Starting phenix.real_space_refine
on Sun Apr 27 11:04:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ivk_60929/04_2025/9ivk_60929_neut.cif"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1806 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2640      2.51       5
     N     654      2.21       5
     O     769      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4077
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2271
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 3, 'TRANS': 274}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 958
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 122, 943
          Classifications: {'peptide': 122}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117}
      Conformer: "B"
        Number of residues, atoms: 122, 943
          Classifications: {'peptide': 122}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117}
          bond proxies already assigned to first conformer: 953
    Chain: "L"
      Number of atoms: 822
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 107, 819
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
      Conformer: "B"
        Number of residues, atoms: 107, 819
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
          bond proxies already assigned to first conformer: 833
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'KY6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.68, per 1000 atoms: 0.90
  Number of scatterers: 4077
  At special positions: 0
  Unit cell: (54.72, 72.96, 143.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     769      8.00
     N     654      7.00
     C    2640      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG ACYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG BCYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG ACYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  89 " - pdb=" SG BCYS L  24 " distance=2.03

  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: 0.95
  Conformation dependent library (CDL) restraints added in 749.8 milliseconds
  

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  968

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 6 sheets defined
      56.4% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 36
      removed outlier: 4.467A  pdb=" N   LYS A  36 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 48
    Processing helix  chain 'A' and resid 48 through 110
    Processing helix  chain 'A' and resid 112 through 133
      removed outlier: 3.567A  pdb=" N   VAL A 116 " --> pdb=" O   ASN A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 171
      removed outlier: 3.572A  pdb=" N   GLU A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 192
    Processing helix  chain 'A' and resid 192 through 243
    Processing helix  chain 'A' and resid 248 through 285
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.866A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
    Processing helix  chain 'L' and resid 94 through 98
      removed outlier: 4.100A  pdb=" N   VAL L  98 " --> pdb=" O   TYR L  95 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.571A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   SER H  55 " --> pdb=" O   PHE H  35 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   PHE H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   TYR H 116 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.571A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   SER H  55 " --> pdb=" O   PHE H  35 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   PHE H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.858A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.858A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    923 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 681
        1.28 -     1.41: 1010
        1.41 -     1.55: 2446
        1.55 -     1.68: 3
        1.68 -     1.81: 22
  Bond restraints: 4162
  Sorted by residual:
  bond pdb=" C   ILE A  50 "
       pdb=" O   ILE A  50 "
    ideal  model  delta    sigma   weight residual
    1.236  1.283 -0.047 1.23e-02 6.61e+03 1.46e+01
  bond pdb=" N   ILE A  48 "
       pdb=" CA  ILE A  48 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 9.50e-03 1.11e+04 1.31e+01
  bond pdb=" N   ILE A 241 "
       pdb=" CA  ILE A 241 "
    ideal  model  delta    sigma   weight residual
    1.452  1.494 -0.041 1.18e-02 7.18e+03 1.24e+01
  bond pdb=" N   ILE A   8 "
       pdb=" CA  ILE A   8 "
    ideal  model  delta    sigma   weight residual
    1.462  1.499 -0.037 1.18e-02 7.18e+03 1.01e+01
  bond pdb=" N   LYS A 239 "
       pdb=" CA  LYS A 239 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.33e-02 5.65e+03 9.97e+00
  ... (remaining 4157 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 5441
        2.39 -     4.78: 173
        4.78 -     7.17: 13
        7.17 -     9.56: 0
        9.56 -    11.95: 3
  Bond angle restraints: 5630
  Sorted by residual:
  angle pdb=" N   LYS A  49 "
        pdb=" CA  LYS A  49 "
        pdb=" C   LYS A  49 "
      ideal   model   delta    sigma   weight residual
     113.19  101.24   11.95 1.19e+00 7.06e-01 1.01e+02
  angle pdb=" N   ILE A  48 "
        pdb=" CA  ILE A  48 "
        pdb=" C   ILE A  48 "
      ideal   model   delta    sigma   weight residual
     113.53  103.86    9.67 9.80e-01 1.04e+00 9.74e+01
  angle pdb=" N   LYS A 240 "
        pdb=" CA  LYS A 240 "
        pdb=" C   LYS A 240 "
      ideal   model   delta    sigma   weight residual
     113.01  102.76   10.25 1.20e+00 6.94e-01 7.29e+01
  angle pdb=" N   PHE A  10 "
        pdb=" CA  PHE A  10 "
        pdb=" C   PHE A  10 "
      ideal   model   delta    sigma   weight residual
     111.36  105.57    5.79 1.09e+00 8.42e-01 2.82e+01
  angle pdb=" CA  THR A 238 "
        pdb=" C   THR A 238 "
        pdb=" O   THR A 238 "
      ideal   model   delta    sigma   weight residual
     120.82  115.70    5.12 1.05e+00 9.07e-01 2.38e+01
  ... (remaining 5625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 2249
       17.53 -    35.06: 209
       35.06 -    52.59: 34
       52.59 -    70.13: 9
       70.13 -    87.66: 12
  Dihedral angle restraints: 2513
    sinusoidal: 1011
      harmonic: 1502
  Sorted by residual:
  dihedral pdb=" CB ACYS L  24 "
           pdb=" SG ACYS L  24 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.56   36.44     1      1.00e+01 1.00e-02 1.88e+01
  dihedral pdb=" C   LYS A 239 "
           pdb=" N   LYS A 239 "
           pdb=" CA  LYS A 239 "
           pdb=" CB  LYS A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.80    9.20     0      2.50e+00 1.60e-01 1.35e+01
  dihedral pdb=" CB  CYS H  25 "
           pdb=" SG  CYS H  25 "
           pdb=" SG ACYS H  99 "
           pdb=" CB ACYS H  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.37   29.63     1      1.00e+01 1.00e-02 1.25e+01
  ... (remaining 2510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 510
       0.060 -    0.120: 84
       0.120 -    0.180: 26
       0.180 -    0.240: 8
       0.240 -    0.299: 5
  Chirality restraints: 633
  Sorted by residual:
  chirality pdb=" CA  LYS A 239 "
            pdb=" N   LYS A 239 "
            pdb=" C   LYS A 239 "
            pdb=" CB  LYS A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  ILE A  50 "
            pdb=" N   ILE A  50 "
            pdb=" C   ILE A  50 "
            pdb=" CB  ILE A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  LYS A  49 "
            pdb=" N   LYS A  49 "
            pdb=" C   LYS A  49 "
            pdb=" CB  LYS A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 630 not shown)

  Planarity restraints: 703
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 242 "   -0.021 2.00e-02 2.50e+03   4.39e-02 1.92e+01
        pdb=" C   LYS A 242 "    0.076 2.00e-02 2.50e+03
        pdb=" O   LYS A 242 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   GLU A 243 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 236 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.44e+00
        pdb=" C   PHE A 236 "    0.050 2.00e-02 2.50e+03
        pdb=" O   PHE A 236 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 237 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A   9 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.36e+00
        pdb=" C   LEU A   9 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU A   9 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A  10 "    0.017 2.00e-02 2.50e+03
  ... (remaining 700 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 649
        2.76 -     3.30: 3955
        3.30 -     3.83: 6991
        3.83 -     4.37: 8130
        4.37 -     4.90: 13792
  Nonbonded interactions: 33517
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H  76 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" NZ  LYS A  41 "
            pdb=" OD1 ASN A 245 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NE2 GLN L  91 "
            pdb=" O   LEU L  97 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NH1 ARG L  25 "
            pdb=" OD2 ASP L  71 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE2 GLU A 212 "
            pdb=" NZ  LYS A 279 "
     model   vdw
     2.289 3.120
  ... (remaining 33512 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=0.50 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.390
  Find NCS groups from input model:        0.050
  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:13.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
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   0.047   4166  Z= 0.392
  Angle     :  0.865  11.946   5638  Z= 0.623
  Chirality :  0.060   0.299    633
  Planarity :  0.005   0.044    703
  Dihedral  : 14.935  87.656   1533
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.67 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.38), residues: 504
  helix:  2.40 (0.31), residues: 258
  sheet: -0.11 (0.50), residues: 109
  loop :  0.38 (0.57), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  97 
 HIS   0.001   0.001   HIS H  38 
 PHE   0.019   0.002   PHE A 151 
 TYR   0.026   0.001   TYR A 260 
 ARG   0.002   0.000   ARG L  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11213 (  306)
  hydrogen bonds       : angle       5.51932 (  923)
  SS BOND              : bond        0.00473 (    4)
  SS BOND              : angle       2.60761 (    8)
  covalent geometry    : bond        0.00571 ( 4162)
  covalent geometry    : angle       0.86005 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7253 (tppp) cc_final: 0.6452 (tmmt)
REVERT: A  118 ASP cc_start: 0.7385 (m-30) cc_final: 0.7040 (m-30)
REVERT: H   72 THR cc_start: 0.8438 (m) cc_final: 0.8232 (m)
REVERT: H   85 GLN cc_start: 0.7999 (tp40) cc_final: 0.7499 (tp40)
  outliers start: 3
  outliers final: 1
  residues processed: 96
  average time/residue: 0.9754
  time to fit residues: 97.3871
Evaluate side-chains
  69 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.175777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.116755 restraints weight = 16759.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 5.43
r_work: 0.3018 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4166  Z= 0.211
  Angle     :  0.593   6.326   5638  Z= 0.312
  Chirality :  0.040   0.139    633
  Planarity :  0.004   0.040    703
  Dihedral  :  4.770  43.091    565
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.14 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.37), residues: 504
  helix:  2.96 (0.29), residues: 263
  sheet:  0.01 (0.50), residues: 103
  loop :  0.49 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.039   0.002   PHE L  84 
 TYR   0.013   0.001   TYR L  92 
 ARG   0.002   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  306)
  hydrogen bonds       : angle       4.17579 (  923)
  SS BOND              : bond        0.00504 (    4)
  SS BOND              : angle       2.31244 (    8)
  covalent geometry    : bond        0.00480 ( 4162)
  covalent geometry    : angle       0.58669 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7314 (tppp) cc_final: 0.6476 (tmmt)
REVERT: A   97 TRP cc_start: 0.7947 (t-100) cc_final: 0.7050 (t-100)
REVERT: A  118 ASP cc_start: 0.7922 (m-30) cc_final: 0.7637 (m-30)
REVERT: A  194 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7636 (mttt)
REVERT: H   85 GLN cc_start: 0.8090 (tp40) cc_final: 0.7709 (tp40)
  outliers start: 12
  outliers final: 6
  residues processed: 77
  average time/residue: 1.0249
  time to fit residues: 82.1685
Evaluate side-chains
  75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.175336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116292 restraints weight = 17156.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 5.41
r_work: 0.3019 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4166  Z= 0.211
  Angle     :  0.593   6.326   5638  Z= 0.312
  Chirality :  0.040   0.139    633
  Planarity :  0.004   0.040    703
  Dihedral  :  4.713  43.091    563
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.66 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.37), residues: 504
  helix:  2.96 (0.29), residues: 263
  sheet:  0.01 (0.50), residues: 103
  loop :  0.49 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.039   0.002   PHE L  84 
 TYR   0.013   0.001   TYR L  92 
 ARG   0.002   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  306)
  hydrogen bonds       : angle       4.17579 (  923)
  SS BOND              : bond        0.00504 (    4)
  SS BOND              : angle       2.31244 (    8)
  covalent geometry    : bond        0.00480 ( 4162)
  covalent geometry    : angle       0.58669 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7324 (tppp) cc_final: 0.6492 (tmmt)
REVERT: A   97 TRP cc_start: 0.7962 (t-100) cc_final: 0.7074 (t-100)
REVERT: A  118 ASP cc_start: 0.7938 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  194 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7655 (mttt)
REVERT: H   85 GLN cc_start: 0.8091 (tp40) cc_final: 0.7757 (tp40)
  outliers start: 7
  outliers final: 6
  residues processed: 70
  average time/residue: 1.0102
  time to fit residues: 73.7429
Evaluate side-chains
  74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.179816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.120476 restraints weight = 15678.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 4.36
r_work: 0.3161 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4166  Z= 0.138
  Angle     :  0.506   6.586   5638  Z= 0.269
  Chirality :  0.037   0.128    633
  Planarity :  0.004   0.038    703
  Dihedral  :  4.585  39.606    563
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.12 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.37), residues: 504
  helix:  3.46 (0.29), residues: 257
  sheet: -0.01 (0.51), residues: 106
  loop :  0.48 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H  50 
 HIS   0.001   0.001   HIS H  38 
 PHE   0.049   0.002   PHE L  84 
 TYR   0.011   0.001   TYR L  92 
 ARG   0.002   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  306)
  hydrogen bonds       : angle       3.76625 (  923)
  SS BOND              : bond        0.00502 (    4)
  SS BOND              : angle       1.78753 (    8)
  covalent geometry    : bond        0.00298 ( 4162)
  covalent geometry    : angle       0.50177 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7098 (tppp) cc_final: 0.6232 (tmmt)
REVERT: A  118 ASP cc_start: 0.7572 (m-30) cc_final: 0.7314 (m-30)
REVERT: A  194 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7382 (mttt)
REVERT: H   85 GLN cc_start: 0.7839 (tp40) cc_final: 0.7319 (tp40)
REVERT: L    4 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (mp-120)
REVERT: L   71 ASP cc_start: 0.8266 (m-30) cc_final: 0.8003 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 75
  average time/residue: 1.0252
  time to fit residues: 80.0479
Evaluate side-chains
  78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain L residue    4 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 35 optimal weight:    9.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.177505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117112 restraints weight = 16918.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 4.49
r_work: 0.3139 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4166  Z= 0.248
  Angle     :  0.579   7.671   5638  Z= 0.302
  Chirality :  0.040   0.149    633
  Planarity :  0.004   0.043    703
  Dihedral  :  4.627  39.529    563
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.12 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.38), residues: 504
  helix:  3.23 (0.29), residues: 263
  sheet: -0.13 (0.51), residues: 106
  loop :  0.57 (0.58), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.048   0.002   PHE L  84 
 TYR   0.011   0.002   TYR L  50 
 ARG   0.006   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  306)
  hydrogen bonds       : angle       3.90015 (  923)
  SS BOND              : bond        0.00460 (    4)
  SS BOND              : angle       1.92150 (    8)
  covalent geometry    : bond        0.00570 ( 4162)
  covalent geometry    : angle       0.57516 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7155 (tppp) cc_final: 0.6291 (tmmt)
REVERT: A  118 ASP cc_start: 0.7692 (m-30) cc_final: 0.7437 (m-30)
REVERT: A  194 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7485 (mttt)
REVERT: H   53 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.9077 (p90)
REVERT: H   63 TYR cc_start: 0.9020 (m-80) cc_final: 0.8807 (m-80)
REVERT: H   85 GLN cc_start: 0.7929 (tp40) cc_final: 0.7516 (tp40)
REVERT: L   82 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7883 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 76
  average time/residue: 0.9070
  time to fit residues: 72.1344
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.178517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.119092 restraints weight = 17976.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 5.00
r_work: 0.3126 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4166  Z= 0.248
  Angle     :  0.579   7.670   5638  Z= 0.302
  Chirality :  0.040   0.149    633
  Planarity :  0.004   0.043    703
  Dihedral  :  4.650  39.529    563
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.50 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.38), residues: 504
  helix:  3.23 (0.29), residues: 263
  sheet: -0.13 (0.51), residues: 106
  loop :  0.57 (0.58), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.048   0.002   PHE L  84 
 TYR   0.011   0.002   TYR L  50 
 ARG   0.006   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  306)
  hydrogen bonds       : angle       3.90016 (  923)
  SS BOND              : bond        0.00461 (    4)
  SS BOND              : angle       1.92154 (    8)
  covalent geometry    : bond        0.00570 ( 4162)
  covalent geometry    : angle       0.57501 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7105 (tppp) cc_final: 0.6242 (tmmt)
REVERT: A  118 ASP cc_start: 0.7551 (m-30) cc_final: 0.7286 (m-30)
REVERT: A  194 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7409 (mttt)
REVERT: H   53 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.9034 (p90)
REVERT: H   63 TYR cc_start: 0.8982 (m-80) cc_final: 0.8757 (m-80)
REVERT: H   85 GLN cc_start: 0.7827 (tp40) cc_final: 0.7420 (tp40)
REVERT: L   82 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7847 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 68
  average time/residue: 0.9882
  time to fit residues: 70.1634
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    0.0040
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.177130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.118616 restraints weight = 12547.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.89
r_work: 0.3151 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4166  Z= 0.245
  Angle     :  0.578   7.658   5638  Z= 0.301
  Chirality :  0.040   0.147    633
  Planarity :  0.004   0.043    703
  Dihedral  :  4.790  39.532    563
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.50 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.38), residues: 504
  helix:  3.23 (0.29), residues: 263
  sheet: -0.13 (0.51), residues: 106
  loop :  0.57 (0.58), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.047   0.002   PHE L  84 
 TYR   0.011   0.002   TYR L  50 
 ARG   0.006   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  306)
  hydrogen bonds       : angle       3.90024 (  923)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       1.92132 (    8)
  covalent geometry    : bond        0.00564 ( 4162)
  covalent geometry    : angle       0.57404 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7159 (tppp) cc_final: 0.6303 (tmmt)
REVERT: A  118 ASP cc_start: 0.7671 (m-30) cc_final: 0.7413 (m-30)
REVERT: A  194 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7482 (mttt)
REVERT: H   53 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.9075 (p90)
REVERT: H   63 TYR cc_start: 0.9021 (m-80) cc_final: 0.8806 (m-80)
REVERT: H   85 GLN cc_start: 0.7932 (tp40) cc_final: 0.7518 (tp40)
REVERT: L   82 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7874 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 68
  average time/residue: 1.1849
  time to fit residues: 83.8107
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.179701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.118180 restraints weight = 22799.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 5.50
r_work: 0.3135 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4166  Z= 0.162
  Angle     :  0.554   9.376   5638  Z= 0.287
  Chirality :  0.038   0.135    633
  Planarity :  0.004   0.041    703
  Dihedral  :  4.645  39.453    563
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.50 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.38), residues: 504
  helix:  3.27 (0.29), residues: 263
  sheet:  0.02 (0.51), residues: 103
  loop :  0.52 (0.57), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.053   0.002   PHE L  84 
 TYR   0.011   0.001   TYR L  92 
 ARG   0.006   0.001   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  306)
  hydrogen bonds       : angle       3.82599 (  923)
  SS BOND              : bond        0.00441 (    4)
  SS BOND              : angle       1.93676 (    8)
  covalent geometry    : bond        0.00363 ( 4162)
  covalent geometry    : angle       0.54965 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7106 (tppp) cc_final: 0.6233 (tmmt)
REVERT: A  118 ASP cc_start: 0.7525 (m-30) cc_final: 0.7265 (m-30)
REVERT: A  194 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7399 (mttt)
REVERT: H   53 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.9014 (p90)
REVERT: H   85 GLN cc_start: 0.7842 (tp40) cc_final: 0.7429 (tp40)
REVERT: L   82 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7837 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 1.2030
  time to fit residues: 85.5213
Evaluate side-chains
  76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.178321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.120272 restraints weight = 12186.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.77
r_work: 0.3156 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4166  Z= 0.162
  Angle     :  0.552   9.326   5638  Z= 0.286
  Chirality :  0.038   0.134    633
  Planarity :  0.004   0.041    703
  Dihedral  :  4.666  39.456    563
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 19.50 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.38), residues: 504
  helix:  3.27 (0.29), residues: 263
  sheet:  0.02 (0.51), residues: 103
  loop :  0.53 (0.57), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.052   0.002   PHE L  84 
 TYR   0.011   0.001   TYR L  92 
 ARG   0.006   0.001   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  306)
  hydrogen bonds       : angle       3.82590 (  923)
  SS BOND              : bond        0.00442 (    4)
  SS BOND              : angle       1.93698 (    8)
  covalent geometry    : bond        0.00363 ( 4162)
  covalent geometry    : angle       0.54773 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7138 (tppp) cc_final: 0.6284 (tmmt)
REVERT: A  118 ASP cc_start: 0.7591 (m-30) cc_final: 0.7334 (m-30)
REVERT: A  194 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7434 (mttt)
REVERT: H   53 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.9040 (p90)
REVERT: H   85 GLN cc_start: 0.7910 (tp40) cc_final: 0.7487 (tp40)
REVERT: L   82 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7850 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 1.0949
  time to fit residues: 81.1665
Evaluate side-chains
  76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0970
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.178768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.118924 restraints weight = 15518.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 4.32
r_work: 0.3165 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4166  Z= 0.147
  Angle     :  0.543   9.474   5638  Z= 0.281
  Chirality :  0.037   0.135    633
  Planarity :  0.004   0.039    703
  Dihedral  :  4.641  39.465    563
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.95 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.38), residues: 504
  helix:  3.45 (0.29), residues: 257
  sheet: -0.11 (0.51), residues: 106
  loop :  0.46 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.053   0.002   PHE L  84 
 TYR   0.011   0.001   TYR L  92 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  306)
  hydrogen bonds       : angle       3.78519 (  923)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       1.91389 (    8)
  covalent geometry    : bond        0.00323 ( 4162)
  covalent geometry    : angle       0.53810 ( 5630)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.7133 (tppp) cc_final: 0.6270 (tmmt)
REVERT: A  118 ASP cc_start: 0.7614 (m-30) cc_final: 0.7358 (m-30)
REVERT: A  194 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7437 (mttt)
REVERT: H   53 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.9043 (p90)
REVERT: H   85 GLN cc_start: 0.7903 (tp40) cc_final: 0.7478 (tp40)
REVERT: L   82 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7865 (pm20)
  outliers start: 7
  outliers final: 4
  residues processed: 71
  average time/residue: 1.1770
  time to fit residues: 87.3135
Evaluate side-chains
  71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain L residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0040
   chunk 13 optimal weight:    0.4980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.180130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119377 restraints weight = 20154.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 5.27
r_work: 0.3146 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4166  Z= 0.147
  Angle     :  0.543   9.474   5638  Z= 0.281
  Chirality :  0.037   0.135    633
  Planarity :  0.004   0.039    703
  Dihedral  :  4.641  39.465    563
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.18 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.38), residues: 504
  helix:  3.45 (0.29), residues: 257
  sheet: -0.11 (0.51), residues: 106
  loop :  0.46 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  97 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.053   0.002   PHE L  84 
 TYR   0.011   0.001   TYR L  92 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  306)
  hydrogen bonds       : angle       3.78519 (  923)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       1.91389 (    8)
  covalent geometry    : bond        0.00323 ( 4162)
  covalent geometry    : angle       0.53810 ( 5630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4091.67 seconds
wall clock time: 71 minutes 21.88 seconds (4281.88 seconds total)