Starting phenix.real_space_refine
on Wed Jul  1 21:15:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_62465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_62465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_62465.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_62465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9knx_62465/07_2026/9knx_62465.map"
  }
  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-dev-6108/lib/python3.11/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: 0.91, per 1000 atoms: 0.34
  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: 0.27
  Conformation dependent library (CDL) restraints added in 112.2 milliseconds
  

  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: 0.05
  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: 0.24

  Time building geometry restraints manager: 0.38 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=" CA5 CDL B 201 "
       pdb=" OA6 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.333  1.441 -0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" CB5 CDL B 201 "
       pdb=" OB6 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.436 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" CA7 CDL B 201 "
       pdb=" OA8 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.331  1.432 -0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" CB7 CDL B 201 "
       pdb=" OB8 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.339  1.435 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" C60 CDL B 201 "
       pdb=" C61 CDL B 201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.607 -0.080 2.00e-02 2.50e+03 1.60e+01
  ... (remaining 2737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 3569
        2.65 -     5.29: 106
        5.29 -     7.94: 12
        7.94 -    10.58: 3
       10.58 -    13.23: 4
  Bond angle restraints: 3694
  Sorted by residual:
  angle pdb=" OB3 CDL B 201 "
        pdb=" PB2 CDL B 201 "
        pdb=" OB4 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     121.80  108.57   13.23 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" OA2 CDL B 201 "
        pdb=" PA1 CDL B 201 "
        pdb=" OA5 CDL B 201 "
      ideal   model   delta    sigma   weight residual
      97.81  110.76  -12.95 3.00e+00 1.11e-01 1.86e+01
  angle pdb=" OA3 CDL B 201 "
        pdb=" PA1 CDL B 201 "
        pdb=" OA4 CDL B 201 "
      ideal   model   delta    sigma   weight residual
     121.92  109.20   12.72 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" OB2 CDL B 201 "
        pdb=" PB2 CDL B 201 "
        pdb=" OB5 CDL B 201 "
      ideal   model   delta    sigma   weight residual
      96.70  109.34  -12.64 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" N   TRP A  34 "
        pdb=" CA  TRP A  34 "
        pdb=" C   TRP A  34 "
      ideal   model   delta    sigma   weight residual
     112.87  108.28    4.59 1.20e+00 6.94e-01 1.46e+01
  ... (remaining 3689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.12: 1434
       16.12 -    32.24: 137
       32.24 -    48.35: 57
       48.35 -    64.47: 26
       64.47 -    80.59: 4
  Dihedral angle restraints: 1658
    sinusoidal: 711
      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 1655 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:             3.430
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.420
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
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      :  0.010   0.108   2743  Z= 0.586
  Angle     :  1.144  13.225   3696  Z= 0.667
  Chirality :  0.062   0.259    387
  Planarity :  0.005   0.036    454
  Dihedral  : 16.580  80.590   1049
  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 are 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/Z
  covalent geometry    : bond        0.00998 /  0.59 ( 2742)
  covalent geometry    : angle       1.13923 /  0.67 ( 3694)
  SS BOND              : bond        0.00748 /  0.39 (    1)
  SS BOND              : angle       4.47585 /  2.62 (    2)
  hydrogen bonds       : bond        0.12628 /  8.66 (  168)
  hydrogen bonds       : angle       6.50125 /  4.46 (  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  : 0.144 
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: 0.0747
  time to fit residues: 5.2963
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  : 0.105 
-------------------------------------------------------------------------------
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...
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 = 0.4335 r_free = 0.4335 target = 0.222732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.177686 restraints weight = 3253.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.182915 restraints weight = 2025.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.185961 restraints weight = 1471.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.188682 restraints weight = 1214.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.189392 restraints weight = 1059.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2743  Z= 0.157
  Angle     :  0.586   9.848   3696  Z= 0.303
  Chirality :  0.041   0.139    387
  Planarity :  0.005   0.045    454
  Dihedral  : 12.261  59.266    459
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.41 %
    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 are not related in a simple way.
  whole:  0.38 (0.46), residues: 323
  helix:  0.81 (0.40), residues: 167
  sheet:  0.24 (0.61), residues: 64
  loop : -0.56 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  45 
 TYR   0.015   0.002   TYR B  85 
 PHE   0.010   0.002   PHE A  57 
 TRP   0.007   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 ( 2742)
  covalent geometry    : angle       0.58566 /  0.30 ( 3694)
  SS BOND              : bond        0.00119 /  0.06 (    1)
  SS BOND              : angle       0.52725 /  0.31 (    2)
  hydrogen bonds       : bond        0.04881 /  3.74 (  168)
  hydrogen bonds       : angle       4.89212 /  3.42 (  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: 5
    poor density    : 47
  time to evaluate  : 0.101 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8528 (mttt) cc_final: 0.8292 (ttmm)
REVERT: A   31 VAL cc_start: 0.8531 (t) cc_final: 0.8199 (p)
REVERT: A   72 LYS cc_start: 0.7866 (tptt) cc_final: 0.7145 (tptt)
REVERT: A  103 MET cc_start: 0.4476 (ptm) cc_final: 0.4250 (ptm)
REVERT: C   60 TYR cc_start: 0.7997 (m-80) cc_final: 0.7345 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 49
  average time/residue: 0.0785
  time to fit residues: 4.5195
Evaluate side-chains
  47 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain A residue   23 MET
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:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0000
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4482

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  84 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 = 0.4372 r_free = 0.4372 target = 0.227512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.185073 restraints weight = 3202.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.189895 restraints weight = 2066.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.193333 restraints weight = 1538.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.194789 restraints weight = 1258.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.196238 restraints weight = 1130.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.3050

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= 0.120
  Angle     :  0.522   7.905   3696  Z= 0.268
  Chirality :  0.040   0.181    387
  Planarity :  0.005   0.047    454
  Dihedral  : 11.471  54.834    459
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.16 %
    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 are not related in a simple way.
  whole:  1.09 (0.47), residues: 323
  helix:  1.54 (0.40), residues: 167
  sheet:  0.28 (0.58), residues: 68
  loop : -0.37 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  72 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.007   0.001   PHE C  68 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.002   0.000   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.12 ( 2742)
  covalent geometry    : angle       0.52218 /  0.27 ( 3694)
  SS BOND              : bond        0.00216 /  0.11 (    1)
  SS BOND              : angle       0.25514 /  0.14 (    2)
  hydrogen bonds       : bond        0.04590 /  3.51 (  168)
  hydrogen bonds       : angle       4.42833 /  3.11 (  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
  50 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: B   27 LYS cc_start: 0.8527 (mttt) cc_final: 0.8289 (ttmm)
REVERT: A   72 LYS cc_start: 0.7942 (tptt) cc_final: 0.7460 (tptt)
REVERT: A  103 MET cc_start: 0.4499 (ptm) cc_final: 0.4276 (ptm)
REVERT: C   60 TYR cc_start: 0.7824 (m-80) cc_final: 0.7181 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 49
  average time/residue: 0.0801
  time to fit residues: 4.6551
Evaluate side-chains
  49 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  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   93 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0170
   chunk 29 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  84 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.228206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.184608 restraints weight = 3224.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.190102 restraints weight = 1997.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.193993 restraints weight = 1436.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.196628 restraints weight = 1143.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.197887 restraints weight = 985.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2743  Z= 0.113
  Angle     :  0.495   6.981   3696  Z= 0.253
  Chirality :  0.039   0.154    387
  Planarity :  0.004   0.048    454
  Dihedral  : 11.052  58.200    459
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.29 %
    Favored  : 83.83 %
  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 are not related in a simple way.
  whole:  1.74 (0.48), residues: 323
  helix:  2.28 (0.41), residues: 165
  sheet:  0.26 (0.58), residues: 68
  loop : -0.21 (0.71), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.007   0.001   PHE A  57 
 TRP   0.004   0.001   TRP B  50 
 HIS   0.003   0.000   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 2742)
  covalent geometry    : angle       0.49512 /  0.25 ( 3694)
  SS BOND              : bond        0.00154 /  0.08 (    1)
  SS BOND              : angle       0.30410 /  0.18 (    2)
  hydrogen bonds       : bond        0.04322 /  3.32 (  168)
  hydrogen bonds       : angle       4.14564 /  2.91 (  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
  53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   18 ASP cc_start: 0.6827 (m-30) cc_final: 0.6488 (m-30)
REVERT: B   23 MET cc_start: 0.7797 (mmt) cc_final: 0.7338 (mmt)
REVERT: A  103 MET cc_start: 0.4592 (ptm) cc_final: 0.4323 (ptm)
REVERT: C   60 TYR cc_start: 0.7855 (m-80) cc_final: 0.7235 (m-80)
REVERT: C   99 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6736 (mm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0752
  time to fit residues: 4.5073
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  : 0.057 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0020
   chunk 22 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.224577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.180087 restraints weight = 3243.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.185531 restraints weight = 2044.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.189282 restraints weight = 1482.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.191574 restraints weight = 1195.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.192670 restraints weight = 1040.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2743  Z= 0.123
  Angle     :  0.488   5.217   3696  Z= 0.256
  Chirality :  0.039   0.155    387
  Planarity :  0.004   0.048    454
  Dihedral  : 10.372  50.620    459
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.54 %
    Favored  : 80.83 %
  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 are not related in a simple way.
  whole:  1.88 (0.48), residues: 323
  helix:  2.43 (0.40), residues: 165
  sheet:  0.23 (0.60), residues: 68
  loop : -0.11 (0.72), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.007   0.001   PHE A  66 
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 2742)
  covalent geometry    : angle       0.48847 /  0.26 ( 3694)
  SS BOND              : bond        0.00065 /  0.03 (    1)
  SS BOND              : angle       0.29416 /  0.17 (    2)
  hydrogen bonds       : bond        0.04415 /  3.38 (  168)
  hydrogen bonds       : angle       4.05617 /  2.85 (  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
  62 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.4567 (ptm) cc_final: 0.4295 (ptm)
REVERT: C    7 SER cc_start: 0.8670 (t) cc_final: 0.8430 (p)
REVERT: C   21 SER cc_start: 0.8835 (p) cc_final: 0.8621 (p)
REVERT: C   32 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8133 (mmt-90)
REVERT: C   60 TYR cc_start: 0.7808 (m-80) cc_final: 0.7272 (m-80)
REVERT: C   83 MET cc_start: 0.8076 (ttp) cc_final: 0.7627 (tpp)
  outliers start: 7
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0421
  time to fit residues: 2.9987
Evaluate side-chains
  60 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5778

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.225222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.181859 restraints weight = 3286.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.186247 restraints weight = 2122.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.190261 restraints weight = 1600.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.192203 restraints weight = 1301.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.192782 restraints weight = 1147.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2743  Z= 0.115
  Angle     :  0.456   5.084   3696  Z= 0.240
  Chirality :  0.038   0.117    387
  Planarity :  0.004   0.048    454
  Dihedral  :  9.935  57.625    459
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.80 %
    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 are not related in a simple way.
  whole:  2.07 (0.48), residues: 323
  helix:  2.62 (0.40), residues: 165
  sheet:  0.12 (0.60), residues: 65
  loop :  0.09 (0.72), residues: 93

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  69 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 2742)
  covalent geometry    : angle       0.45633 /  0.24 ( 3694)
  SS BOND              : bond        0.00127 /  0.07 (    1)
  SS BOND              : angle       0.25740 /  0.14 (    2)
  hydrogen bonds       : bond        0.04172 /  3.20 (  168)
  hydrogen bonds       : angle       3.89976 /  2.75 (  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
  57 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.4524 (ptm) cc_final: 0.4244 (ptm)
REVERT: C   32 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8087 (mmt-90)
REVERT: C   52 ASP cc_start: 0.8095 (m-30) cc_final: 0.7857 (m-30)
REVERT: C   60 TYR cc_start: 0.7649 (m-80) cc_final: 0.7073 (m-80)
  outliers start: 5
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0722
  time to fit residues: 4.6344
Evaluate side-chains
  56 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0970
   overall best weight:    0.3336

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.227699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.184321 restraints weight = 3257.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.189295 restraints weight = 2095.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.192525 restraints weight = 1554.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.193926 restraints weight = 1278.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.196099 restraints weight = 1153.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2743  Z= 0.106
  Angle     :  0.473   7.027   3696  Z= 0.243
  Chirality :  0.039   0.116    387
  Planarity :  0.004   0.047    454
  Dihedral  :  9.602  59.981    459
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 20.30 %
    Favored  : 78.57 %
  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 are not related in a simple way.
  whole:  2.22 (0.48), residues: 323
  helix:  2.71 (0.39), residues: 165
  sheet:  0.12 (0.60), residues: 65
  loop :  0.29 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  45 
 TYR   0.011   0.001   TYR B  85 
 PHE   0.009   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/Z
  covalent geometry    : bond        0.00226 /  0.11 ( 2742)
  covalent geometry    : angle       0.47299 /  0.24 ( 3694)
  SS BOND              : bond        0.00159 /  0.08 (    1)
  SS BOND              : angle       0.25063 /  0.14 (    2)
  hydrogen bonds       : bond        0.04061 /  3.10 (  168)
  hydrogen bonds       : angle       3.86648 /  2.71 (  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
  54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   72 LYS cc_start: 0.8048 (tptt) cc_final: 0.7351 (tptt)
REVERT: A  103 MET cc_start: 0.4532 (ptm) cc_final: 0.4325 (ptm)
REVERT: C   30 THR cc_start: 0.8068 (m) cc_final: 0.7854 (m)
REVERT: C   52 ASP cc_start: 0.8033 (m-30) cc_final: 0.7824 (m-30)
REVERT: C   60 TYR cc_start: 0.7631 (m-80) cc_final: 0.7016 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0586
  time to fit residues: 3.8179
Evaluate side-chains
  53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain A residue   38 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.223592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.181405 restraints weight = 3283.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.186471 restraints weight = 2084.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.189900 restraints weight = 1522.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.191908 restraints weight = 1229.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.192996 restraints weight = 1078.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2743  Z= 0.118
  Angle     :  0.482   6.595   3696  Z= 0.256
  Chirality :  0.039   0.116    387
  Planarity :  0.004   0.047    454
  Dihedral  :  9.637  53.926    459
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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 are not related in a simple way.
  whole:  2.34 (0.49), residues: 323
  helix:  2.76 (0.40), residues: 165
  sheet:  0.27 (0.61), residues: 65
  loop :  0.37 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 113 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.013   0.001   PHE C  68 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 2742)
  covalent geometry    : angle       0.48187 /  0.26 ( 3694)
  SS BOND              : bond        0.00130 /  0.07 (    1)
  SS BOND              : angle       0.29990 /  0.16 (    2)
  hydrogen bonds       : bond        0.04212 /  3.19 (  168)
  hydrogen bonds       : angle       3.90745 /  2.75 (  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
  58 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   72 LYS cc_start: 0.8082 (tptt) cc_final: 0.7391 (tptt)
REVERT: A  103 MET cc_start: 0.4632 (ptm) cc_final: 0.4418 (ptm)
REVERT: C   30 THR cc_start: 0.8081 (m) cc_final: 0.7845 (m)
REVERT: C   52 ASP cc_start: 0.8192 (m-30) cc_final: 0.7751 (m-30)
REVERT: C   60 TYR cc_start: 0.7633 (m-80) cc_final: 0.7021 (m-80)
  outliers start: 6
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0565
  time to fit residues: 3.8880
Evaluate side-chains
  57 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0670
   chunk 6 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.224004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.180440 restraints weight = 3302.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.185389 restraints weight = 2129.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.188664 restraints weight = 1586.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.191093 restraints weight = 1302.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.192253 restraints weight = 1140.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2743  Z= 0.123
  Angle     :  0.482   5.257   3696  Z= 0.261
  Chirality :  0.040   0.115    387
  Planarity :  0.004   0.046    454
  Dihedral  :  9.622  52.609    459
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.17 %
    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 are not related in a simple way.
  whole:  2.38 (0.49), residues: 323
  helix:  2.78 (0.40), residues: 165
  sheet:  0.30 (0.61), residues: 65
  loop :  0.40 (0.74), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  45 
 TYR   0.014   0.001   TYR A  62 
 PHE   0.013   0.002   PHE C  68 
 TRP   0.005   0.001   TRP A  28 
 HIS   0.004   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 2742)
  covalent geometry    : angle       0.48209 /  0.26 ( 3694)
  SS BOND              : bond        0.00158 /  0.08 (    1)
  SS BOND              : angle       0.36828 /  0.20 (    2)
  hydrogen bonds       : bond        0.04254 /  3.24 (  168)
  hydrogen bonds       : angle       3.92246 /  2.76 (  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
  57 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8185 (mptt)
REVERT: A   72 LYS cc_start: 0.8087 (tptt) cc_final: 0.7380 (tptt)
REVERT: A  103 MET cc_start: 0.4604 (ptm) cc_final: 0.4377 (ptm)
REVERT: C   52 ASP cc_start: 0.8288 (m-30) cc_final: 0.8047 (m-30)
REVERT: C   60 TYR cc_start: 0.7650 (m-80) cc_final: 0.7031 (m-80)
  outliers start: 5
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0641
  time to fit residues: 4.3337
Evaluate side-chains
  56 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
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 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.223131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.181536 restraints weight = 3308.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.186284 restraints weight = 2099.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.189845 restraints weight = 1543.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.191961 restraints weight = 1246.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.193615 restraints weight = 1084.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2743  Z= 0.121
  Angle     :  0.516   9.811   3696  Z= 0.267
  Chirality :  0.039   0.115    387
  Planarity :  0.004   0.046    454
  Dihedral  :  9.584  52.978    459
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.55 %
    Favored  : 78.57 %
  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 are not related in a simple way.
  whole:  2.44 (0.49), residues: 323
  helix:  2.82 (0.40), residues: 165
  sheet:  0.39 (0.61), residues: 65
  loop :  0.37 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  19 
 TYR   0.014   0.001   TYR A  62 
 PHE   0.010   0.001   PHE C  68 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 2742)
  covalent geometry    : angle       0.51582 /  0.27 ( 3694)
  SS BOND              : bond        0.00142 /  0.07 (    1)
  SS BOND              : angle       0.37463 /  0.20 (    2)
  hydrogen bonds       : bond        0.04258 /  3.22 (  168)
  hydrogen bonds       : angle       3.88210 /  2.75 (  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: 5
    poor density    : 54
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8182 (mptt)
REVERT: A   72 LYS cc_start: 0.8098 (tptt) cc_final: 0.7392 (tptt)
REVERT: A  103 MET cc_start: 0.4671 (ptm) cc_final: 0.4439 (ptm)
REVERT: C    7 SER cc_start: 0.8776 (t) cc_final: 0.8536 (p)
REVERT: C   52 ASP cc_start: 0.8266 (m-30) cc_final: 0.8050 (m-30)
REVERT: C   60 TYR cc_start: 0.7607 (m-80) cc_final: 0.7065 (m-80)
  outliers start: 5
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0396
  time to fit residues: 2.8173
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  : 0.057 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.222494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.180166 restraints weight = 3292.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.185097 restraints weight = 2131.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.187725 restraints weight = 1572.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.190595 restraints weight = 1306.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.191357 restraints weight = 1128.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.4583

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= 0.128
  Angle     :  0.504   7.010   3696  Z= 0.267
  Chirality :  0.039   0.115    387
  Planarity :  0.004   0.046    454
  Dihedral  :  9.637  53.194    459
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.28
  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 are not related in a simple way.
  whole:  2.40 (0.49), residues: 323
  helix:  2.79 (0.40), residues: 165
  sheet:  0.38 (0.61), residues: 65
  loop :  0.35 (0.73), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.014   0.001   TYR A  62 
 PHE   0.008   0.001   PHE C  68 
 TRP   0.005   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  84 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 2742)
  covalent geometry    : angle       0.50421 /  0.27 ( 3694)
  SS BOND              : bond        0.00158 /  0.08 (    1)
  SS BOND              : angle       0.43831 /  0.23 (    2)
  hydrogen bonds       : bond        0.04307 /  3.27 (  168)
  hydrogen bonds       : angle       3.90475 /  2.77 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 821.58 seconds
wall clock time: 14 minutes 50.27 seconds (890.27 seconds total)