Starting phenix.real_space_refine
on Wed Sep 17 08:01:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b9r_44389/09_2025/9b9r_44389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b9r_44389/09_2025/9b9r_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_44389/09_2025/9b9r_44389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b9r_44389/09_2025/9b9r_44389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b9r_44389/09_2025/9b9r_44389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b9r_44389/09_2025/9b9r_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-2.0-5805/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: 1.44, per 1000 atoms: 0.21
  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: 0.53
  Conformation dependent library (CDL) restraints added in 258.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.19
  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: 1.43

  Time building geometry restraints manager: 0.79 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:             0.430
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.070
  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:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.790
-------------------------------------------------------------------------------
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 aren 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  : 0.146 
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: 0.1128
  time to fit residues: 30.2970
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 aren 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  : 0.152 
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   35 PHE cc_start: 0.8610 (m-80) cc_final: 0.8410 (m-80)
REVERT: B   36 LYS cc_start: 0.9559 (mttt) cc_final: 0.9353 (mmmm)
REVERT: B   82 ASP cc_start: 0.8363 (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: 0.8927 (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: 0.8344 (ttp-170)
REVERT: D   64 MET cc_start: 0.8745 (ppp) cc_final: 0.7994 (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: 0.1079
  time to fit residues: 20.8079
Evaluate side-chains
  131 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 = 0.3376 r_free = 0.3376 target = 0.063643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.055534 restraints weight = 48908.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.058208 restraints weight = 20399.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059949 restraints weight = 10692.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.061052 restraints weight = 6278.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.061783 restraints weight = 3925.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.6707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3560  Z= 0.130
  Angle     :  0.559   4.391   4808  Z= 0.308
  Chirality :  0.037   0.170    560
  Planarity :  0.003   0.020    608
  Dihedral  :  3.832  14.050    464
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.35 %
    Favored  : 76.82 %
  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:  1.99 (0.37), residues: 428
  helix:  1.80 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.45 (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        0.00281 ( 3560)
  covalent geometry    : angle       0.55881 ( 4808)
  hydrogen bonds       : bond        0.03784 (  233)
  hydrogen bonds       : angle       4.32049 (  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: 7
    poor density    : 136
  time to evaluate  : 0.249 
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: A   45 CYS cc_start: 0.9437 (t) cc_final: 0.8863 (t)
REVERT: A   68 ASP cc_start: 0.9607 (t70) cc_final: 0.9355 (t0)
REVERT: A   70 GLU cc_start: 0.9518 (tp30) cc_final: 0.9278 (tp30)
REVERT: A   90 MET cc_start: 0.5584 (mmm) cc_final: 0.5153 (mmm)
REVERT: B    8 GLU cc_start: 0.9184 (mp0) cc_final: 0.8824 (mp0)
REVERT: B   82 ASP cc_start: 0.8379 (m-30) cc_final: 0.7880 (t70)
REVERT: B   83 MET cc_start: 0.8404 (tmt) cc_final: 0.7713 (tmm)
REVERT: B   86 THR cc_start: 0.8290 (p) cc_final: 0.8005 (p)
REVERT: C   75 GLU cc_start: 0.9257 (mp0) cc_final: 0.8950 (mp0)
REVERT: C   84 MET cc_start: 0.9429 (ttp) cc_final: 0.9174 (tpp)
REVERT: D    9 GLN cc_start: 0.9264 (pt0) cc_final: 0.8905 (mp10)
REVERT: D   17 GLN cc_start: 0.9256 (pt0) cc_final: 0.9034 (pt0)
REVERT: D   64 MET cc_start: 0.8856 (ppp) cc_final: 0.8098 (ppp)
REVERT: D   68 ASP cc_start: 0.9323 (t0) cc_final: 0.9083 (t0)
REVERT: D   82 ASP cc_start: 0.9147 (m-30) cc_final: 0.8925 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 140
  average time/residue: 0.0995
  time to fit residues: 18.4893
Evaluate side-chains
  123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
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:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 32 optimal weight:    4.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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  20 HIS ** 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 = 0.3307 r_free = 0.3307 target = 0.061006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.052944 restraints weight = 51350.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.055683 restraints weight = 21483.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.057423 restraints weight = 11121.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.058557 restraints weight = 6453.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.059266 restraints weight = 4012.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.7945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3560  Z= 0.207
  Angle     :  0.615   6.617   4808  Z= 0.341
  Chirality :  0.038   0.189    560
  Planarity :  0.003   0.018    608
  Dihedral  :  3.858  14.541    464
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.05 %
    Favored  : 76.04 %
  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:  1.63 (0.37), residues: 428
  helix:  1.57 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.19 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.012   0.001   TYR D  16 
 PHE   0.013   0.002   PHE A  77 
 HIS   0.005   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3560)
  covalent geometry    : angle       0.61483 ( 4808)
  hydrogen bonds       : bond        0.03903 (  233)
  hydrogen bonds       : angle       4.72105 (  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
  130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.130 
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: A    8 GLU cc_start: 0.9140 (mp0) cc_final: 0.8735 (mp0)
REVERT: B    8 GLU cc_start: 0.9242 (mp0) cc_final: 0.9024 (mp0)
REVERT: B   82 ASP cc_start: 0.8480 (m-30) cc_final: 0.7874 (t70)
REVERT: B   83 MET cc_start: 0.8453 (tmt) cc_final: 0.7743 (tmm)
REVERT: B   86 THR cc_start: 0.8596 (p) cc_final: 0.8336 (p)
REVERT: D   64 MET cc_start: 0.8946 (ppp) cc_final: 0.8133 (ppp)
REVERT: D   68 ASP cc_start: 0.9397 (t0) cc_final: 0.9147 (t0)
REVERT: D   82 ASP cc_start: 0.9234 (m-30) cc_final: 0.8983 (m-30)
REVERT: D   99 VAL cc_start: 0.9645 (t) cc_final: 0.9441 (p)
  outliers start: 15
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1055
  time to fit residues: 17.0588
Evaluate side-chains
  123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  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 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   98 ASP
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:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
C 107 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.060612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.052852 restraints weight = 50713.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.055476 restraints weight = 20789.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.057134 restraints weight = 10738.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.058264 restraints weight = 6340.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.058913 restraints weight = 3880.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.8197

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= 0.125
  Angle     :  0.561   6.537   4808  Z= 0.303
  Chirality :  0.037   0.172    560
  Planarity :  0.003   0.018    608
  Dihedral  :  3.871  14.888    464
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.96 %
    Favored  : 73.44 %
  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 aren not related in a simple way.
  whole:  1.82 (0.37), residues: 428
  helix:  1.78 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop :  0.10 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  39 
 TYR   0.011   0.001   TYR D  16 
 PHE   0.010   0.001   PHE D  77 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3560)
  covalent geometry    : angle       0.56116 ( 4808)
  hydrogen bonds       : bond        0.03451 (  233)
  hydrogen bonds       : angle       4.35968 (  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
  125 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.144 
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: A    8 GLU cc_start: 0.9146 (mp0) cc_final: 0.8735 (mp0)
REVERT: B    8 GLU cc_start: 0.9280 (mp0) cc_final: 0.9040 (mp0)
REVERT: B   15 ASN cc_start: 0.9095 (m-40) cc_final: 0.8735 (m110)
REVERT: B   17 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8812 (mt0)
REVERT: B   22 GLN cc_start: 0.9439 (tp40) cc_final: 0.9151 (mp10)
REVERT: B   82 ASP cc_start: 0.8572 (m-30) cc_final: 0.8049 (t0)
REVERT: B   83 MET cc_start: 0.8559 (tmt) cc_final: 0.8047 (tmm)
REVERT: B   86 THR cc_start: 0.8702 (p) cc_final: 0.8416 (p)
REVERT: D   64 MET cc_start: 0.9012 (ppp) cc_final: 0.8202 (ppp)
REVERT: D   68 ASP cc_start: 0.9366 (t0) cc_final: 0.9110 (t0)
REVERT: D   82 ASP cc_start: 0.9194 (m-30) cc_final: 0.8965 (m-30)
  outliers start: 10
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1026
  time to fit residues: 16.1602
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  : 0.188 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  20 HIS
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.060371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.052444 restraints weight = 51911.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.055096 restraints weight = 21260.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.056812 restraints weight = 11053.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.057950 restraints weight = 6412.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.058674 restraints weight = 3977.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.8561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3560  Z= 0.144
  Angle     :  0.595   7.999   4808  Z= 0.323
  Chirality :  0.037   0.166    560
  Planarity :  0.003   0.017    608
  Dihedral  :  3.822  13.467    464
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 24.74 %
    Favored  : 72.40 %
  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:  1.67 (0.37), residues: 428
  helix:  1.70 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.05 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  33 
 TYR   0.012   0.001   TYR D  16 
 PHE   0.009   0.001   PHE A  77 
 HIS   0.004   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3560)
  covalent geometry    : angle       0.59513 ( 4808)
  hydrogen bonds       : bond        0.03448 (  233)
  hydrogen bonds       : angle       4.44491 (  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
  129 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.187 
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    8 GLU cc_start: 0.9255 (mp0) cc_final: 0.9027 (mp0)
REVERT: B   15 ASN cc_start: 0.9006 (m-40) cc_final: 0.8582 (m110)
REVERT: B   82 ASP cc_start: 0.8724 (m-30) cc_final: 0.8189 (t0)
REVERT: B   83 MET cc_start: 0.8667 (tmt) cc_final: 0.8136 (tmm)
REVERT: D   33 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8084 (ttp-170)
REVERT: D   64 MET cc_start: 0.9019 (ppp) cc_final: 0.8225 (ppp)
REVERT: D   68 ASP cc_start: 0.9351 (t0) cc_final: 0.9100 (t0)
REVERT: D   82 ASP cc_start: 0.9224 (m-30) cc_final: 0.8968 (m-30)
REVERT: D   91 LEU cc_start: 0.8867 (mt) cc_final: 0.8373 (mm)
  outliers start: 11
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1025
  time to fit residues: 16.4919
Evaluate side-chains
  127 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.059886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.052197 restraints weight = 51863.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.054779 restraints weight = 21583.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.056449 restraints weight = 11248.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.057499 restraints weight = 6530.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.058233 restraints weight = 4112.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.8861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3560  Z= 0.143
  Angle     :  0.616   6.244   4808  Z= 0.330
  Chirality :  0.037   0.159    560
  Planarity :  0.002   0.016    608
  Dihedral  :  3.824  12.839    464
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 27.08 %
    Favored  : 70.83 %
  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:  1.65 (0.38), residues: 428
  helix:  1.74 (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   0.003   0.000   ARG D  33 
 TYR   0.011   0.001   TYR D  16 
 PHE   0.011   0.001   PHE A   7 
 HIS   0.004   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3560)
  covalent geometry    : angle       0.61583 ( 4808)
  hydrogen bonds       : bond        0.03298 (  233)
  hydrogen bonds       : angle       4.40523 (  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
  123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.194 
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: A    8 GLU cc_start: 0.9135 (mp0) cc_final: 0.8930 (mp0)
REVERT: B    8 GLU cc_start: 0.9244 (mp0) cc_final: 0.9020 (mp0)
REVERT: B   82 ASP cc_start: 0.8806 (m-30) cc_final: 0.8084 (t0)
REVERT: B   83 MET cc_start: 0.8834 (tmt) cc_final: 0.8219 (tmm)
REVERT: C    9 GLN cc_start: 0.9390 (pt0) cc_final: 0.8889 (mp10)
REVERT: D   33 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.8120 (ttp-170)
REVERT: D   64 MET cc_start: 0.9003 (ppp) cc_final: 0.8202 (ppp)
REVERT: D   68 ASP cc_start: 0.9359 (t0) cc_final: 0.9123 (t0)
REVERT: D   82 ASP cc_start: 0.9229 (m-30) cc_final: 0.9023 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1090
  time to fit residues: 16.8703
Evaluate side-chains
  117 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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   87 SER
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:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.060319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.052716 restraints weight = 51238.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.055284 restraints weight = 20698.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.056961 restraints weight = 10662.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.058019 restraints weight = 6159.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.058730 restraints weight = 3829.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.9080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3560  Z= 0.126
  Angle     :  0.603   6.083   4808  Z= 0.321
  Chirality :  0.037   0.160    560
  Planarity :  0.002   0.017    608
  Dihedral  :  3.767  12.193    464
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 27.86 %
    Favored  : 70.57 %
  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:  1.73 (0.38), residues: 428
  helix:  1.83 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -0.23 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.008   0.001   PHE D  49 
 HIS   0.004   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3560)
  covalent geometry    : angle       0.60262 ( 4808)
  hydrogen bonds       : bond        0.03116 (  233)
  hydrogen bonds       : angle       4.32454 (  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
  122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.214 
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: A   97 MET cc_start: 0.8879 (ptp) cc_final: 0.8584 (pmm)
REVERT: B    8 GLU cc_start: 0.9258 (mp0) cc_final: 0.9053 (mp0)
REVERT: B   82 ASP cc_start: 0.8800 (m-30) cc_final: 0.8080 (t0)
REVERT: B   83 MET cc_start: 0.8808 (tmt) cc_final: 0.8214 (tmm)
REVERT: D   33 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.8124 (ttp-170)
REVERT: D   64 MET cc_start: 0.8962 (ppp) cc_final: 0.8165 (ppp)
REVERT: D   68 ASP cc_start: 0.9337 (t0) cc_final: 0.9099 (t0)
REVERT: D   82 ASP cc_start: 0.9229 (m-30) cc_final: 0.9001 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 118
  average time/residue: 0.1102
  time to fit residues: 17.1148
Evaluate side-chains
  119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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   45 CYS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3289 r_free = 0.3289 target = 0.060406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.052418 restraints weight = 51963.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.055042 restraints weight = 21234.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.056779 restraints weight = 11079.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.057910 restraints weight = 6461.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.058665 restraints weight = 4075.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.9256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3560  Z= 0.135
  Angle     :  0.608   6.197   4808  Z= 0.328
  Chirality :  0.037   0.154    560
  Planarity :  0.002   0.018    608
  Dihedral  :  3.723  12.324    464
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 27.34 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.90 (0.38), residues: 428
  helix:  1.96 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.10 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.016   0.001   PHE A   7 
 HIS   0.003   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3560)
  covalent geometry    : angle       0.60750 ( 4808)
  hydrogen bonds       : bond        0.03062 (  233)
  hydrogen bonds       : angle       4.29787 (  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
  117 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.162 
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   97 MET cc_start: 0.9018 (ptp) cc_final: 0.8731 (pmm)
REVERT: B    8 GLU cc_start: 0.9242 (mp0) cc_final: 0.9036 (mp0)
REVERT: B   82 ASP cc_start: 0.8822 (m-30) cc_final: 0.8123 (t0)
REVERT: B   83 MET cc_start: 0.8939 (tmt) cc_final: 0.8697 (tmm)
REVERT: D    9 GLN cc_start: 0.9263 (pt0) cc_final: 0.8984 (pt0)
REVERT: D   33 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8088 (ttp-170)
REVERT: D   64 MET cc_start: 0.8972 (ppp) cc_final: 0.8168 (ppp)
REVERT: D   68 ASP cc_start: 0.9349 (t0) cc_final: 0.9113 (t0)
REVERT: D   82 ASP cc_start: 0.9264 (m-30) cc_final: 0.9038 (m-30)
  outliers start: 6
  outliers final: 6
  residues processed: 113
  average time/residue: 0.1039
  time to fit residues: 15.4138
Evaluate side-chains
  117 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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   45 CYS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain C residue   94 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 35 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.060276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.052438 restraints weight = 51074.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.054994 restraints weight = 20966.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.056697 restraints weight = 10915.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.057823 restraints weight = 6371.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.058572 restraints weight = 3962.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.9412

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= 0.131
  Angle     :  0.619   7.143   4808  Z= 0.332
  Chirality :  0.037   0.153    560
  Planarity :  0.002   0.019    608
  Dihedral  :  3.726  12.036    464
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 26.30 %
    Favored  : 72.40 %
  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:  1.91 (0.39), residues: 428
  helix:  1.94 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.04 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.010   0.001   TYR D  16 
 PHE   0.009   0.001   PHE A   7 
 HIS   0.003   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3560)
  covalent geometry    : angle       0.61942 ( 4808)
  hydrogen bonds       : bond        0.03034 (  233)
  hydrogen bonds       : angle       4.24664 (  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
  117 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.207 
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: A   97 MET cc_start: 0.9026 (ptp) cc_final: 0.8776 (pmm)
REVERT: A  109 ASN cc_start: 0.9324 (m110) cc_final: 0.8844 (p0)
REVERT: B    8 GLU cc_start: 0.9236 (mp0) cc_final: 0.9036 (mp0)
REVERT: B   82 ASP cc_start: 0.8818 (m-30) cc_final: 0.8104 (t0)
REVERT: B   83 MET cc_start: 0.8967 (tmt) cc_final: 0.8316 (tmm)
REVERT: D    9 GLN cc_start: 0.9267 (pt0) cc_final: 0.8953 (pt0)
REVERT: D   33 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8070 (ttp-170)
REVERT: D   64 MET cc_start: 0.8995 (ppp) cc_final: 0.8195 (ppp)
REVERT: D   68 ASP cc_start: 0.9340 (t0) cc_final: 0.9096 (t0)
REVERT: D   82 ASP cc_start: 0.9277 (m-30) cc_final: 0.9067 (m-30)
  outliers start: 5
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1127
  time to fit residues: 16.5949
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  : 0.136 
-------------------------------------------------------------------------------
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   45 CYS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.060031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052323 restraints weight = 50739.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054821 restraints weight = 20862.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.056502 restraints weight = 10862.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.057605 restraints weight = 6306.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.058342 restraints weight = 3952.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.9575

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     :  0.635   9.191   4808  Z= 0.338
  Chirality :  0.037   0.155    560
  Planarity :  0.002   0.018    608
  Dihedral  :  3.708  11.929    464
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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 aren not related in a simple way.
  whole:  1.92 (0.39), residues: 428
  helix:  1.93 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop :  0.01 (0.44), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.011   0.001   TYR D  16 
 PHE   0.009   0.001   PHE A   7 
 HIS   0.003   0.001   HIS C   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3560)
  covalent geometry    : angle       0.63543 ( 4808)
  hydrogen bonds       : bond        0.03035 (  233)
  hydrogen bonds       : angle       4.26004 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1647.70 seconds
wall clock time: 28 minutes 45.65 seconds (1725.65 seconds total)