Starting phenix.real_space_refine
on Sat May 10 03:20:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqi_38578/05_2025/8xqi_38578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqi_38578/05_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_38578/05_2025/8xqi_38578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqi_38578/05_2025/8xqi_38578.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqi_38578/05_2025/8xqi_38578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqi_38578/05_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-5687/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: 3.43, per 1000 atoms: 0.71
  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: 1.27
  Conformation dependent library (CDL) restraints added in 585.5 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: 1.27

  Time building geometry restraints manager: 1.43 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.810
  Find NCS groups from input model:        0.240
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.510
-------------------------------------------------------------------------------
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  : 0.524 
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: 0.1878
  time to fit residues: 22.5820
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  : 0.522 
-------------------------------------------------------------------------------
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  : 0.534 
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: 0.1690
  time to fit residues: 23.8185
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  : 0.522 
-------------------------------------------------------------------------------
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:    0.9990
   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:    0.6980

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.150823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.129558 restraints weight = 5881.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.51
r_work: 0.3432 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.0987

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= 0.214
  Angle     :  0.593   8.223   6820  Z= 0.303
  Chirality :  0.041   0.157    799
  Planarity :  0.005   0.034    806
  Dihedral  :  5.153  34.165    791
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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:  1.07 (0.33), residues: 591
  helix:  1.45 (0.23), residues: 466
  sheet: -0.91 (1.73), residues: 10
  loop : -2.18 (0.55), residues: 115

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05234 (  378)
  hydrogen bonds       : angle       4.80009 ( 1125)
  SS BOND              : bond        0.00419 (    3)
  SS BOND              : angle       1.75214 (    6)
  covalent geometry    : bond        0.00505 ( 4986)
  covalent geometry    : angle       0.59113 ( 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
  121 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.487 
Fit side-chains
REVERT: B  288 MET cc_start: 0.7293 (tmm) cc_final: 0.6997 (tmm)
REVERT: B  309 TYR cc_start: 0.7575 (m-80) cc_final: 0.7159 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 118
  average time/residue: 0.1648
  time to fit residues: 24.7306
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  : 0.543 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 51 optimal weight:    0.3980
   chunk 50 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.152132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.129867 restraints weight = 6019.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.62
r_work: 0.3436 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1167

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= 0.160
  Angle     :  0.548   7.395   6820  Z= 0.280
  Chirality :  0.039   0.155    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.923  33.816    791
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.54 %
    Favored  : 78.35 %
  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:  1.23 (0.33), residues: 591
  helix:  1.58 (0.22), residues: 466
  sheet: -0.93 (1.67), residues: 10
  loop : -2.21 (0.53), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  24 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.016   0.001   PHE A 307 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04753 (  378)
  hydrogen bonds       : angle       4.67655 ( 1125)
  SS BOND              : bond        0.00248 (    3)
  SS BOND              : angle       1.62692 (    6)
  covalent geometry    : bond        0.00363 ( 4986)
  covalent geometry    : angle       0.54579 ( 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
  124 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.487 
Fit side-chains
REVERT: B  133 ARG cc_start: 0.7062 (ptp90) cc_final: 0.6541 (ptp90)
REVERT: B  288 MET cc_start: 0.7339 (tmm) cc_final: 0.7042 (tmm)
REVERT: B  308 LEU cc_start: 0.8340 (mt) cc_final: 0.8065 (mt)
REVERT: B  309 TYR cc_start: 0.7589 (m-80) cc_final: 0.6940 (m-80)
  outliers start: 11
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1596
  time to fit residues: 24.4695
Evaluate side-chains
  114 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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   40 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0570
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 47 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0980
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.2498

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.153366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.131201 restraints weight = 5998.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.61
r_work: 0.3455 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4989  Z= 0.133
  Angle     :  0.533   7.059   6820  Z= 0.270
  Chirality :  0.038   0.159    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.735  32.109    791
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.50 %
    Favored  : 76.63 %
  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:  1.46 (0.33), residues: 591
  helix:  1.75 (0.22), residues: 470
  sheet:  None (None), residues: 0
  loop : -2.26 (0.51), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 279 
 HIS   0.001   0.000   HIS A 265 
 PHE   0.014   0.001   PHE B 307 
 TYR   0.008   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04462 (  378)
  hydrogen bonds       : angle       4.55926 ( 1125)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       1.36813 (    6)
  covalent geometry    : bond        0.00288 ( 4986)
  covalent geometry    : angle       0.53123 ( 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
  122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A  188 VAL cc_start: 0.8290 (m) cc_final: 0.7973 (p)
REVERT: B  133 ARG cc_start: 0.7058 (ptp90) cc_final: 0.6705 (ptp90)
REVERT: B  273 LEU cc_start: 0.8073 (tt) cc_final: 0.7833 (tp)
REVERT: B  288 MET cc_start: 0.7319 (tmm) cc_final: 0.7008 (tmm)
REVERT: B  309 TYR cc_start: 0.7530 (m-80) cc_final: 0.6796 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1778
  time to fit residues: 26.5396
Evaluate side-chains
  114 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ARG
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  197 TRP
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:    0.8980
   chunk 35 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.151589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.130126 restraints weight = 5957.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.56
r_work: 0.3432 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4989  Z= 0.171
  Angle     :  0.558   7.579   6820  Z= 0.283
  Chirality :  0.040   0.160    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.800  31.432    791
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.31 %
    Favored  : 76.63 %
  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:  1.40 (0.33), residues: 591
  helix:  1.70 (0.22), residues: 469
  sheet: -0.91 (1.60), residues: 10
  loop : -2.28 (0.53), residues: 112

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   0.016   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        0.04729 (  378)
  hydrogen bonds       : angle       4.57682 ( 1125)
  SS BOND              : bond        0.00425 (    3)
  SS BOND              : angle       1.92750 (    6)
  covalent geometry    : bond        0.00400 ( 4986)
  covalent geometry    : angle       0.55548 ( 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
  128 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.6472 (mmp-170) cc_final: 0.6271 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8358 (m) cc_final: 0.8046 (p)
REVERT: B  133 ARG cc_start: 0.7076 (ptp90) cc_final: 0.6748 (ptp90)
REVERT: B  288 MET cc_start: 0.7326 (tmm) cc_final: 0.7020 (tmm)
REVERT: B  307 PHE cc_start: 0.7684 (m-80) cc_final: 0.7483 (m-80)
REVERT: B  309 TYR cc_start: 0.7633 (m-80) cc_final: 0.6951 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1670
  time to fit residues: 26.0263
Evaluate side-chains
  122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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 A residue  305 ASN
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:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.152219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131117 restraints weight = 5840.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 1.50
r_work: 0.3446 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4989  Z= 0.159
  Angle     :  0.555   7.275   6820  Z= 0.281
  Chirality :  0.039   0.172    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.755  31.384    791
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.65 %
    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:  1.41 (0.33), residues: 591
  helix:  1.71 (0.22), residues: 469
  sheet: -0.90 (1.60), residues: 10
  loop : -2.25 (0.53), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 195 
 HIS   0.003   0.001   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        0.04598 (  378)
  hydrogen bonds       : angle       4.56975 ( 1125)
  SS BOND              : bond        0.00308 (    3)
  SS BOND              : angle       1.64580 (    6)
  covalent geometry    : bond        0.00368 ( 4986)
  covalent geometry    : angle       0.55326 ( 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
  125 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  188 VAL cc_start: 0.8371 (m) cc_final: 0.8076 (p)
REVERT: B  133 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6780 (ptp90)
REVERT: B  288 MET cc_start: 0.7326 (tmm) cc_final: 0.7029 (tmm)
REVERT: B  307 PHE cc_start: 0.7683 (m-80) cc_final: 0.7441 (m-80)
REVERT: B  309 TYR cc_start: 0.7620 (m-80) cc_final: 0.6907 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1968
  time to fit residues: 29.8271
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  : 0.532 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 53 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   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 = 0.3851 r_free = 0.3851 target = 0.151894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.130913 restraints weight = 5933.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.50
r_work: 0.3444 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1644

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= 0.164
  Angle     :  0.572   8.248   6820  Z= 0.288
  Chirality :  0.039   0.168    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.737  30.859    791
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.65 %
    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:  1.39 (0.33), residues: 591
  helix:  1.68 (0.22), residues: 469
  sheet: -0.91 (1.53), residues: 10
  loop : -2.23 (0.53), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 279 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.009   0.001   PHE B 101 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.004   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  378)
  hydrogen bonds       : angle       4.56768 ( 1125)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       1.61833 (    6)
  covalent geometry    : bond        0.00383 ( 4986)
  covalent geometry    : angle       0.57040 ( 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
  127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3884 (tmtt)
REVERT: A  188 VAL cc_start: 0.8385 (m) cc_final: 0.8089 (p)
REVERT: B  133 ARG cc_start: 0.7061 (ptp90) cc_final: 0.6794 (ptp90)
REVERT: B  288 MET cc_start: 0.7329 (tmm) cc_final: 0.7030 (tmm)
REVERT: B  307 PHE cc_start: 0.7703 (m-80) cc_final: 0.7437 (m-80)
REVERT: B  309 TYR cc_start: 0.7653 (m-80) cc_final: 0.6938 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1718
  time to fit residues: 26.7744
Evaluate side-chains
  124 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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  197 TRP
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:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 41 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    0.1980
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.3296

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.153002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.131591 restraints weight = 5863.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.53
r_work: 0.3455 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4989  Z= 0.143
  Angle     :  0.564   8.659   6820  Z= 0.283
  Chirality :  0.039   0.158    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.631  30.157    791
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.03 %
    Favored  : 75.48 %
  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:  1.51 (0.33), residues: 591
  helix:  1.76 (0.22), residues: 470
  sheet:  None (None), residues: 0
  loop : -2.14 (0.50), residues: 121

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   0.016   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        0.04446 (  378)
  hydrogen bonds       : angle       4.51302 ( 1125)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       1.94696 (    6)
  covalent geometry    : bond        0.00322 ( 4986)
  covalent geometry    : angle       0.56167 ( 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
  123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.3817 (OUTLIER) cc_final: 0.3579 (tmtt)
REVERT: A  127 ARG cc_start: 0.6250 (mmp-170) cc_final: 0.5922 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8358 (m) cc_final: 0.8067 (p)
REVERT: B  288 MET cc_start: 0.7319 (tmm) cc_final: 0.6999 (tmm)
REVERT: B  307 PHE cc_start: 0.7672 (m-80) cc_final: 0.7316 (m-80)
REVERT: B  309 TYR cc_start: 0.7576 (m-80) cc_final: 0.6780 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 119
  average time/residue: 0.1770
  time to fit residues: 26.6881
Evaluate side-chains
  119 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.151837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130834 restraints weight = 5906.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.50
r_work: 0.3440 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4989  Z= 0.173
  Angle     :  0.590   8.613   6820  Z= 0.297
  Chirality :  0.040   0.172    799
  Planarity :  0.004   0.033    806
  Dihedral  :  4.714  30.015    791
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.61 %
    Favored  : 75.29 %
  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:  1.40 (0.33), residues: 591
  helix:  1.68 (0.22), residues: 469
  sheet: -0.90 (1.50), residues: 10
  loop : -2.17 (0.53), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  24 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.009   0.001   PHE B  97 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04689 (  378)
  hydrogen bonds       : angle       4.55007 ( 1125)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       2.00257 (    6)
  covalent geometry    : bond        0.00407 ( 4986)
  covalent geometry    : angle       0.58773 ( 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
  126 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.3876 (OUTLIER) cc_final: 0.3574 (tmtt)
REVERT: A  127 ARG cc_start: 0.6300 (mmp-170) cc_final: 0.6012 (mmp-170)
REVERT: A  188 VAL cc_start: 0.8381 (m) cc_final: 0.8074 (p)
REVERT: B  288 MET cc_start: 0.7317 (tmm) cc_final: 0.7001 (tmm)
REVERT: B  307 PHE cc_start: 0.7737 (m-80) cc_final: 0.7316 (m-80)
REVERT: B  309 TYR cc_start: 0.7649 (m-80) cc_final: 0.6935 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1742
  time to fit residues: 27.1624
Evaluate side-chains
  124 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 53 optimal weight:    0.0980
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.1980

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.154232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.132786 restraints weight = 5975.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.53
r_work: 0.3460 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
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      :  0.003   0.038   4989  Z= 0.128
  Angle     :  0.565   9.213   6820  Z= 0.284
  Chirality :  0.038   0.152    799
  Planarity :  0.004   0.034    806
  Dihedral  :  4.546  29.309    791
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.75 %
    Favored  : 74.52 %
  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:  1.63 (0.33), residues: 591
  helix:  1.82 (0.22), residues: 471
  sheet:  None (None), residues: 0
  loop : -1.99 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 195 
 HIS   0.001   0.000   HIS B 265 
 PHE   0.017   0.001   PHE A 307 
 TYR   0.007   0.001   TYR B 107 
 ARG   0.004   0.000   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  378)
  hydrogen bonds       : angle       4.47140 ( 1125)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.71370 (    6)
  covalent geometry    : bond        0.00271 ( 4986)
  covalent geometry    : angle       0.56294 ( 6814)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2638.20 seconds
wall clock time: 46 minutes 28.29 seconds (2788.29 seconds total)