Starting phenix.real_space_refine
on Wed Sep 17 03:15:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9knx_62465/09_2025/9knx_62465.cif"
  }
  resolution = 3.72
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      17      5.16       5
     C    1736      2.51       5
     N     452      2.21       5
     O     468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2675
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 1000
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 707
          Classifications: {'peptide': 89}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 84}
    Chain: "C"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 879
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "B"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 89
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
  Time building chain proxies: 0.94, per 1000 atoms: 0.35
  Number of scatterers: 2675
  At special positions: 0
  Unit cell: (79.23, 66.69, 95.19, 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      17     16.00
     P       2     15.00
     O     468      8.00
     N     452      7.00
     C    1736      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.02

  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: 0.37
  Conformation dependent library (CDL) restraints added in 121.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  606

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 3 sheets defined
      59.9% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 24
    Processing helix  chain 'B' and resid 25 through 27
      No H-bonds generated for 'chain 'B' and resid 25 through 27'
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 40 through 60
      removed outlier: 4.267A  pdb=" N   TRP B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      Proline residue:  B  46  - end of helix
      removed outlier: 3.824A  pdb=" N   GLY B  51 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LEU B  52 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 87
      removed outlier: 3.555A  pdb=" N   LEU B  87 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 127
      removed outlier: 3.580A  pdb=" N   PHE B  97 " --> pdb=" O   ASN B  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 34
      removed outlier: 3.963A  pdb=" N   PHE A  27 " --> pdb=" O   MET A  23 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TRP A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   GLY A  29 " --> pdb=" O   THR A  25 " (cutoff:3.500A)
      Proline residue:  A  30  - end of helix
    Processing helix  chain 'A' and resid 34 through 44
      removed outlier: 3.626A  pdb=" N   ILE A  38 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 73
    Processing helix  chain 'A' and resid 77 through 108
    Processing helix  chain 'C' and resid 62 through 65
    Processing helix  chain 'C' and resid 74 through 76
      No H-bonds generated for 'chain 'C' and resid 74 through 76'
    Processing helix  chain 'C' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.404A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   SER C 114 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL C  12 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   MET C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ALA C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.404A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   SER C 114 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL C  12 " --> pdb=" O   SER C 114 " (cutoff:3.500A)

    172 hydrogen bonds defined for protein.
    480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.41

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 399
        1.30 -     1.43: 761
        1.43 -     1.56: 1540
        1.56 -     1.69: 14
        1.69 -     1.81: 28
  Bond restraints: 2742
  Sorted by residual:
  bond pdb=" CB7 CDL B 201 "
       pdb=" OB8 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.435 -0.101 1.10e-02 8.26e+03 8.42e+01
  bond pdb=" CA7 CDL B 201 "
       pdb=" OA8 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.432 -0.098 1.10e-02 8.26e+03 7.86e+01
  bond pdb=" CA5 CDL B 201 "
       pdb=" OA6 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.342  1.441 -0.099 1.50e-02 4.44e+03 4.36e+01
  bond pdb=" CB5 CDL B 201 "
       pdb=" OB6 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.342  1.436 -0.094 1.50e-02 4.44e+03 3.93e+01
  bond pdb=" OB2 CDL B 201 "
       pdb=" PB2 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.579  1.670 -0.091 1.50e-02 4.44e+03 3.65e+01
  ... (remaining 2737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 3422
        1.88 -     3.76: 231
        3.76 -     5.64: 30
        5.64 -     7.53: 5
        7.53 -     9.41: 6
  Bond angle restraints: 3694
  Sorted by residual:
  angle pdb=" C51 CDL B 201 "
        pdb=" CB5 CDL B 201 "
        pdb=" OB6 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     111.33  119.43   -8.10 1.32e+00 5.72e-01 3.75e+01
  angle pdb=" C11 CDL B 201 "
        pdb=" CA5 CDL B 201 "
        pdb=" OA6 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     111.33  119.40   -8.07 1.32e+00 5.72e-01 3.72e+01
  angle pdb=" C71 CDL B 201 "
        pdb=" CB7 CDL B 201 "
        pdb=" OB8 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     111.64  120.73   -9.09 1.65e+00 3.69e-01 3.05e+01
  angle pdb=" C31 CDL B 201 "
        pdb=" CA7 CDL B 201 "
        pdb=" OA8 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     111.64  120.52   -8.88 1.65e+00 3.69e-01 2.91e+01
  angle pdb=" CA3 CDL B 201 "
        pdb=" OA5 CDL B 201 "
        pdb=" PA1 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     121.27  116.53    4.74 1.00e+00 1.00e+00 2.25e+01
  ... (remaining 3689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.12: 1427
       16.12 -    32.24: 134
       32.24 -    48.35: 52
       48.35 -    64.47: 25
       64.47 -    80.59: 4
  Dihedral angle restraints: 1642
    sinusoidal: 695
      harmonic: 947
  Sorted by residual:
  dihedral pdb=" C   THR A  56 "
           pdb=" N   THR A  56 "
           pdb=" CA  THR A  56 "
           pdb=" CB  THR A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.90    8.90     0      2.50e+00 1.60e-01 1.27e+01
  dihedral pdb=" C   PHE A  27 "
           pdb=" N   PHE A  27 "
           pdb=" CA  PHE A  27 "
           pdb=" CB  PHE A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.64    8.04     0      2.50e+00 1.60e-01 1.03e+01
  dihedral pdb=" N   ASN B  33 "
           pdb=" CA  ASN B  33 "
           pdb=" CB  ASN B  33 "
           pdb=" CG  ASN B  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.74   59.74     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 272
       0.052 -    0.104: 78
       0.104 -    0.155: 24
       0.155 -    0.207: 9
       0.207 -    0.259: 4
  Chirality restraints: 387
  Sorted by residual:
  chirality pdb=" CA  VAL C  98 "
            pdb=" N   VAL C  98 "
            pdb=" C   VAL C  98 "
            pdb=" CB  VAL C  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PHE A  27 "
            pdb=" N   PHE A  27 "
            pdb=" C   PHE A  27 "
            pdb=" CB  PHE A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL A  73 "
            pdb=" CA  VAL A  73 "
            pdb=" CG1 VAL A  73 "
            pdb=" CG2 VAL A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 384 not shown)

  Planarity restraints: 454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C  50 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.94e+00
        pdb=" C   ALA C  50 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ALA C  50 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE C  51 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  54 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.79e+00
        pdb=" C   ARG A  54 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG A  54 "    0.013 2.00e-02 2.50e+03
        pdb=" N   MET A  55 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  71 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   GLN B  71 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLN B  71 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER B  72 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 451 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 558
        2.78 -     3.31: 2471
        3.31 -     3.84: 4368
        3.84 -     4.37: 5125
        4.37 -     4.90: 8531
  Nonbonded interactions: 21053
  Sorted by model distance:
  nonbonded pdb=" O   CYS A  60 "
            pdb=" OG  SER A  63 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   LEU B  22 "
            pdb=" NH2 ARG B  29 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NZ  LYS B  49 "
            pdb=" OD1 ASN B 100 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD2 ASP B  59 "
            pdb=" OG  SER A  52 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OA6 CDL B 201 "
            pdb=" OA8 CDL B 201 "
     model   vdw
     2.400 2.432
  ... (remaining 21048 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.160
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.900
  Find NCS groups from input model:        0.010
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
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      :  0.011   0.105   2743  Z= 0.689
  Angle     :  1.060   9.408   3696  Z= 0.697
  Chirality :  0.062   0.259    387
  Planarity :  0.005   0.036    454
  Dihedral  : 16.420  80.590   1033
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  7.89 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -1.45 (0.44), residues: 323
  helix: -1.31 (0.33), residues: 168
  sheet:  0.03 (0.62), residues: 66
  loop : -0.50 (0.75), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  62 
 TYR   0.014   0.001   TYR B  85 
 PHE   0.020   0.002   PHE A  69 
 TRP   0.011   0.002   TRP B  44 
 HIS   0.004   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.01108 ( 2742)
  covalent geometry    : angle       1.05526 ( 3694)
  SS BOND              : bond        0.00748 (    1)
  SS BOND              : angle       4.47585 (    2)
  hydrogen bonds       : bond        0.12628 (  168)
  hydrogen bonds       : angle       6.50125 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B   27 LYS cc_start: 0.8347 (mttt) cc_final: 0.8123 (tttt)
REVERT: A   72 LYS cc_start: 0.7641 (tptt) cc_final: 0.7359 (tptt)
REVERT: C   60 TYR cc_start: 0.7520 (m-80) cc_final: 0.7140 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0688
  time to fit residues: 4.8485
Evaluate side-chains
  48 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  93 ASN
** A  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.215532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.168283 restraints weight = 3199.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.173448 restraints weight = 2003.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.176776 restraints weight = 1464.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.179433 restraints weight = 1194.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.180667 restraints weight = 1039.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2743  Z= 0.153
  Angle     :  0.578   9.497   3696  Z= 0.300
  Chirality :  0.041   0.152    387
  Planarity :  0.005   0.045    454
  Dihedral  : 13.090  66.016    443
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.78 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.37 (0.46), residues: 323
  helix:  0.79 (0.40), residues: 167
  sheet:  0.22 (0.61), residues: 64
  loop : -0.52 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.015   0.001   TYR B  85 
 PHE   0.010   0.002   PHE A  57 
 TRP   0.006   0.001   TRP B  50 
 HIS   0.002   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2742)
  covalent geometry    : angle       0.57762 ( 3694)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.57057 (    2)
  hydrogen bonds       : bond        0.04962 (  168)
  hydrogen bonds       : angle       4.91260 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.097 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8510 (mttt) cc_final: 0.8290 (ttmm)
REVERT: A   72 LYS cc_start: 0.7855 (tptt) cc_final: 0.7489 (tptm)
REVERT: A  103 MET cc_start: 0.4544 (ptm) cc_final: 0.4315 (ptm)
REVERT: C   60 TYR cc_start: 0.7972 (m-80) cc_final: 0.7313 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.0690
  time to fit residues: 4.0640
Evaluate side-chains
  47 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   78 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:   40.0000
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0060
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.226200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.183521 restraints weight = 3219.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.188402 restraints weight = 2089.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.191195 restraints weight = 1555.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.193852 restraints weight = 1299.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.195004 restraints weight = 1136.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2743  Z= 0.131
  Angle     :  0.534   7.848   3696  Z= 0.273
  Chirality :  0.040   0.195    387
  Planarity :  0.005   0.047    454
  Dihedral  : 11.629  56.328    443
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.91 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.13 (0.47), residues: 323
  helix:  1.58 (0.40), residues: 167
  sheet:  0.28 (0.59), residues: 68
  loop : -0.36 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.009   0.001   PHE C  68 
 TRP   0.006   0.001   TRP C  36 
 HIS   0.003   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2742)
  covalent geometry    : angle       0.53365 ( 3694)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.25332 (    2)
  hydrogen bonds       : bond        0.04710 (  168)
  hydrogen bonds       : angle       4.46311 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 MET cc_start: 0.8019 (tpp) cc_final: 0.7411 (mpp)
REVERT: B   27 LYS cc_start: 0.8546 (mttt) cc_final: 0.8286 (ttmm)
REVERT: A   72 LYS cc_start: 0.7946 (tptt) cc_final: 0.7340 (tptt)
REVERT: A  103 MET cc_start: 0.4547 (ptm) cc_final: 0.4318 (ptm)
REVERT: C   60 TYR cc_start: 0.7875 (m-80) cc_final: 0.7259 (m-80)
  outliers start: 4
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0816
  time to fit residues: 4.7517
Evaluate side-chains
  51 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0010
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7192

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.224484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.181936 restraints weight = 3220.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.186680 restraints weight = 2102.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.189586 restraints weight = 1568.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.192161 restraints weight = 1304.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.193318 restraints weight = 1138.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2743  Z= 0.132
  Angle     :  0.513   6.087   3696  Z= 0.266
  Chirality :  0.040   0.174    387
  Planarity :  0.004   0.049    454
  Dihedral  : 10.178  55.473    443
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.29 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.64 (0.48), residues: 323
  helix:  2.14 (0.41), residues: 165
  sheet:  0.29 (0.58), residues: 68
  loop : -0.19 (0.71), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  32 
 TYR   0.014   0.001   TYR B  85 
 PHE   0.009   0.001   PHE A  57 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2742)
  covalent geometry    : angle       0.51318 ( 3694)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.41329 (    2)
  hydrogen bonds       : bond        0.04484 (  168)
  hydrogen bonds       : angle       4.25863 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: B   18 ASP cc_start: 0.6962 (m-30) cc_final: 0.6670 (m-30)
REVERT: B   23 MET cc_start: 0.7999 (tpp) cc_final: 0.7363 (mpp)
REVERT: A  103 MET cc_start: 0.4629 (ptm) cc_final: 0.4359 (ptm)
REVERT: C   29 VAL cc_start: 0.8182 (t) cc_final: 0.7959 (p)
REVERT: C   32 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8184 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7839 (m-80) cc_final: 0.7275 (m-80)
REVERT: C   83 MET cc_start: 0.7992 (ttp) cc_final: 0.7561 (tpp)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0797
  time to fit residues: 4.9682
Evaluate side-chains
  55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0770
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.226290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.182779 restraints weight = 3237.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.188252 restraints weight = 2027.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.191941 restraints weight = 1464.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.193797 restraints weight = 1178.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.194310 restraints weight = 1037.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2743  Z= 0.111
  Angle     :  0.473   5.720   3696  Z= 0.247
  Chirality :  0.039   0.144    387
  Planarity :  0.004   0.046    454
  Dihedral  :  9.406  55.693    443
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.67 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.48), residues: 323
  helix:  2.56 (0.40), residues: 165
  sheet:  0.27 (0.59), residues: 68
  loop : -0.09 (0.72), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  45 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.005   0.001   PHE A  57 
 TRP   0.005   0.001   TRP A  34 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 2742)
  covalent geometry    : angle       0.47358 ( 3694)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.24597 (    2)
  hydrogen bonds       : bond        0.04269 (  168)
  hydrogen bonds       : angle       3.97786 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 MET cc_start: 0.7977 (tpp) cc_final: 0.7465 (mpp)
REVERT: B   27 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8012 (ttmm)
REVERT: A  103 MET cc_start: 0.4547 (ptm) cc_final: 0.4277 (ptm)
REVERT: C   32 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8221 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7744 (m-80) cc_final: 0.7191 (m-80)
REVERT: C   83 MET cc_start: 0.8069 (ttp) cc_final: 0.7642 (tpp)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0711
  time to fit residues: 4.4845
Evaluate side-chains
  53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:   40.0000
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.222918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.178441 restraints weight = 3260.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.183586 restraints weight = 2067.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.187340 restraints weight = 1514.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.188901 restraints weight = 1224.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.188901 restraints weight = 1089.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2743  Z= 0.131
  Angle     :  0.490   6.135   3696  Z= 0.256
  Chirality :  0.039   0.124    387
  Planarity :  0.004   0.047    454
  Dihedral  :  9.351  56.789    443
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.05 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.97 (0.48), residues: 323
  helix:  2.53 (0.40), residues: 165
  sheet:  0.09 (0.59), residues: 65
  loop :  0.04 (0.72), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  32 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.007   0.001   PHE B  80 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2742)
  covalent geometry    : angle       0.48962 ( 3694)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.31950 (    2)
  hydrogen bonds       : bond        0.04379 (  168)
  hydrogen bonds       : angle       3.97502 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.103 
Fit side-chains
REVERT: B   23 MET cc_start: 0.8037 (tpp) cc_final: 0.7347 (mpp)
REVERT: B   27 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8036 (ttmm)
REVERT: A   72 LYS cc_start: 0.8094 (tptt) cc_final: 0.7397 (tptt)
REVERT: A  103 MET cc_start: 0.4453 (ptm) cc_final: 0.4175 (ptm)
REVERT: C   32 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8235 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7563 (m-80) cc_final: 0.7006 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0724
  time to fit residues: 4.5062
Evaluate side-chains
  53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0060
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.225484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.181365 restraints weight = 3230.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.186652 restraints weight = 2052.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.189753 restraints weight = 1496.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.192745 restraints weight = 1227.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.194034 restraints weight = 1052.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2743  Z= 0.110
  Angle     :  0.477   5.919   3696  Z= 0.247
  Chirality :  0.039   0.125    387
  Planarity :  0.004   0.046    454
  Dihedral  :  9.009  58.055    443
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.05 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.48), residues: 323
  helix:  2.63 (0.40), residues: 165
  sheet:  0.12 (0.59), residues: 65
  loop :  0.13 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  67 
 TYR   0.011   0.001   TYR B  85 
 PHE   0.011   0.001   PHE C  68 
 TRP   0.005   0.001   TRP A  34 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2742)
  covalent geometry    : angle       0.47672 ( 3694)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.27136 (    2)
  hydrogen bonds       : bond        0.04199 (  168)
  hydrogen bonds       : angle       3.91049 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B   23 MET cc_start: 0.7959 (tpp) cc_final: 0.7423 (mpp)
REVERT: B   27 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8017 (ttmm)
REVERT: A   72 LYS cc_start: 0.8090 (tptt) cc_final: 0.7411 (tptt)
REVERT: A  103 MET cc_start: 0.4570 (ptm) cc_final: 0.4359 (ptm)
REVERT: C   18 LEU cc_start: 0.7462 (tp) cc_final: 0.7212 (mp)
REVERT: C   32 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8306 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7604 (m-80) cc_final: 0.7025 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0739
  time to fit residues: 4.4853
Evaluate side-chains
  52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.221119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.178100 restraints weight = 3251.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.183050 restraints weight = 2088.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.186524 restraints weight = 1546.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.187945 restraints weight = 1257.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.187945 restraints weight = 1123.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2743  Z= 0.130
  Angle     :  0.504   6.232   3696  Z= 0.270
  Chirality :  0.040   0.129    387
  Planarity :  0.004   0.047    454
  Dihedral  :  9.225  59.977    443
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.05 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.48), residues: 323
  helix:  2.60 (0.40), residues: 165
  sheet:  0.23 (0.60), residues: 65
  loop :  0.18 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  32 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.015   0.002   PHE C  68 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2742)
  covalent geometry    : angle       0.50377 ( 3694)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.31086 (    2)
  hydrogen bonds       : bond        0.04415 (  168)
  hydrogen bonds       : angle       4.00343 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.101 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8104 (ttmm)
REVERT: A   72 LYS cc_start: 0.8089 (tptt) cc_final: 0.7436 (tptt)
REVERT: A  103 MET cc_start: 0.4638 (ptm) cc_final: 0.4425 (ptm)
REVERT: C   32 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8324 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7609 (m-80) cc_final: 0.7059 (m-80)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0750
  time to fit residues: 4.6551
Evaluate side-chains
  52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   93 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.4698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.224888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.181554 restraints weight = 3267.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.186860 restraints weight = 2061.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.190602 restraints weight = 1501.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.192815 restraints weight = 1202.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.193586 restraints weight = 1043.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.4387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   2743  Z= 0.112
  Angle     :  0.478   5.939   3696  Z= 0.256
  Chirality :  0.039   0.121    387
  Planarity :  0.004   0.047    454
  Dihedral  :  8.899  55.136    443
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.42 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.49), residues: 323
  helix:  2.71 (0.40), residues: 165
  sheet:  0.29 (0.61), residues: 65
  loop :  0.33 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  39 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.013   0.001   PHE C  68 
 TRP   0.005   0.001   TRP A  34 
 HIS   0.002   0.000   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 2742)
  covalent geometry    : angle       0.47808 ( 3694)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.39611 (    2)
  hydrogen bonds       : bond        0.04207 (  168)
  hydrogen bonds       : angle       3.89975 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.096 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8177 (mptt)
REVERT: A   72 LYS cc_start: 0.8074 (tptt) cc_final: 0.7427 (tptt)
REVERT: A  103 MET cc_start: 0.4653 (ptm) cc_final: 0.4422 (ptm)
REVERT: C    7 SER cc_start: 0.8717 (t) cc_final: 0.8432 (p)
REVERT: C   60 TYR cc_start: 0.7559 (m-80) cc_final: 0.6936 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 54
  average time/residue: 0.0641
  time to fit residues: 4.2036
Evaluate side-chains
  55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   62 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.220933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.178826 restraints weight = 3307.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.183302 restraints weight = 2142.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.186843 restraints weight = 1586.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.188757 restraints weight = 1283.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.190602 restraints weight = 1129.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2743  Z= 0.133
  Angle     :  0.507   9.301   3696  Z= 0.267
  Chirality :  0.040   0.117    387
  Planarity :  0.005   0.047    454
  Dihedral  :  9.097  57.470    443
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.80 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.48), residues: 323
  helix:  2.77 (0.40), residues: 165
  sheet:  0.23 (0.58), residues: 68
  loop :  0.19 (0.73), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  68 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.010   0.002   PHE C  68 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2742)
  covalent geometry    : angle       0.50733 ( 3694)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.41145 (    2)
  hydrogen bonds       : bond        0.04337 (  168)
  hydrogen bonds       : angle       3.89997 (  480)

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

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

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  646 Ramachandran restraints generated.
    323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.095 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8202 (mptt)
REVERT: A   72 LYS cc_start: 0.8118 (tptt) cc_final: 0.7460 (tptt)
REVERT: A  103 MET cc_start: 0.4634 (ptm) cc_final: 0.4402 (ptm)
REVERT: C    7 SER cc_start: 0.8707 (t) cc_final: 0.8407 (p)
REVERT: C   60 TYR cc_start: 0.7611 (m-80) cc_final: 0.7119 (m-80)
  outliers start: 6
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0533
  time to fit residues: 3.8397
Evaluate side-chains
  58 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 21 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.222974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.180445 restraints weight = 3287.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.185737 restraints weight = 2076.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.189223 restraints weight = 1508.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.191588 restraints weight = 1213.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.192792 restraints weight = 1048.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2743  Z= 0.121
  Angle     :  0.505   7.544   3696  Z= 0.266
  Chirality :  0.039   0.120    387
  Planarity :  0.004   0.046    454
  Dihedral  :  8.788  50.955    443
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.30 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.49), residues: 323
  helix:  2.75 (0.40), residues: 166
  sheet:  0.19 (0.60), residues: 65
  loop :  0.34 (0.73), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  32 
 TYR   0.013   0.001   TYR A  62 
 PHE   0.009   0.001   PHE C  68 
 TRP   0.005   0.001   TRP A  28 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2742)
  covalent geometry    : angle       0.50462 ( 3694)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       0.41710 (    2)
  hydrogen bonds       : bond        0.04237 (  168)
  hydrogen bonds       : angle       3.89941 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 890.27 seconds
wall clock time: 15 minutes 59.28 seconds (959.28 seconds total)