Starting phenix.real_space_refine
on Tue Feb  3 20:40:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b9r_44389/02_2026/9b9r_44389.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    2220      2.51       5
     N     612      2.21       5
     O     624      1.98       5
     H    3436      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6928
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 1732
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 1732
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 1732
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 1732
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
  Time building chain proxies: 1.36, per 1000 atoms: 0.20
  Number of scatterers: 6928
  At special positions: 0
  Unit cell: (95.85, 71.55, 87.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O     624      8.00
     N     612      7.00
     C    2220      6.00
     H    3436      1.00
    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: 0.56
  Conformation dependent library (CDL) restraints added in 201.5 milliseconds
  

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  856

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      66.9% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 21
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.550A  pdb=" N   TYR A  85 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 106
    Processing helix  chain 'A' and resid 108 through 119
    Processing helix  chain 'B' and resid 5 through 21
    Processing helix  chain 'B' and resid 38 through 46
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 73 through 87
    Processing helix  chain 'B' and resid 95 through 106
    Processing helix  chain 'B' and resid 108 through 120
    Processing helix  chain 'C' and resid 5 through 21
    Processing helix  chain 'C' and resid 38 through 46
    Processing helix  chain 'C' and resid 46 through 54
    Processing helix  chain 'C' and resid 73 through 87
    Processing helix  chain 'C' and resid 95 through 106
    Processing helix  chain 'C' and resid 108 through 120
    Processing helix  chain 'D' and resid 5 through 21
    Processing helix  chain 'D' and resid 38 through 46
    Processing helix  chain 'D' and resid 46 through 53
    Processing helix  chain 'D' and resid 73 through 87
    Processing helix  chain 'D' and resid 95 through 106
    Processing helix  chain 'D' and resid 108 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37
    Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 37
    Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 37
    Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 37

    233 hydrogen bonds defined for protein.
    675 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3420
        1.03 -     1.23: 16
        1.23 -     1.42: 1532
        1.42 -     1.62: 1972
        1.62 -     1.81: 56
  Bond restraints: 6996
  Sorted by residual:
  bond pdb=" CA  VAL A 111 "
       pdb=" C   VAL A 111 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.012 1.39e-02 5.18e+03 7.43e-01
  bond pdb=" N   VAL A  99 "
       pdb=" CA  VAL A  99 "
    ideal  model  delta    sigma   weight residual
    1.459  1.448  0.011 1.30e-02 5.92e+03 7.19e-01
  bond pdb=" CA  VAL C  41 "
       pdb=" C   VAL C  41 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.33e-02 5.65e+03 6.66e-01
  bond pdb=" CA  VAL B 111 "
       pdb=" C   VAL B 111 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.39e-02 5.18e+03 6.37e-01
  bond pdb=" CA  ASP A  98 "
       pdb=" C   ASP A  98 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.010 1.32e-02 5.74e+03 6.31e-01
  ... (remaining 6991 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 12264
        1.56 -     3.13: 275
        3.13 -     4.69: 14
        4.69 -     6.25: 6
        6.25 -     7.82: 1
  Bond angle restraints: 12560
  Sorted by residual:
  angle pdb=" N   VAL A  99 "
        pdb=" CA  VAL A  99 "
        pdb=" C   VAL A  99 "
      ideal   model   delta    sigma   weight residual
     111.09  106.37    4.72 1.25e+00 6.40e-01 1.43e+01
  angle pdb=" N   GLY C  92 "
        pdb=" CA  GLY C  92 "
        pdb=" C   GLY C  92 "
      ideal   model   delta    sigma   weight residual
     113.18  105.36    7.82 2.37e+00 1.78e-01 1.09e+01
  angle pdb=" C   ASP D  25 "
        pdb=" N   CYS D  26 "
        pdb=" CA  CYS D  26 "
      ideal   model   delta    sigma   weight residual
     121.75  116.88    4.87 1.73e+00 3.34e-01 7.92e+00
  angle pdb=" N   GLY D  31 "
        pdb=" CA  GLY D  31 "
        pdb=" C   GLY D  31 "
      ideal   model   delta    sigma   weight residual
     111.02  105.82    5.20 1.86e+00 2.89e-01 7.81e+00
  angle pdb=" N   GLY B  31 "
        pdb=" CA  GLY B  31 "
        pdb=" C   GLY B  31 "
      ideal   model   delta    sigma   weight residual
     111.02  105.89    5.13 1.86e+00 2.89e-01 7.60e+00
  ... (remaining 12555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.01: 3072
       13.01 -    26.01: 171
       26.01 -    39.02: 24
       39.02 -    52.02: 29
       52.02 -    65.03: 8
  Dihedral angle restraints: 3304
    sinusoidal: 1716
      harmonic: 1588
  Sorted by residual:
  dihedral pdb=" CA  ASP C  68 "
           pdb=" CB  ASP C  68 "
           pdb=" CG  ASP C  68 "
           pdb=" OD1 ASP C  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.44   53.44     1      2.00e+01 2.50e-03 9.70e+00
  dihedral pdb=" CA  ASP A  68 "
           pdb=" CB  ASP A  68 "
           pdb=" CG  ASP A  68 "
           pdb=" OD1 ASP A  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.96   50.96     1      2.00e+01 2.50e-03 8.88e+00
  dihedral pdb=" CB  MET B  97 "
           pdb=" CG  MET B  97 "
           pdb=" SD  MET B  97 "
           pdb=" CE  MET B  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.23   49.23     3      1.50e+01 4.44e-03 8.75e+00
  ... (remaining 3301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 402
       0.033 -    0.066: 91
       0.066 -    0.099: 53
       0.099 -    0.132: 7
       0.132 -    0.165: 7
  Chirality restraints: 560
  Sorted by residual:
  chirality pdb=" CA  ILE D  28 "
            pdb=" N   ILE D  28 "
            pdb=" C   ILE D  28 "
            pdb=" CB  ILE D  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.83e-01
  chirality pdb=" CA  ILE B  28 "
            pdb=" N   ILE B  28 "
            pdb=" C   ILE B  28 "
            pdb=" CB  ILE B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CA  ILE A  28 "
            pdb=" N   ILE A  28 "
            pdb=" C   ILE A  28 "
            pdb=" CB  ILE A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 557 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C  40 "   -0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   SER C  40 "    0.064 2.00e-02 2.50e+03
        pdb=" O   SER C  40 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL C  41 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  97 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.95e+00
        pdb=" C   MET A  97 "    0.046 2.00e-02 2.50e+03
        pdb=" O   MET A  97 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A  98 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 110 "    0.011 2.00e-02 2.50e+03   2.28e-02 5.18e+00
        pdb=" C   SER B 110 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   SER B 110 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 111 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 113
        2.12 -     2.74: 12115
        2.74 -     3.36: 19705
        3.36 -     3.98: 24861
        3.98 -     4.60: 39064
  Nonbonded interactions: 95858
  Sorted by model distance:
  nonbonded pdb=" HG  SER B  46 "
            pdb=" O   LEU B 106 "
     model   vdw
     1.498 2.450
  nonbonded pdb=" HG  SER A  46 "
            pdb=" O   LEU A 106 "
     model   vdw
     1.573 2.450
  nonbonded pdb=" O   ASP D  82 "
            pdb=" HG1 THR D  86 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" O   ASP B  82 "
            pdb=" HG1 THR B  86 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" O   ASP A  82 "
            pdb=" HG1 THR A  86 "
     model   vdw
     1.667 2.450
  ... (remaining 95853 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'
  selection = chain 'D'
}

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:             0.570
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.430
  Find NCS groups from input model:        0.080
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3560  Z= 0.147
  Angle     :  0.680   7.817   4808  Z= 0.458
  Chirality :  0.039   0.165    560
  Planarity :  0.005   0.037    608
  Dihedral  : 11.042  65.027   1244
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  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 are not related in a simple way.
  whole:  0.53 (0.33), residues: 428
  helix:  0.35 (0.25), residues: 284
  sheet:  None (None), residues: 0
  loop :  0.72 (0.43), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  39 
 TYR   0.017   0.003   TYR A  85 
 PHE   0.014   0.002   PHE D  11 
 HIS   0.007   0.002   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3560)
  covalent geometry    : angle       0.68035 ( 4808)
  hydrogen bonds       : bond        0.11359 (  233)
  hydrogen bonds       : angle       4.99487 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASP cc_start: 0.9283 (t70) cc_final: 0.8848 (t0)
REVERT: B   35 PHE cc_start: 0.8604 (m-80) cc_final: 0.7837 (m-80)
REVERT: B   82 ASP cc_start: 0.8346 (m-30) cc_final: 0.7846 (t0)
REVERT: B   97 MET cc_start: 0.9353 (tpt) cc_final: 0.9079 (tmm)
REVERT: B   98 ASP cc_start: 0.9216 (m-30) cc_final: 0.8315 (m-30)
REVERT: C   41 VAL cc_start: 0.9239 (t) cc_final: 0.8863 (m)
REVERT: C   45 CYS cc_start: 0.7349 (m) cc_final: 0.7068 (m)
REVERT: C  111 VAL cc_start: 0.9186 (t) cc_final: 0.8954 (t)
REVERT: D   15 ASN cc_start: 0.9305 (t0) cc_final: 0.9026 (t0)
REVERT: D   16 TYR cc_start: 0.8588 (t80) cc_final: 0.8346 (t80)
REVERT: D   20 HIS cc_start: 0.8943 (m-70) cc_final: 0.8502 (m90)
REVERT: D   30 VAL cc_start: 0.8675 (t) cc_final: 0.8414 (p)
REVERT: D   68 ASP cc_start: 0.9508 (t0) cc_final: 0.9217 (t0)
REVERT: D   82 ASP cc_start: 0.9171 (m-30) cc_final: 0.8968 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1255
  time to fit residues: 33.4875
Evaluate side-chains
  143 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
B  15 ASN
B  20 HIS
** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
C 105 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.062635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.054946 restraints weight = 49679.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.057606 restraints weight = 20399.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.059250 restraints weight = 10442.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.060293 restraints weight = 6010.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.061044 restraints weight = 3714.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3560  Z= 0.196
  Angle     :  0.618   4.806   4808  Z= 0.354
  Chirality :  0.039   0.157    560
  Planarity :  0.003   0.022    608
  Dihedral  :  3.912  15.160    464
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.45 %
    Favored  : 79.95 %
  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 are not related in a simple way.
  whole:  1.80 (0.36), residues: 428
  helix:  1.56 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.62 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.013   0.001   TYR C  16 
 PHE   0.016   0.002   PHE A  49 
 HIS   0.007   0.002   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3560)
  covalent geometry    : angle       0.61781 ( 4808)
  hydrogen bonds       : bond        0.04209 (  233)
  hydrogen bonds       : angle       4.55208 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9189 (mp0) cc_final: 0.8777 (mp0)
REVERT: A   68 ASP cc_start: 0.9592 (t70) cc_final: 0.9357 (t0)
REVERT: A   90 MET cc_start: 0.5716 (mmm) cc_final: 0.5127 (mmm)
REVERT: B    8 GLU cc_start: 0.9134 (mp0) cc_final: 0.8808 (mp0)
REVERT: B   36 LYS cc_start: 0.9559 (mttt) cc_final: 0.9353 (mmmm)
REVERT: B   82 ASP cc_start: 0.8364 (m-30) cc_final: 0.7855 (t70)
REVERT: B   83 MET cc_start: 0.8350 (tmt) cc_final: 0.7593 (tmm)
REVERT: B   86 THR cc_start: 0.8141 (p) cc_final: 0.7832 (p)
REVERT: B   98 ASP cc_start: 0.9414 (m-30) cc_final: 0.8436 (m-30)
REVERT: D    9 GLN cc_start: 0.9311 (pt0) cc_final: 0.9012 (mp10)
REVERT: D   16 TYR cc_start: 0.8951 (t80) cc_final: 0.8652 (t80)
REVERT: D   17 GLN cc_start: 0.9275 (pt0) cc_final: 0.8928 (pt0)
REVERT: D   20 HIS cc_start: 0.8840 (m-70) cc_final: 0.8475 (m-70)
REVERT: D   33 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8343 (ttp-170)
REVERT: D   64 MET cc_start: 0.8745 (ppp) cc_final: 0.7993 (ppp)
REVERT: D   68 ASP cc_start: 0.9473 (t0) cc_final: 0.9103 (t0)
REVERT: D   82 ASP cc_start: 0.9201 (m-30) cc_final: 0.8922 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 151
  average time/residue: 0.1137
  time to fit residues: 21.9581
Evaluate side-chains
  130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 HIS
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  112 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
D  17 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.055221 restraints weight = 49236.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.057889 restraints weight = 20614.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.059571 restraints weight = 10783.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.060682 restraints weight = 6418.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061395 restraints weight = 4008.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.6749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3560  Z= 0.140
  Angle     :  0.564   4.385   4808  Z= 0.312
  Chirality :  0.037   0.170    560
  Planarity :  0.003   0.019    608
  Dihedral  :  3.833  14.088    464
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.35 %
    Favored  : 76.56 %
  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 are not related in a simple way.
  whole:  1.93 (0.37), residues: 428
  helix:  1.75 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.43 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.004   0.001   TYR C  16 
 PHE   0.009   0.001   PHE A  77 
 HIS   0.005   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3560)
  covalent geometry    : angle       0.56428 ( 4808)
  hydrogen bonds       : bond        0.03812 (  233)
  hydrogen bonds       : angle       4.35440 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 CYS cc_start: 0.9420 (t) cc_final: 0.8862 (t)
REVERT: A   68 ASP cc_start: 0.9608 (t70) cc_final: 0.9359 (t0)
REVERT: A   70 GLU cc_start: 0.9528 (tp30) cc_final: 0.9301 (tp30)
REVERT: A   90 MET cc_start: 0.5606 (mmm) cc_final: 0.5167 (mmm)
REVERT: B    8 GLU cc_start: 0.9181 (mp0) cc_final: 0.8818 (mp0)
REVERT: B   82 ASP cc_start: 0.8384 (m-30) cc_final: 0.7875 (t70)
REVERT: B   83 MET cc_start: 0.8424 (tmt) cc_final: 0.7711 (tmm)
REVERT: B   86 THR cc_start: 0.8318 (p) cc_final: 0.7965 (p)
REVERT: C   75 GLU cc_start: 0.9256 (mp0) cc_final: 0.8950 (mp0)
REVERT: C   84 MET cc_start: 0.9437 (ttp) cc_final: 0.9172 (tpp)
REVERT: D    9 GLN cc_start: 0.9268 (pt0) cc_final: 0.8913 (mp10)
REVERT: D   64 MET cc_start: 0.8860 (ppp) cc_final: 0.8105 (ppp)
REVERT: D   68 ASP cc_start: 0.9330 (t0) cc_final: 0.9090 (t0)
REVERT: D   82 ASP cc_start: 0.9153 (m-30) cc_final: 0.8931 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 140
  average time/residue: 0.0935
  time to fit residues: 17.4223
Evaluate side-chains
  127 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain D residue  112 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.061906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.054142 restraints weight = 49904.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.056771 restraints weight = 20561.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.058387 restraints weight = 10631.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.059522 restraints weight = 6299.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.060225 restraints weight = 3864.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.7544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3560  Z= 0.148
  Angle     :  0.581   6.345   4808  Z= 0.314
  Chirality :  0.038   0.192    560
  Planarity :  0.003   0.016    608
  Dihedral  :  3.787  12.914    464
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.40 %
    Favored  : 75.00 %
  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 are not related in a simple way.
  whole:  1.83 (0.37), residues: 428
  helix:  1.72 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.29 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.009   0.001   TYR D  16 
 PHE   0.009   0.001   PHE D  77 
 HIS   0.004   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3560)
  covalent geometry    : angle       0.58136 ( 4808)
  hydrogen bonds       : bond        0.03643 (  233)
  hydrogen bonds       : angle       4.48201 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9118 (mp0) cc_final: 0.8721 (mp0)
REVERT: A   70 GLU cc_start: 0.9518 (tp30) cc_final: 0.9277 (tp30)
REVERT: A   90 MET cc_start: 0.5633 (mmm) cc_final: 0.5166 (mmm)
REVERT: B    8 GLU cc_start: 0.9238 (mp0) cc_final: 0.8999 (mp0)
REVERT: B   68 ASP cc_start: 0.8582 (t70) cc_final: 0.8345 (t70)
REVERT: B   82 ASP cc_start: 0.8315 (m-30) cc_final: 0.7790 (t0)
REVERT: B   83 MET cc_start: 0.8283 (tmt) cc_final: 0.7441 (tmm)
REVERT: B   86 THR cc_start: 0.8120 (p) cc_final: 0.7772 (p)
REVERT: C   75 GLU cc_start: 0.9279 (mp0) cc_final: 0.9075 (mp0)
REVERT: D    9 GLN cc_start: 0.9288 (pt0) cc_final: 0.9050 (mp10)
REVERT: D   64 MET cc_start: 0.8904 (ppp) cc_final: 0.8078 (ppp)
REVERT: D   68 ASP cc_start: 0.9364 (t0) cc_final: 0.9113 (t0)
REVERT: D   82 ASP cc_start: 0.9170 (m-30) cc_final: 0.8936 (m-30)
REVERT: D   83 MET cc_start: 0.9340 (tmm) cc_final: 0.9132 (tmm)
  outliers start: 10
  outliers final: 10
  residues processed: 123
  average time/residue: 0.0983
  time to fit residues: 16.0210
Evaluate side-chains
  122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  112 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053686 restraints weight = 50770.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.056413 restraints weight = 21384.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.058086 restraints weight = 11206.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.059263 restraints weight = 6710.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.060014 restraints weight = 4157.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.7895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3560  Z= 0.122
  Angle     :  0.544   4.870   4808  Z= 0.297
  Chirality :  0.037   0.176    560
  Planarity :  0.002   0.016    608
  Dihedral  :  3.726  13.097    464
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.44 %
    Favored  : 74.48 %
  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 are not related in a simple way.
  whole:  1.97 (0.38), residues: 428
  helix:  1.88 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.19 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.009   0.001   PHE D  77 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3560)
  covalent geometry    : angle       0.54427 ( 4808)
  hydrogen bonds       : bond        0.03413 (  233)
  hydrogen bonds       : angle       4.33162 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9143 (mp0) cc_final: 0.8733 (mp0)
REVERT: A   70 GLU cc_start: 0.9549 (tp30) cc_final: 0.9328 (tp30)
REVERT: A   90 MET cc_start: 0.6279 (mmm) cc_final: 0.5826 (mmm)
REVERT: A  109 ASN cc_start: 0.9131 (m110) cc_final: 0.8704 (p0)
REVERT: B    8 GLU cc_start: 0.9273 (mp0) cc_final: 0.9037 (mp0)
REVERT: B   82 ASP cc_start: 0.8376 (m-30) cc_final: 0.7845 (t70)
REVERT: B   83 MET cc_start: 0.8422 (tmt) cc_final: 0.7934 (tmm)
REVERT: B   86 THR cc_start: 0.8300 (p) cc_final: 0.7984 (p)
REVERT: D    9 GLN cc_start: 0.9270 (pt0) cc_final: 0.9048 (mp10)
REVERT: D   64 MET cc_start: 0.8953 (ppp) cc_final: 0.8155 (ppp)
REVERT: D   68 ASP cc_start: 0.9356 (t0) cc_final: 0.9096 (t0)
REVERT: D   82 ASP cc_start: 0.9183 (m-30) cc_final: 0.8957 (m-30)
REVERT: D   83 MET cc_start: 0.9399 (tmm) cc_final: 0.9143 (tmm)
  outliers start: 8
  outliers final: 8
  residues processed: 127
  average time/residue: 0.1117
  time to fit residues: 18.6767
Evaluate side-chains
  123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  112 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  20 HIS
B  17 GLN
** C  20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.057723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.050103 restraints weight = 53778.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.052571 restraints weight = 22055.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.054250 restraints weight = 11539.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.055294 restraints weight = 6683.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.056010 restraints weight = 4151.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.9127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3560  Z= 0.255
  Angle     :  0.658   6.051   4808  Z= 0.376
  Chirality :  0.038   0.167    560
  Planarity :  0.004   0.029    608
  Dihedral  :  4.052  15.797    464
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.22 %
    Favored  : 71.88 %
  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 are not related in a simple way.
  whole:  1.03 (0.36), residues: 428
  helix:  1.17 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.19 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  33 
 TYR   0.015   0.002   TYR D  16 
 PHE   0.020   0.003   PHE B   3 
 HIS   0.010   0.002   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 3560)
  covalent geometry    : angle       0.65796 ( 4808)
  hydrogen bonds       : bond        0.04039 (  233)
  hydrogen bonds       : angle       4.94307 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9153 (pt0)
REVERT: B   68 ASP cc_start: 0.8504 (t70) cc_final: 0.8015 (t70)
REVERT: B   82 ASP cc_start: 0.8823 (m-30) cc_final: 0.8171 (t0)
REVERT: B   86 THR cc_start: 0.8710 (p) cc_final: 0.8319 (p)
REVERT: B  110 SER cc_start: 0.9401 (m) cc_final: 0.8835 (p)
REVERT: D   64 MET cc_start: 0.9043 (ppp) cc_final: 0.8307 (ppp)
REVERT: D   68 ASP cc_start: 0.9415 (t0) cc_final: 0.9201 (t0)
REVERT: D   82 ASP cc_start: 0.9346 (m-30) cc_final: 0.9120 (m-30)
REVERT: D   83 MET cc_start: 0.9534 (tmm) cc_final: 0.9237 (tmm)
REVERT: D  110 SER cc_start: 0.9564 (p) cc_final: 0.9245 (p)
  outliers start: 15
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1050
  time to fit residues: 16.2765
Evaluate side-chains
  121 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   25 ASP
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  112 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.059032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.051142 restraints weight = 51464.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.053737 restraints weight = 21020.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.055442 restraints weight = 10909.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.056520 restraints weight = 6322.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.057267 restraints weight = 3972.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.9210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3560  Z= 0.137
  Angle     :  0.639   6.747   4808  Z= 0.343
  Chirality :  0.038   0.157    560
  Planarity :  0.002   0.021    608
  Dihedral  :  4.005  13.534    464
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 26.04 %
    Favored  : 71.61 %
  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 are not related in a simple way.
  whole:  1.48 (0.38), residues: 428
  helix:  1.53 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.05 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  18 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.010   0.001   PHE A  77 
 HIS   0.004   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3560)
  covalent geometry    : angle       0.63878 ( 4808)
  hydrogen bonds       : bond        0.03407 (  233)
  hydrogen bonds       : angle       4.40134 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9135 (mp0) cc_final: 0.8929 (mp0)
REVERT: A   97 MET cc_start: 0.8916 (ptp) cc_final: 0.8696 (pmm)
REVERT: B   22 GLN cc_start: 0.9415 (tp40) cc_final: 0.9177 (mp10)
REVERT: B   82 ASP cc_start: 0.8789 (m-30) cc_final: 0.8112 (t0)
REVERT: B   86 THR cc_start: 0.8752 (p) cc_final: 0.8372 (p)
REVERT: D   33 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7888 (ttp-170)
REVERT: D   64 MET cc_start: 0.9068 (ppp) cc_final: 0.8271 (ppp)
REVERT: D   68 ASP cc_start: 0.9375 (t0) cc_final: 0.9135 (t0)
REVERT: D   82 ASP cc_start: 0.9323 (m-30) cc_final: 0.9114 (m-30)
REVERT: D   83 MET cc_start: 0.9494 (tmm) cc_final: 0.9147 (tmm)
REVERT: D  110 SER cc_start: 0.9532 (p) cc_final: 0.9222 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 112
  average time/residue: 0.1146
  time to fit residues: 16.8172
Evaluate side-chains
  116 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue  100 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.059276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.051556 restraints weight = 51402.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.054110 restraints weight = 21166.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.055763 restraints weight = 11004.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.056869 restraints weight = 6395.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.057599 restraints weight = 4006.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.9385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3560  Z= 0.131
  Angle     :  0.619   6.291   4808  Z= 0.330
  Chirality :  0.037   0.158    560
  Planarity :  0.002   0.020    608
  Dihedral  :  3.872  13.793    464
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 26.56 %
    Favored  : 72.14 %
  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 are not related in a simple way.
  whole:  1.61 (0.38), residues: 428
  helix:  1.70 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.19 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  33 
 TYR   0.011   0.001   TYR D  16 
 PHE   0.008   0.001   PHE A  77 
 HIS   0.003   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3560)
  covalent geometry    : angle       0.61890 ( 4808)
  hydrogen bonds       : bond        0.03202 (  233)
  hydrogen bonds       : angle       4.32900 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9142 (mp0) cc_final: 0.8939 (mp0)
REVERT: B   82 ASP cc_start: 0.8796 (m-30) cc_final: 0.8113 (t0)
REVERT: B   86 THR cc_start: 0.8771 (p) cc_final: 0.8373 (p)
REVERT: D    9 GLN cc_start: 0.9280 (pt0) cc_final: 0.8986 (pt0)
REVERT: D   64 MET cc_start: 0.9025 (ppp) cc_final: 0.8232 (ppp)
REVERT: D   68 ASP cc_start: 0.9354 (t0) cc_final: 0.9102 (t0)
REVERT: D   83 MET cc_start: 0.9483 (tmm) cc_final: 0.9124 (tmm)
  outliers start: 5
  outliers final: 5
  residues processed: 111
  average time/residue: 0.1133
  time to fit residues: 16.5458
Evaluate side-chains
  115 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain D residue   84 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.059220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.051243 restraints weight = 52515.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053864 restraints weight = 21792.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.055489 restraints weight = 11379.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.056662 restraints weight = 6820.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.057443 restraints weight = 4245.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.9580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3560  Z= 0.146
  Angle     :  0.629   7.443   4808  Z= 0.341
  Chirality :  0.037   0.153    560
  Planarity :  0.002   0.020    608
  Dihedral  :  3.831  13.200    464
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 26.56 %
    Favored  : 71.61 %
  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 are not related in a simple way.
  whole:  1.48 (0.38), residues: 428
  helix:  1.62 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.28 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  50 
 TYR   0.011   0.001   TYR D  16 
 PHE   0.009   0.001   PHE A  77 
 HIS   0.003   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3560)
  covalent geometry    : angle       0.62899 ( 4808)
  hydrogen bonds       : bond        0.03174 (  233)
  hydrogen bonds       : angle       4.38565 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.9175 (mp0) cc_final: 0.8962 (mp0)
REVERT: A   97 MET cc_start: 0.9030 (ptp) cc_final: 0.8793 (pmm)
REVERT: B   82 ASP cc_start: 0.8774 (m-30) cc_final: 0.8098 (t0)
REVERT: B   86 THR cc_start: 0.8825 (p) cc_final: 0.8402 (p)
REVERT: D    9 GLN cc_start: 0.9274 (pt0) cc_final: 0.8970 (pt0)
REVERT: D   64 MET cc_start: 0.9041 (ppp) cc_final: 0.8245 (ppp)
REVERT: D   68 ASP cc_start: 0.9364 (t0) cc_final: 0.9119 (t0)
REVERT: D   83 MET cc_start: 0.9486 (tmm) cc_final: 0.9106 (tmm)
  outliers start: 7
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1017
  time to fit residues: 14.5225
Evaluate side-chains
  113 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.058865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.051267 restraints weight = 51985.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.053764 restraints weight = 21418.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.055391 restraints weight = 11085.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.056533 restraints weight = 6418.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.057247 restraints weight = 3941.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.9723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3560  Z= 0.133
  Angle     :  0.636   8.566   4808  Z= 0.339
  Chirality :  0.037   0.155    560
  Planarity :  0.002   0.020    608
  Dihedral  :  3.823  12.764    464
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 27.08 %
    Favored  : 71.61 %
  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 are not related in a simple way.
  whole:  1.60 (0.38), residues: 428
  helix:  1.69 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.20 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  39 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.008   0.001   PHE A  77 
 HIS   0.003   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3560)
  covalent geometry    : angle       0.63646 ( 4808)
  hydrogen bonds       : bond        0.03115 (  233)
  hydrogen bonds       : angle       4.31909 (  675)

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

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

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 ASP cc_start: 0.8735 (m-30) cc_final: 0.8209 (t0)
REVERT: B   86 THR cc_start: 0.8824 (p) cc_final: 0.8424 (p)
REVERT: D    9 GLN cc_start: 0.9268 (pt0) cc_final: 0.8956 (pt0)
REVERT: D   33 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.8062 (ttp-170)
REVERT: D   64 MET cc_start: 0.9038 (ppp) cc_final: 0.8262 (ppp)
REVERT: D   68 ASP cc_start: 0.9336 (t0) cc_final: 0.9088 (t0)
REVERT: D   83 MET cc_start: 0.9474 (tmm) cc_final: 0.8999 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1065
  time to fit residues: 14.9035
Evaluate side-chains
  110 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   84 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.058414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.050903 restraints weight = 52231.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.053378 restraints weight = 21487.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.055004 restraints weight = 11258.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.056058 restraints weight = 6527.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.056801 restraints weight = 4087.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.9927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3560  Z= 0.182
  Angle     :  0.669   8.414   4808  Z= 0.362
  Chirality :  0.037   0.151    560
  Planarity :  0.003   0.020    608
  Dihedral  :  3.904  13.542    464
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 26.82 %
    Favored  : 71.61 %
  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 are not related in a simple way.
  whole:  1.50 (0.38), residues: 428
  helix:  1.60 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.13 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.013   0.001   TYR D  16 
 PHE   0.011   0.002   PHE A   7 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3560)
  covalent geometry    : angle       0.66892 ( 4808)
  hydrogen bonds       : bond        0.03271 (  233)
  hydrogen bonds       : angle       4.54132 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1640.03 seconds
wall clock time: 28 minutes 35.58 seconds (1715.58 seconds total)