001   TYR A 113 
 PHE   0.014   0.001   PHE A 178 
 TRP   0.006   0.001   TRP A 265 
 HIS   0.001   0.000   HIS A 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3977)
  covalent geometry    : angle       0.51990 ( 5609)
  hydrogen bonds       : bond        0.04572 (  104)
  hydrogen bonds       : angle       3.87453 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6195 (mm-30)
REVERT: A  239 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7350 (mtpt)
REVERT: A  270 MET cc_start: 0.7532 (mmp) cc_final: 0.7222 (mpp)
REVERT: A  285 SER cc_start: 0.8581 (t) cc_final: 0.8259 (m)
REVERT: A  286 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7853 (ttmm)
REVERT: A  312 LYS cc_start: 0.7282 (mmtt) cc_final: 0.7061 (mmtt)
  outliers start: 8
  outliers final: 4
  residues processed: 59
  average time/residue: 0.6734
  time to fit residues: 40.8518
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  239 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0060
   chunk 29 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.2596

-------------------------------------------------------------------------------
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 = 0.4333 r_free = 0.4333 target = 0.186410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.159592 restraints weight = 5153.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.03
r_work: 0.3921 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3977  Z= 0.126
  Angle     :  0.540   8.911   5609  Z= 0.271
  Chirality :  0.037   0.152    652
  Planarity :  0.004   0.045    527
  Dihedral  : 20.626 100.230   1139
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 23.53 %
    Favored  : 75.16 %
  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: -0.63 (0.49), residues: 331
  helix:  1.03 (0.49), residues: 126
  sheet: -1.42 (0.58), residues: 81
  loop : -1.10 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.006   0.001   TYR A 113 
 PHE   0.014   0.001   PHE A 178 
 TRP   0.006   0.001   TRP A 222 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3977)
  covalent geometry    : angle       0.54014 ( 5609)
  hydrogen bonds       : bond        0.04615 (  104)
  hydrogen bonds       : angle       3.87750 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6238 (mm-30)
REVERT: A  239 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7340 (mtpt)
REVERT: A  270 MET cc_start: 0.7543 (mmp) cc_final: 0.7230 (mpp)
REVERT: A  285 SER cc_start: 0.8591 (t) cc_final: 0.8255 (m)
REVERT: A  286 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7832 (ttmm)
REVERT: A  312 LYS cc_start: 0.7304 (mmtt) cc_final: 0.7089 (mmtt)
  outliers start: 4
  outliers final: 3
  residues processed: 58
  average time/residue: 0.7187
  time to fit residues: 42.7312
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  239 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4313 r_free = 0.4313 target = 0.185023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.157043 restraints weight = 5070.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.15
r_work: 0.3882 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3977  Z= 0.181
  Angle     :  0.566   9.903   5609  Z= 0.285
  Chirality :  0.039   0.164    652
  Planarity :  0.004   0.045    527
  Dihedral  : 20.556 101.792   1139
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.86 %
    Favored  : 74.18 %
  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: -0.65 (0.48), residues: 331
  helix:  1.06 (0.50), residues: 125
  sheet: -1.55 (0.56), residues: 81
  loop : -1.05 (0.58), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.009   0.001   TYR A 248 
 PHE   0.018   0.002   PHE A 125 
 TRP   0.006   0.002   TRP A 222 
 HIS   0.001   0.000   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 3977)
  covalent geometry    : angle       0.56625 ( 5609)
  hydrogen bonds       : bond        0.05082 (  104)
  hydrogen bonds       : angle       3.95749 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6249 (mm-30)
REVERT: A  239 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7321 (mtpt)
REVERT: A  270 MET cc_start: 0.7599 (mmp) cc_final: 0.7279 (mpp)
REVERT: A  285 SER cc_start: 0.8596 (t) cc_final: 0.8234 (m)
REVERT: A  286 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7758 (ttpp)
REVERT: A  312 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7118 (mmtt)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.6648
  time to fit residues: 40.2601
Evaluate side-chains
  62 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  239 LYS
Chi-restraints excluded: chain A residue  332 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4292 r_free = 0.4292 target = 0.183066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.155412 restraints weight = 5152.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.08
r_work: 0.3862 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3977  Z= 0.220
  Angle     :  0.639   9.981   5609  Z= 0.318
  Chirality :  0.041   0.169    652
  Planarity :  0.004   0.051    527
  Dihedral  : 20.564 103.597   1139
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 24.18 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.78 (0.48), residues: 331
  helix:  0.98 (0.50), residues: 125
  sheet: -1.60 (0.56), residues: 79
  loop : -1.18 (0.57), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 391 
 TYR   0.012   0.002   TYR A 248 
 PHE   0.021   0.002   PHE A 125 
 TRP   0.007   0.002   TRP A 296 
 HIS   0.002   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 3977)
  covalent geometry    : angle       0.63902 ( 5609)
  hydrogen bonds       : bond        0.05736 (  104)
  hydrogen bonds       : angle       4.06317 (  268)

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

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

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  662 Ramachandran restraints generated.
    331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6127 (mm-30)
REVERT: A  270 MET cc_start: 0.7626 (mmp) cc_final: 0.7286 (mpp)
REVERT: A  285 SER cc_start: 0.8615 (t) cc_final: 0.8260 (m)
REVERT: A  286 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7731 (ttpp)
REVERT: A  312 LYS cc_start: 0.7409 (mmtt) cc_final: 0.7154 (mmtt)
  outliers start: 6
  outliers final: 5
  residues processed: 62
  average time/residue: 0.7010
  time to fit residues: 44.5774
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  239 LYS
Chi-restraints excluded: chain A residue  303 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.183639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.155761 restraints weight = 5077.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 2.08
r_work: 0.3869 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3977  Z= 0.191
  Angle     :  0.624  11.282   5609  Z= 0.309
  Chirality :  0.040   0.194    652
  Planarity :  0.005   0.047    527
  Dihedral  : 20.536 102.951   1139
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 24.18 %
    Favored  : 73.53 %
  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: -0.79 (0.48), residues: 331
  helix:  0.94 (0.49), residues: 125
  sheet: -1.61 (0.57), residues: 79
  loop : -1.16 (0.57), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 109 
 TYR   0.009   0.001   TYR A 248 
 PHE   0.018   0.002   PHE A 125 
 TRP   0.009   0.002   TRP A 373 
 HIS   0.001   0.000   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 3977)
  covalent geometry    : angle       0.62353 ( 5609)
  hydrogen bonds       : bond        0.05436 (  104)
  hydrogen bonds       : angle       4.03892 (  268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1625.91 seconds
wall clock time: 28 minutes 27.74 seconds (1707.74 seconds total)