Starting phenix.real_space_refine
on Wed Sep 17 04:46:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqv_45824/09_2025/9cqv_45824.map"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  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: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.27, per 1000 atoms: 0.28
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (81.585, 72.765, 66.885, 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)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 175.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 0 sheets defined
      87.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.554A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.512A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.990A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.031A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.670A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.866A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.635A  pdb=" N   GLY D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.982A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    341 hydrogen bonds defined for protein.
    978 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: 0.68

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 1629
        1.38 -     1.55: 2938
        1.55 -     1.72: 9
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.500 -0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" N   VAL D  23 "
       pdb=" CA  VAL D  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.499 -0.040 1.21e-02 6.83e+03 1.07e+01
  bond pdb=" N   VAL B  18 "
       pdb=" CA  VAL B  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.20e-02 6.94e+03 8.75e+00
  bond pdb=" N   ASN B  80 "
       pdb=" CA  ASN B  80 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.16e-02 7.43e+03 8.45e+00
  bond pdb=" N   THR C  38 "
       pdb=" CA  THR C  38 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.43e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 5880
        1.36 -     2.72: 308
        2.72 -     4.08: 110
        4.08 -     5.44: 29
        5.44 -     6.80: 3
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" C   PHE C  36 "
        pdb=" N   PRO C  37 "
        pdb=" CA  PRO C  37 "
      ideal   model   delta    sigma   weight residual
     118.85  124.27   -5.42 1.09e+00 8.42e-01 2.47e+01
  angle pdb=" CA  LEU B  81 "
        pdb=" C   LEU B  81 "
        pdb=" O   LEU B  81 "
      ideal   model   delta    sigma   weight residual
     120.55  116.25    4.30 1.06e+00 8.90e-01 1.65e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     111.14  115.07   -3.93 1.08e+00 8.57e-01 1.33e+01
  angle pdb=" N   VAL D 137 "
        pdb=" CA  VAL D 137 "
        pdb=" C   VAL D 137 "
      ideal   model   delta    sigma   weight residual
     110.72  107.25    3.47 1.01e+00 9.80e-01 1.18e+01
  angle pdb=" CA  LYS C  40 "
        pdb=" C   LYS C  40 "
        pdb=" O   LYS C  40 "
      ideal   model   delta    sigma   weight residual
     120.55  116.97    3.58 1.06e+00 8.90e-01 1.14e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 2257
       15.99 -    31.98: 227
       31.98 -    47.97: 93
       47.97 -    63.96: 29
       63.96 -    79.95: 8
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CG  ARG A  92 "
           pdb=" CD  ARG A  92 "
           pdb=" NE  ARG A  92 "
           pdb=" CZ  ARG A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.81  -50.19     2      1.50e+01 4.44e-03 1.26e+01
  dihedral pdb=" C2D HEM A 201 "
           pdb=" C3D HEM A 201 "
           pdb=" CAD HEM A 201 "
           pdb=" CBD HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -100.05  -79.95     2      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" C2D HEM B 201 "
           pdb=" C3D HEM B 201 "
           pdb=" CAD HEM B 201 "
           pdb=" CBD HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -78.97   78.97     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 560
       0.058 -    0.116: 100
       0.116 -    0.175: 25
       0.175 -    0.233: 5
       0.233 -    0.291: 2
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL D 134 "
            pdb=" CA  VAL D 134 "
            pdb=" CG1 VAL D 134 "
            pdb=" CG2 VAL D 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL B  18 "
            pdb=" CA  VAL B  18 "
            pdb=" CG1 VAL B  18 "
            pdb=" CG2 VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  40 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" C   LYS C  40 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LYS C  40 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   THR C  41 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  99 "   -0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 100 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO B 124 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.024 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 419
        2.74 -     3.28: 4311
        3.28 -     3.82: 7885
        3.82 -     4.36: 9191
        4.36 -     4.90: 15788
  Nonbonded interactions: 37594
  Sorted by model distance:
  nonbonded pdb=" OG  SER C   3 "
            pdb=" OD1 ASP C   6 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OE1 GLU D 101 "
            pdb=" NH1 ARG D 104 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OE1 GLU B 101 "
            pdb=" NH1 ARG B 104 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   PRO A 114 "
            pdb=" NE2 HIS B 116 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.379 3.120
  ... (remaining 37589 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.460
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.280
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.165   4614  Z= 0.332
  Angle     :  0.790   6.804   6330  Z= 0.516
  Chirality :  0.052   0.291    692
  Planarity :  0.006   0.045    790
  Dihedral  : 16.702  79.948   1562
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.74 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.35), residues: 558
  helix:  2.48 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.13 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  92 
 TYR   0.009   0.002   TYR A  24 
 PHE   0.015   0.001   PHE C  36 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 4610)
  covalent geometry    : angle       0.79010 ( 6330)
  hydrogen bonds       : bond        0.12235 (  341)
  hydrogen bonds       : angle       4.89783 (  978)
  Misc. bond           : bond        0.10715 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  139 LYS cc_start: 0.4413 (OUTLIER) cc_final: 0.3384 (ptpt)
REVERT: A  140 TYR cc_start: -0.0282 (OUTLIER) cc_final: -0.0601 (m-80)
REVERT: D   17 LYS cc_start: 0.8177 (mptp) cc_final: 0.7810 (mtpt)
REVERT: D   90 GLU cc_start: 0.7980 (tt0) cc_final: 0.7328 (tp30)
  outliers start: 14
  outliers final: 5
  residues processed: 72
  average time/residue: 0.7240
  time to fit residues: 53.6948
Evaluate side-chains
  65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
B 131 GLN
C  68 ASN
D  19 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.129884 restraints weight = 4550.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.60
r_work: 0.3447 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.0797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   4614  Z= 0.126
  Angle     :  0.568   6.498   6330  Z= 0.264
  Chirality :  0.039   0.126    692
  Planarity :  0.006   0.044    790
  Dihedral  : 10.271  80.317    630
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 13.66 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.17 (0.36), residues: 558
  helix:  2.55 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.39 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.010   0.001   PHE B 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4610)
  covalent geometry    : angle       0.56842 ( 6330)
  hydrogen bonds       : bond        0.03530 (  341)
  hydrogen bonds       : angle       3.96650 (  978)
  Misc. bond           : bond        0.06372 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.177 
Fit side-chains
REVERT: B   90 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7069 (tm-30)
REVERT: B   95 LYS cc_start: 0.7750 (tttt) cc_final: 0.7342 (mptt)
REVERT: D   17 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (mtpt)
REVERT: D   66 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8022 (mtmm)
REVERT: D   82 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7516 (tttt)
REVERT: D   90 GLU cc_start: 0.8041 (tt0) cc_final: 0.7410 (tp30)
  outliers start: 20
  outliers final: 7
  residues processed: 73
  average time/residue: 0.7360
  time to fit residues: 55.2786
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
B 131 GLN
C   9 ASN
C  68 ASN
D  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128938 restraints weight = 4565.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.62
r_work: 0.3434 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   4614  Z= 0.130
  Angle     :  0.570   6.263   6330  Z= 0.264
  Chirality :  0.039   0.163    692
  Planarity :  0.006   0.045    790
  Dihedral  :  9.954  81.296    623
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 14.54 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.35), residues: 558
  helix:  2.52 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.35 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4610)
  covalent geometry    : angle       0.56986 ( 6330)
  hydrogen bonds       : bond        0.03629 (  341)
  hydrogen bonds       : angle       3.90717 (  978)
  Misc. bond           : bond        0.06844 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7825 (tptp) cc_final: 0.7298 (mptt)
REVERT: B   90 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6779 (mt-10)
REVERT: B   95 LYS cc_start: 0.7698 (tttt) cc_final: 0.7372 (mptt)
REVERT: D   17 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8004 (mtpt)
REVERT: D   26 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7649 (tt0)
REVERT: D   66 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7975 (mtmm)
REVERT: D   82 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7449 (tttt)
REVERT: D   90 GLU cc_start: 0.7950 (tt0) cc_final: 0.7333 (tm-30)
  outliers start: 21
  outliers final: 9
  residues processed: 71
  average time/residue: 0.7472
  time to fit residues: 54.6193
Evaluate side-chains
  70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  80 ASN
B 117 HIS
C   9 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.147711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128125 restraints weight = 4551.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.60
r_work: 0.3417 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.137
  Angle     :  0.577   6.381   6330  Z= 0.267
  Chirality :  0.040   0.125    692
  Planarity :  0.006   0.045    790
  Dihedral  :  9.769  82.181    621
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.42 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.35), residues: 558
  helix:  2.48 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.20 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4610)
  covalent geometry    : angle       0.57683 ( 6330)
  hydrogen bonds       : bond        0.03707 (  341)
  hydrogen bonds       : angle       3.90712 (  978)
  Misc. bond           : bond        0.07406 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7935 (tptp) cc_final: 0.7476 (mptt)
REVERT: B   26 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7467 (mm-30)
REVERT: B   90 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6927 (mt-10)
REVERT: B   95 LYS cc_start: 0.7758 (tttt) cc_final: 0.7469 (mptt)
REVERT: D   17 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8105 (mtpt)
REVERT: D   26 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7690 (tt0)
REVERT: D   66 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8030 (mtmm)
REVERT: D   82 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7522 (tttt)
REVERT: D   90 GLU cc_start: 0.7958 (tt0) cc_final: 0.7407 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 73
  average time/residue: 0.7310
  time to fit residues: 54.9128
Evaluate side-chains
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN
D  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.146323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.126234 restraints weight = 4531.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.65
r_work: 0.3418 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   4614  Z= 0.145
  Angle     :  0.588   6.618   6330  Z= 0.272
  Chirality :  0.040   0.126    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.733  82.688    621
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.98 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 442
  sheet:  None (None), residues: 0
  loop :  0.34 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.010   0.001   PHE B 118 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4610)
  covalent geometry    : angle       0.58818 ( 6330)
  hydrogen bonds       : bond        0.03859 (  341)
  hydrogen bonds       : angle       3.91824 (  978)
  Misc. bond           : bond        0.07603 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7851 (tptp) cc_final: 0.7401 (mptt)
REVERT: B   26 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7383 (mm-30)
REVERT: B   90 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6798 (mt-10)
REVERT: B   95 LYS cc_start: 0.7730 (tttt) cc_final: 0.7449 (mptt)
REVERT: D   17 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8045 (mtpt)
REVERT: D   26 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7651 (tt0)
REVERT: D   66 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7982 (mtmm)
REVERT: D   82 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7344 (tppt)
REVERT: D   90 GLU cc_start: 0.7896 (tt0) cc_final: 0.7290 (tm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 72
  average time/residue: 0.7268
  time to fit residues: 53.9218
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   chunk 32 optimal weight:    0.3980
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.147779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.128092 restraints weight = 4535.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.59
r_work: 0.3430 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   4614  Z= 0.122
  Angle     :  0.566   5.985   6330  Z= 0.261
  Chirality :  0.039   0.129    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.584  81.166    621
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.20 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.17 (0.36), residues: 558
  helix:  2.49 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.57 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  92 
 TYR   0.006   0.001   TYR B  35 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4610)
  covalent geometry    : angle       0.56573 ( 6330)
  hydrogen bonds       : bond        0.03366 (  341)
  hydrogen bonds       : angle       3.80641 (  978)
  Misc. bond           : bond        0.06475 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7884 (tptp) cc_final: 0.7511 (mptt)
REVERT: B   21 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.5872 (m-30)
REVERT: B   26 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7461 (mm-30)
REVERT: B   90 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6946 (mt-10)
REVERT: B   95 LYS cc_start: 0.7730 (tttt) cc_final: 0.7522 (mptt)
REVERT: D   17 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8119 (mtpt)
REVERT: D   66 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7986 (mtmm)
REVERT: D   82 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7410 (tppt)
REVERT: D   90 GLU cc_start: 0.7978 (tt0) cc_final: 0.7424 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 70
  average time/residue: 0.7252
  time to fit residues: 52.2120
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.147312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127794 restraints weight = 4619.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.61
r_work: 0.3419 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   4614  Z= 0.140
  Angle     :  0.587   6.725   6330  Z= 0.272
  Chirality :  0.040   0.127    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.514  82.004    619
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.64 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.57 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4610)
  covalent geometry    : angle       0.58655 ( 6330)
  hydrogen bonds       : bond        0.03739 (  341)
  hydrogen bonds       : angle       3.87628 (  978)
  Misc. bond           : bond        0.07570 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7889 (tptp) cc_final: 0.7516 (mptt)
REVERT: B   21 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5856 (m-30)
REVERT: B   26 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7408 (mm-30)
REVERT: B   90 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6841 (mt-10)
REVERT: B   95 LYS cc_start: 0.7741 (tttt) cc_final: 0.7511 (mptt)
REVERT: D   17 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8083 (mtpt)
REVERT: D   66 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7985 (mtmm)
REVERT: D   82 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7382 (tppt)
REVERT: D   90 GLU cc_start: 0.7924 (tt0) cc_final: 0.7326 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.7519
  time to fit residues: 54.1459
Evaluate side-chains
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.147419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127954 restraints weight = 4580.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.61
r_work: 0.3423 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.137
  Angle     :  0.583   6.528   6330  Z= 0.270
  Chirality :  0.040   0.125    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.514  82.031    619
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.08 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.36), residues: 558
  helix:  2.41 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.60 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4610)
  covalent geometry    : angle       0.58286 ( 6330)
  hydrogen bonds       : bond        0.03672 (  341)
  hydrogen bonds       : angle       3.86953 (  978)
  Misc. bond           : bond        0.07335 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7877 (tptp) cc_final: 0.7486 (mptt)
REVERT: B   21 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5828 (m-30)
REVERT: B   26 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7403 (mm-30)
REVERT: B   90 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6826 (mt-10)
REVERT: B   95 LYS cc_start: 0.7706 (tttt) cc_final: 0.7497 (mptt)
REVERT: D   17 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (mtpt)
REVERT: D   66 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7971 (mtmm)
REVERT: D   82 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7388 (tppt)
REVERT: D   90 GLU cc_start: 0.7945 (tt0) cc_final: 0.7333 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 70
  average time/residue: 0.7479
  time to fit residues: 53.9412
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.146497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.126624 restraints weight = 4519.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.63
r_work: 0.3421 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   4614  Z= 0.135
  Angle     :  0.579   6.473   6330  Z= 0.269
  Chirality :  0.040   0.126    692
  Planarity :  0.006   0.047    790
  Dihedral  :  9.515  81.846    619
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.74 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.09 (0.36), residues: 558
  helix:  2.42 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.60 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 104 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4610)
  covalent geometry    : angle       0.57900 ( 6330)
  hydrogen bonds       : bond        0.03651 (  341)
  hydrogen bonds       : angle       3.86935 (  978)
  Misc. bond           : bond        0.07250 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7854 (tptp) cc_final: 0.7457 (mptt)
REVERT: B   21 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5800 (m-30)
REVERT: B   26 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7390 (mm-30)
REVERT: B   90 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6788 (mt-10)
REVERT: B   95 LYS cc_start: 0.7698 (tttt) cc_final: 0.7481 (mptt)
REVERT: D   17 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8061 (mtpt)
REVERT: D   66 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7957 (mtmm)
REVERT: D   82 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7377 (tppt)
REVERT: D   90 GLU cc_start: 0.7925 (tt0) cc_final: 0.7300 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 68
  average time/residue: 0.7612
  time to fit residues: 53.2775
Evaluate side-chains
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.146806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.126911 restraints weight = 4521.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.64
r_work: 0.3426 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   4614  Z= 0.132
  Angle     :  0.577   6.436   6330  Z= 0.268
  Chirality :  0.040   0.127    692
  Planarity :  0.006   0.047    790
  Dihedral  :  9.495  81.597    619
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.74 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.11 (0.36), residues: 558
  helix:  2.44 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.58 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 104 
 TYR   0.006   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4610)
  covalent geometry    : angle       0.57738 ( 6330)
  hydrogen bonds       : bond        0.03570 (  341)
  hydrogen bonds       : angle       3.85286 (  978)
  Misc. bond           : bond        0.07087 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7860 (tptp) cc_final: 0.7468 (mptt)
REVERT: B   21 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5794 (m-30)
REVERT: B   26 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7403 (mm-30)
REVERT: B   90 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6781 (mt-10)
REVERT: B   95 LYS cc_start: 0.7715 (tttt) cc_final: 0.7485 (mptt)
REVERT: D   17 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8051 (mtpt)
REVERT: D   66 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7954 (mtmm)
REVERT: D   82 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7382 (tppt)
REVERT: D   90 GLU cc_start: 0.7927 (tt0) cc_final: 0.7305 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 68
  average time/residue: 0.7689
  time to fit residues: 53.7765
Evaluate side-chains
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.147401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.127478 restraints weight = 4501.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.64
r_work: 0.3429 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   4614  Z= 0.125
  Angle     :  0.568   6.280   6330  Z= 0.263
  Chirality :  0.039   0.126    692
  Planarity :  0.006   0.048    790
  Dihedral  :  9.450  81.304    619
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.74 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.16 (0.36), residues: 558
  helix:  2.49 (0.25), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.56 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 104 
 TYR   0.006   0.001   TYR B  35 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4610)
  covalent geometry    : angle       0.56826 ( 6330)
  hydrogen bonds       : bond        0.03432 (  341)
  hydrogen bonds       : angle       3.82131 (  978)
  Misc. bond           : bond        0.06883 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1750.45 seconds
wall clock time: 30 minutes 45.37 seconds (1845.37 seconds total)