Starting phenix.real_space_refine
on Sun Apr 27 06:32:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqi_38578/04_2025/8xqi_38578.cif"
  }
  resolution = 3.25
  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=   0.015
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: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    3225      2.51       5
     N     768      2.21       5
     O     808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4842
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2330
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2456
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 11, 'TRANS': 294}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.75, per 1000 atoms: 0.77
  Number of scatterers: 4842
  At special positions: 0
  Unit cell: (105.04, 56.16, 81.12, 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      41     16.00
     O     808      8.00
     N     768      7.00
     C    3225      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 181 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  19 " - pdb=" SG  CYS B 281 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 181 " distance=2.04

  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: 1.12
  Conformation dependent library (CDL) restraints added in 588.8 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      85.1% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 56
    Processing helix  chain 'A' and resid 62 through 91
      removed outlier: 4.051A  pdb=" N   ILE A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 97 through 132
      removed outlier: 4.343A  pdb=" N   PHE A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 3.516A  pdb=" N   ARG A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 167
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 172 through 176
      removed outlier: 3.518A  pdb=" N   ASN A 175 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   THR A 176 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 176'
    Processing helix  chain 'A' and resid 193 through 210
    Processing helix  chain 'A' and resid 210 through 232
    Processing helix  chain 'A' and resid 242 through 278
      removed outlier: 4.173A  pdb=" N   LEU A 246 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 280 through 313
      Proline residue:  A 292  - end of helix
      removed outlier: 4.541A  pdb=" N   SER A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   CYS A 303 " --> pdb=" O   TYR A 299 " (cutoff:3.500A)
      Proline residue:  A 306  - end of helix
    Processing helix  chain 'A' and resid 313 through 322
    Processing helix  chain 'B' and resid 29 through 56
    Processing helix  chain 'B' and resid 62 through 91
      removed outlier: 3.908A  pdb=" N   ILE B  66 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   PHE B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR B  81 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
      Proline residue:  B  83  - end of helix
    Processing helix  chain 'B' and resid 98 through 132
    Processing helix  chain 'B' and resid 134 through 144
      removed outlier: 4.532A  pdb=" N   ALA B 138 " --> pdb=" O   PRO B 134 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ARG B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 167
      Proline residue:  B 163  - end of helix
    Processing helix  chain 'B' and resid 172 through 176
      removed outlier: 3.611A  pdb=" N   ASN B 175 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 210
    Processing helix  chain 'B' and resid 210 through 232
      removed outlier: 3.782A  pdb=" N   HIS B 231 " --> pdb=" O   THR B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 278
      removed outlier: 5.880A  pdb=" N   LEU B 246 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU B 247 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      Proline residue:  B 263  - end of helix
      removed outlier: 3.909A  pdb=" N   LEU B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 310
      Proline residue:  B 292  - end of helix
      removed outlier: 4.469A  pdb=" N   SER B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   CYS B 303 " --> pdb=" O   TYR B 299 " (cutoff:3.500A)
      Proline residue:  B 306  - end of helix
    Processing helix  chain 'B' and resid 314 through 322
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171
    Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 171

    378 hydrogen bonds defined for protein.
    1125 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: 1.39

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1418
        1.35 -     1.47: 1388
        1.47 -     1.58: 2119
        1.58 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 4986
  Sorted by residual:
  bond pdb=" N   GLN A 318 "
       pdb=" CA  GLN A 318 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.92e+00
  bond pdb=" N   GLN B 318 "
       pdb=" CA  GLN B 318 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.28e-02 6.10e+03 4.90e+00
  bond pdb=" N   CYS A 320 "
       pdb=" CA  CYS A 320 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.66e+00
  bond pdb=" N   CYS B 320 "
       pdb=" CA  CYS B 320 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.33e+00
  bond pdb=" N   ALA A 319 "
       pdb=" CA  ALA A 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.21e-02 6.83e+03 3.37e+00
  ... (remaining 4981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 6658
        1.84 -     3.68: 128
        3.68 -     5.52: 20
        5.52 -     7.36: 6
        7.36 -     9.20: 2
  Bond angle restraints: 6814
  Sorted by residual:
  angle pdb=" CB  MET A  36 "
        pdb=" CG  MET A  36 "
        pdb=" SD  MET A  36 "
      ideal   model   delta    sigma   weight residual
     112.70  121.90   -9.20 3.00e+00 1.11e-01 9.41e+00
  angle pdb=" CA  THR A 321 "
        pdb=" CB  THR A 321 "
        pdb=" OG1 THR A 321 "
      ideal   model   delta    sigma   weight residual
     109.60  105.68    3.92 1.50e+00 4.44e-01 6.84e+00
  angle pdb=" CA  CYS A 320 "
        pdb=" C   CYS A 320 "
        pdb=" O   CYS A 320 "
      ideal   model   delta    sigma   weight residual
     120.82  118.12    2.70 1.05e+00 9.07e-01 6.61e+00
  angle pdb=" CA  THR B 321 "
        pdb=" CB  THR B 321 "
        pdb=" OG1 THR B 321 "
      ideal   model   delta    sigma   weight residual
     109.60  105.75    3.85 1.50e+00 4.44e-01 6.58e+00
  angle pdb=" N   THR B 321 "
        pdb=" CA  THR B 321 "
        pdb=" C   THR B 321 "
      ideal   model   delta    sigma   weight residual
     111.28  108.64    2.64 1.09e+00 8.42e-01 5.85e+00
  ... (remaining 6809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.16: 2529
       13.16 -    26.33: 284
       26.33 -    39.49: 109
       39.49 -    52.65: 36
       52.65 -    65.82: 11
  Dihedral angle restraints: 2969
    sinusoidal: 1204
      harmonic: 1765
  Sorted by residual:
  dihedral pdb=" CA  PHE B 210 "
           pdb=" C   PHE B 210 "
           pdb=" N   VAL B 211 "
           pdb=" CA  VAL B 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.21  -16.79     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   VAL A 211 "
           pdb=" CA  VAL A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.93  -16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  ILE A 228 "
           pdb=" C   ILE A 228 "
           pdb=" N   ALA A 229 "
           pdb=" CA  ALA A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.55   15.45     0      5.00e+00 4.00e-02 9.55e+00
  ... (remaining 2966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 591
       0.040 -    0.080: 148
       0.080 -    0.121: 53
       0.121 -    0.161: 6
       0.161 -    0.201: 1
  Chirality restraints: 799
  Sorted by residual:
  chirality pdb=" CB  VAL B  79 "
            pdb=" CA  VAL B  79 "
            pdb=" CG1 VAL B  79 "
            pdb=" CG2 VAL B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CG  LEU A 304 "
            pdb=" CB  LEU A 304 "
            pdb=" CD1 LEU A 304 "
            pdb=" CD2 LEU A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CB  THR A 170 "
            pdb=" CA  THR A 170 "
            pdb=" OG1 THR A 170 "
            pdb=" CG2 THR A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.01e-01
  ... (remaining 796 not shown)

  Planarity restraints: 806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 162 "   -0.026 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO B 163 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 163 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 163 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 162 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.28e+00
        pdb=" N   PRO A 163 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 163 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 163 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 305 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B 306 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 306 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 306 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 803 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 543
        2.74 -     3.28: 5065
        3.28 -     3.82: 8515
        3.82 -     4.36: 9763
        4.36 -     4.90: 16657
  Nonbonded interactions: 40543
  Sorted by model distance:
  nonbonded pdb=" O   MET B 272 "
            pdb=" OG  SER B 275 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   GLY B 200 "
            pdb=" OG  SER B 204 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   GLY A 200 "
            pdb=" OG  SER A 204 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   MET A 272 "
            pdb=" OG  SER A 275 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" NH2 ARG B 168 "
            pdb=" O   CYS B 181 "
     model   vdw
     2.423 3.120
  ... (remaining 40538 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 24 through 234 or resid 243 through 322 or resid 401))
}

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:             1.260
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.910
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
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      :  0.004   0.041   4989  Z= 0.210
  Angle     :  0.666   9.202   6820  Z= 0.367
  Chirality :  0.042   0.201    799
  Planarity :  0.005   0.038    806
  Dihedral  : 13.883  65.815   1820
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.54 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.08 (0.34), residues: 591
  helix:  1.47 (0.23), residues: 459
  sheet: -0.69 (1.80), residues: 10
  loop : -2.06 (0.54), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 154 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.017   0.002   PHE B  67 
 TYR   0.011   0.001   TYR B 107 
 ARG   0.007   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10342 (  378)
  hydrogen bonds       : angle       5.27774 ( 1125)
  SS BOND              : bond        0.00366 (    3)
  SS BOND              : angle       1.90763 (    6)
  covalent geometry    : bond        0.00423 ( 4986)
  covalent geometry    : angle       0.66412 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.510 
Fit side-chains
REVERT: B  288 MET cc_start: 0.6589 (tmm) cc_final: 0.6333 (tmm)
REVERT: B  309 TYR cc_start: 0.7402 (m-80) cc_final: 0.7008 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1798
  time to fit residues: 21.7605
Evaluate side-chains
  97 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 44 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.2980
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.152905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.130653 restraints weight = 5940.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.60
r_work: 0.3443 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.0670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4989  Z= 0.162
  Angle     :  0.561   7.639   6820  Z= 0.287
  Chirality :  0.039   0.134    799
  Planarity :  0.005   0.036    806
  Dihedral  :  5.143  36.309    791
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.24 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.33 (0.34), residues: 591
  helix:  1.62 (0.23), residues: 466
  sheet: -0.84 (1.76), residues: 10
  loop : -2.03 (0.56), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 154 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.015   0.001   PHE A 307 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.005   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05075 (  378)
  hydrogen bonds       : angle       4.79441 ( 1125)
  SS BOND              : bond        0.00235 (    3)
  SS BOND              : angle       1.35622 (    6)
  covalent geometry    : bond        0.00363 ( 4986)
  covalent geometry    : angle       0.55968 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.512 
Fit side-chains
REVERT: B  288 MET cc_start: 0.7312 (tmm) cc_final: 0.7002 (tmm)
REVERT: B  309 TYR cc_start: 0.7449 (m-80) cc_final: 0.6982 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1695
  time to fit residues: 24.1511
Evaluate side-chains
  109 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.151084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.129262 restraints weight = 5886.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.58
r_work: 0.3419 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4989  Z= 0.211
  Angle     :  0.590   8.151   6820  Z= 0.301
  Chirality :  0.041   0.163    799
  Planarity :  0.005   0.034    806
  Dihedral  :  5.142  34.378    791
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.97 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.10 (0.33), residues: 591
  helix:  1.47 (0.23), residues: 466
  sheet: -0.94 (1.73), residues: 10
  loop : -2.17 (0.55), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 265 
 PHE   0.011   0.002   PHE B  67 
 TYR   0.011   0.001   TYR B 107 
 ARG   0.006   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05174 (  378)
  hydrogen bonds       : angle       4.79496 ( 1125)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       1.72762 (    6)
  covalent geometry    : bond        0.00498 ( 4986)
  covalent geometry    : angle       0.58786 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 1.134 
Fit side-chains
REVERT: B  288 MET cc_start: 0.7322 (tmm) cc_final: 0.7025 (tmm)
REVERT: B  309 TYR cc_start: 0.7577 (m-80) cc_final: 0.7097 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 119
  average time/residue: 0.2101
  time to fit residues: 32.3625
Evaluate side-chains
  117 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.150910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.128474 restraints weight = 5998.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.63
r_work: 0.3410 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4989  Z= 0.204
  Angle     :  0.580   7.933   6820  Z= 0.296
  Chirality :  0.041   0.163    799
  Planarity :  0.005   0.034    806
  Dihedral  :  5.078  33.898    791
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.92 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.33), residues: 591
  helix:  1.39 (0.22), residues: 466
  sheet: -0.90 (1.66), residues: 10
  loop : -2.28 (0.53), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  24 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.016   0.002   PHE A 307 
 TYR   0.011   0.001   TYR B 107 
 ARG   0.004   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05092 (  378)
  hydrogen bonds       : angle       4.76634 ( 1125)
  SS BOND              : bond        0.00439 (    3)
  SS BOND              : angle       1.98286 (    6)
  covalent geometry    : bond        0.00482 ( 4986)
  covalent geometry    : angle       0.57700 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.524 
Fit side-chains
REVERT: B  288 MET cc_start: 0.7328 (tmm) cc_final: 0.7033 (tmm)
REVERT: B  307 PHE cc_start: 0.7721 (m-80) cc_final: 0.7513 (m-80)
REVERT: B  309 TYR cc_start: 0.7675 (m-80) cc_final: 0.7112 (m-80)
REVERT: B  317 ARG cc_start: 0.5903 (mtp180) cc_final: 0.5699 (mtp180)
  outliers start: 10
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1677
  time to fit residues: 25.6059
Evaluate side-chains
  116 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0040
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.3992

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.152009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129838 restraints weight = 6026.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.62
r_work: 0.3437 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4989  Z= 0.155
  Angle     :  0.551   7.235   6820  Z= 0.280
  Chirality :  0.039   0.164    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.877  33.042    791
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.50 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.28 (0.33), residues: 591
  helix:  1.60 (0.22), residues: 468
  sheet: -0.98 (1.65), residues: 10
  loop : -2.24 (0.54), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 279 
 HIS   0.002   0.000   HIS A 265 
 PHE   0.015   0.001   PHE A 307 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  378)
  hydrogen bonds       : angle       4.64009 ( 1125)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       1.53323 (    6)
  covalent geometry    : bond        0.00351 ( 4986)
  covalent geometry    : angle       0.54903 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.6475 (mmm160) cc_final: 0.6014 (mmp-170)
REVERT: B  133 ARG cc_start: 0.7032 (ptp90) cc_final: 0.6607 (ptp90)
REVERT: B  288 MET cc_start: 0.7340 (tmm) cc_final: 0.7019 (tmm)
REVERT: B  307 PHE cc_start: 0.7715 (m-80) cc_final: 0.7424 (m-80)
REVERT: B  308 LEU cc_start: 0.8343 (mt) cc_final: 0.8043 (mt)
REVERT: B  309 TYR cc_start: 0.7635 (m-80) cc_final: 0.6941 (m-80)
  outliers start: 14
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1570
  time to fit residues: 24.7867
Evaluate side-chains
  119 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.151430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.129209 restraints weight = 6040.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.62
r_work: 0.3424 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4989  Z= 0.166
  Angle     :  0.562   7.412   6820  Z= 0.284
  Chirality :  0.040   0.163    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.832  32.014    791
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.88 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.27 (0.33), residues: 591
  helix:  1.60 (0.22), residues: 468
  sheet: -0.91 (1.58), residues: 10
  loop : -2.23 (0.53), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  378)
  hydrogen bonds       : angle       4.61167 ( 1125)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.86040 (    6)
  covalent geometry    : bond        0.00384 ( 4986)
  covalent geometry    : angle       0.55951 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.6359 (mmm160) cc_final: 0.5935 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8352 (m) cc_final: 0.8036 (p)
REVERT: A  222 PHE cc_start: 0.8119 (t80) cc_final: 0.7839 (t80)
REVERT: B  133 ARG cc_start: 0.7151 (ptp90) cc_final: 0.6819 (ptp90)
REVERT: B  288 MET cc_start: 0.7337 (tmm) cc_final: 0.7030 (tmm)
REVERT: B  307 PHE cc_start: 0.7752 (m-80) cc_final: 0.7444 (m-80)
REVERT: B  309 TYR cc_start: 0.7660 (m-80) cc_final: 0.6955 (m-80)
REVERT: B  317 ARG cc_start: 0.5851 (mtp180) cc_final: 0.5646 (mtp180)
  outliers start: 14
  outliers final: 11
  residues processed: 122
  average time/residue: 0.1734
  time to fit residues: 26.9687
Evaluate side-chains
  121 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  197 TRP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0670
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.3118

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.152834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130877 restraints weight = 5920.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.59
r_work: 0.3439 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4989  Z= 0.139
  Angle     :  0.538   7.195   6820  Z= 0.273
  Chirality :  0.039   0.161    799
  Planarity :  0.004   0.034    806
  Dihedral  :  4.700  31.265    791
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.07 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.44 (0.33), residues: 591
  helix:  1.73 (0.22), residues: 469
  sheet: -0.81 (1.64), residues: 10
  loop : -2.28 (0.53), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 195 
 HIS   0.002   0.000   HIS A 265 
 PHE   0.014   0.001   PHE A 307 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04456 (  378)
  hydrogen bonds       : angle       4.54485 ( 1125)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       1.55600 (    6)
  covalent geometry    : bond        0.00312 ( 4986)
  covalent geometry    : angle       0.53606 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.6268 (mmm160) cc_final: 0.5904 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8341 (m) cc_final: 0.8037 (p)
REVERT: A  222 PHE cc_start: 0.8084 (t80) cc_final: 0.7851 (t80)
REVERT: B  133 ARG cc_start: 0.7119 (ptp90) cc_final: 0.6856 (ptt-90)
REVERT: B  288 MET cc_start: 0.7344 (tmm) cc_final: 0.7038 (tmm)
REVERT: B  307 PHE cc_start: 0.7701 (m-80) cc_final: 0.7358 (m-80)
REVERT: B  309 TYR cc_start: 0.7601 (m-80) cc_final: 0.6806 (m-80)
REVERT: B  317 ARG cc_start: 0.5772 (mtp180) cc_final: 0.5570 (mtp180)
  outliers start: 13
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1833
  time to fit residues: 27.4665
Evaluate side-chains
  120 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  197 TRP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 53 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.150834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.128780 restraints weight = 6001.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.61
r_work: 0.3408 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   4989  Z= 0.192
  Angle     :  0.584   7.820   6820  Z= 0.295
  Chirality :  0.041   0.172    799
  Planarity :  0.005   0.034    806
  Dihedral  :  4.849  31.100    791
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.26 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.24 (0.33), residues: 591
  helix:  1.57 (0.22), residues: 468
  sheet: -0.89 (1.54), residues: 10
  loop : -2.22 (0.53), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.009   0.001   PHE B 101 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04869 (  378)
  hydrogen bonds       : angle       4.60545 ( 1125)
  SS BOND              : bond        0.00449 (    3)
  SS BOND              : angle       1.76026 (    6)
  covalent geometry    : bond        0.00457 ( 4986)
  covalent geometry    : angle       0.58197 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.3869 (OUTLIER) cc_final: 0.3575 (tmtt)
REVERT: A  127 ARG cc_start: 0.6305 (mmm160) cc_final: 0.5946 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8399 (m) cc_final: 0.8102 (p)
REVERT: B  133 ARG cc_start: 0.7090 (ptp90) cc_final: 0.6836 (ptp90)
REVERT: B  288 MET cc_start: 0.7340 (tmm) cc_final: 0.7034 (tmm)
REVERT: B  307 PHE cc_start: 0.7778 (m-80) cc_final: 0.7309 (m-80)
REVERT: B  309 TYR cc_start: 0.7702 (m-80) cc_final: 0.7012 (m-80)
REVERT: B  317 ARG cc_start: 0.5807 (mtp180) cc_final: 0.5600 (mtp180)
  outliers start: 13
  outliers final: 10
  residues processed: 122
  average time/residue: 0.2032
  time to fit residues: 31.5519
Evaluate side-chains
  123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 19 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.151523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.129602 restraints weight = 5880.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.59
r_work: 0.3426 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4989  Z= 0.169
  Angle     :  0.581   7.267   6820  Z= 0.294
  Chirality :  0.040   0.172    799
  Planarity :  0.004   0.035    806
  Dihedral  :  4.785  31.453    791
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.69 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.27 (0.33), residues: 591
  helix:  1.58 (0.22), residues: 468
  sheet: -1.05 (1.53), residues: 10
  loop : -2.15 (0.53), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.018   0.001   PHE A 307 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  378)
  hydrogen bonds       : angle       4.59339 ( 1125)
  SS BOND              : bond        0.00373 (    3)
  SS BOND              : angle       2.04648 (    6)
  covalent geometry    : bond        0.00394 ( 4986)
  covalent geometry    : angle       0.57770 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.4168 (OUTLIER) cc_final: 0.3374 (tmtt)
REVERT: A  188 VAL cc_start: 0.8399 (m) cc_final: 0.8115 (p)
REVERT: B  133 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6813 (ptp90)
REVERT: B  288 MET cc_start: 0.7344 (tmm) cc_final: 0.7038 (tmm)
REVERT: B  307 PHE cc_start: 0.7765 (m-80) cc_final: 0.7294 (m-80)
REVERT: B  309 TYR cc_start: 0.7685 (m-80) cc_final: 0.6958 (m-80)
REVERT: B  317 ARG cc_start: 0.5785 (mtp180) cc_final: 0.5581 (mtp180)
  outliers start: 15
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1624
  time to fit residues: 25.3808
Evaluate side-chains
  122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  197 TRP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.149496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127304 restraints weight = 5992.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.63
r_work: 0.3412 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4989  Z= 0.194
  Angle     :  0.608   9.083   6820  Z= 0.307
  Chirality :  0.041   0.175    799
  Planarity :  0.005   0.036    806
  Dihedral  :  4.861  31.259    791
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.22 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.15 (0.33), residues: 591
  helix:  1.49 (0.22), residues: 468
  sheet: -1.06 (1.47), residues: 10
  loop : -2.12 (0.53), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  24 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.011   0.001   PHE A 307 
 TYR   0.011   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  378)
  hydrogen bonds       : angle       4.62907 ( 1125)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       2.07713 (    6)
  covalent geometry    : bond        0.00461 ( 4986)
  covalent geometry    : angle       0.60562 ( 6814)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.3918 (OUTLIER) cc_final: 0.3132 (tmtt)
REVERT: A  188 VAL cc_start: 0.8419 (m) cc_final: 0.8142 (p)
REVERT: B  288 MET cc_start: 0.7353 (tmm) cc_final: 0.7038 (tmm)
REVERT: B  307 PHE cc_start: 0.7798 (m-80) cc_final: 0.7234 (m-80)
REVERT: B  309 TYR cc_start: 0.7724 (m-80) cc_final: 0.7026 (m-80)
REVERT: B  317 ARG cc_start: 0.5681 (mtp180) cc_final: 0.5477 (mtp180)
  outliers start: 10
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1873
  time to fit residues: 28.3842
Evaluate side-chains
  120 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  296 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.150696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.128503 restraints weight = 5990.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.63
r_work: 0.3429 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4989  Z= 0.155
  Angle     :  0.586   8.739   6820  Z= 0.296
  Chirality :  0.040   0.167    799
  Planarity :  0.004   0.035    806
  Dihedral  :  4.743  31.244    791
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.22 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.25 (0.33), residues: 591
  helix:  1.56 (0.22), residues: 470
  sheet:  None (None), residues: 0
  loop : -2.10 (0.50), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 195 
 HIS   0.001   0.000   HIS B 265 
 PHE   0.021   0.001   PHE A 307 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04631 (  378)
  hydrogen bonds       : angle       4.57331 ( 1125)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       1.86763 (    6)
  covalent geometry    : bond        0.00352 ( 4986)
  covalent geometry    : angle       0.58378 ( 6814)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2867.85 seconds
wall clock time: 51 minutes 40.27 seconds (3100.27 seconds total)