Starting phenix.real_space_refine
on Wed Mar  5 19:25:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2025/7wb5_32395.cif"
  }
  resolution = 3.7
  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=   0.022
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      15      5.16       5
     C    2077      2.51       5
     N     533      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3256
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 928
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.43, per 1000 atoms: 1.05
  Number of scatterers: 3256
  At special positions: 0
  Unit cell: (72.36, 88.56, 72.36, 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      15     16.00
     O     631      8.00
     N     533      7.00
     C    2077      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN R 343 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 400.5 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 12 sheets defined
      4.4% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'R' and resid 349 through 353
    Processing helix  chain 'R' and resid 364 through 370
      removed outlier: 4.598A  pdb=" N   LEU R 368 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.682A  pdb=" N   LYS H  12 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47
      removed outlier: 3.906A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51
      removed outlier: 3.533A  pdb=" N   TRP H  50 " --> pdb=" O   THR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.846A  pdb=" N   ILE L  21 " --> pdb=" O   LEU L  73 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU L  73 " --> pdb=" O   ILE L  21 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER L  63 " --> pdb=" O   THR L  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.595A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 103 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54
      removed outlier: 3.572A  pdb=" N   GLN L  53 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.884A  pdb=" N   ILE R 434 " --> pdb=" O   VAL R 511 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   CYS R 432 " --> pdb=" O   LEU R 513 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358
    Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474

    73 hydrogen bonds defined for protein.
    171 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 734
        1.33 -     1.45: 857
        1.45 -     1.57: 1735
        1.57 -     1.69: 1
        1.69 -     1.82: 18
  Bond restraints: 3345
  Sorted by residual:
  bond pdb=" CA  SER R 438 "
       pdb=" CB  SER R 438 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.35e-02 5.49e+03 1.53e+01
  bond pdb=" CA  SER R 349 "
       pdb=" CB  SER R 349 "
    ideal  model  delta    sigma   weight residual
    1.529  1.467  0.062 1.64e-02 3.72e+03 1.43e+01
  bond pdb=" N   LEU R 452 "
       pdb=" CA  LEU R 452 "
    ideal  model  delta    sigma   weight residual
    1.452  1.495 -0.043 1.22e-02 6.72e+03 1.23e+01
  bond pdb=" N   VAL R 433 "
       pdb=" CA  VAL R 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" N   LYS R 378 "
       pdb=" CA  LYS R 378 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.041 1.29e-02 6.01e+03 1.03e+01
  ... (remaining 3340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 4160
        2.59 -     5.17: 364
        5.17 -     7.76: 19
        7.76 -    10.34: 3
       10.34 -    12.93: 2
  Bond angle restraints: 4548
  Sorted by residual:
  angle pdb=" CA  PRO L  80 "
        pdb=" N   PRO L  80 "
        pdb=" CD  PRO L  80 "
      ideal   model   delta    sigma   weight residual
     112.00   99.07   12.93 1.40e+00 5.10e-01 8.52e+01
  angle pdb=" CA  TRP R 436 "
        pdb=" CB  TRP R 436 "
        pdb=" CG  TRP R 436 "
      ideal   model   delta    sigma   weight residual
     113.60  123.83  -10.23 1.90e+00 2.77e-01 2.90e+01
  angle pdb=" CA  PHE R 400 "
        pdb=" CB  PHE R 400 "
        pdb=" CG  PHE R 400 "
      ideal   model   delta    sigma   weight residual
     113.80  118.30   -4.50 1.00e+00 1.00e+00 2.03e+01
  angle pdb=" N   PRO L  80 "
        pdb=" CD  PRO L  80 "
        pdb=" CG  PRO L  80 "
      ideal   model   delta    sigma   weight residual
     103.20   96.90    6.30 1.50e+00 4.44e-01 1.77e+01
  angle pdb=" N   LEU R 387 "
        pdb=" CA  LEU R 387 "
        pdb=" C   LEU R 387 "
      ideal   model   delta    sigma   weight residual
     114.75  109.56    5.19 1.26e+00 6.30e-01 1.69e+01
  ... (remaining 4543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.52: 1718
       21.52 -    43.04: 173
       43.04 -    64.55: 66
       64.55 -    86.07: 12
       86.07 -   107.59: 12
  Dihedral angle restraints: 1981
    sinusoidal: 801
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CA  VAL L  29 "
           pdb=" C   VAL L  29 "
           pdb=" N   SER L  30 "
           pdb=" CA  SER L  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.90  -40.10     0      5.00e+00 4.00e-02 6.43e+01
  dihedral pdb=" CA  PHE H 106 "
           pdb=" C   PHE H 106 "
           pdb=" N   ASP H 107 "
           pdb=" CA  ASP H 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.68  -33.32     0      5.00e+00 4.00e-02 4.44e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.78  -43.78     1      1.00e+01 1.00e-02 2.67e+01
  ... (remaining 1978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 417
       0.119 -    0.238: 63
       0.238 -    0.356: 5
       0.356 -    0.475: 0
       0.475 -    0.593: 2
  Chirality restraints: 487
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-02 2.50e+03 6.89e+01
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.29e+01
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN R 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.81   -0.59 2.00e-01 2.50e+01 8.81e+00
  ... (remaining 484 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "    0.304 2.00e-02 2.50e+03   2.62e-01 8.61e+02
        pdb=" C7  NAG A   2 "   -0.065 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.009 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "   -0.453 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "    0.205 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.292 2.00e-02 2.50e+03   2.51e-01 7.91e+02
        pdb=" C7  NAG A   1 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.164 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.443 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN L  79 "   -0.111 5.00e-02 4.00e+02   1.57e-01 3.92e+01
        pdb=" N   PRO L  80 "    0.270 5.00e-02 4.00e+02
        pdb=" CA  PRO L  80 "   -0.083 5.00e-02 4.00e+02
        pdb=" CD  PRO L  80 "   -0.076 5.00e-02 4.00e+02
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 281
        2.73 -     3.27: 3255
        3.27 -     3.82: 5356
        3.82 -     4.36: 6706
        4.36 -     4.90: 11080
  Nonbonded interactions: 26678
  Sorted by model distance:
  nonbonded pdb=" O   ILE L  21 "
            pdb=" OG1 THR L  72 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OG  SER H   7 "
            pdb=" OG  SER H  21 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLN H   6 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER L  26 "
            pdb=" OE1 GLN L  27 "
     model   vdw
     2.405 3.040
  nonbonded pdb=" O   VAL H  76 "
            pdb=" OG  SER H  77 "
     model   vdw
     2.421 3.040
  ... (remaining 26673 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.360
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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      :  0.011   0.132   3345  Z= 0.690
  Angle     :  1.407  12.925   4548  Z= 0.926
  Chirality :  0.090   0.593    487
  Planarity :  0.018   0.262    581
  Dihedral  : 21.949 107.591   1220
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  2.24 %
    Allowed  : 18.16 %
    Favored  : 79.60 %
  Rotamer:
    Outliers : 14.00 %
    Allowed  :  7.43 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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: -4.90 (0.36), residues: 402
  helix: -4.22 (0.64), residues: 21
  sheet: -3.58 (0.39), residues: 121
  loop : -3.14 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.092   0.006   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.023   0.003   PHE R 400 
 TYR   0.024   0.003   TYR L  49 
 ARG   0.007   0.001   ARG L  61 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt)
REVERT: L   74 THR cc_start: 0.7091 (m) cc_final: 0.6553 (m)
REVERT: L   79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7818 (mp10)
REVERT: R  369 TYR cc_start: 0.7978 (t80) cc_final: 0.7755 (t80)
REVERT: R  387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt)
REVERT: R  454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7654 (mtp-110)
REVERT: R  493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30)
  outliers start: 49
  outliers final: 12
  residues processed: 150
  average time/residue: 0.1849
  time to fit residues: 32.3962
Evaluate side-chains
  122 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  410 ILE
Chi-restraints excluded: chain R residue  422 ASN
Chi-restraints excluded: chain R residue  425 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  454 ARG
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  493 GLN
Chi-restraints excluded: chain R residue  516 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H  35 ASN
H  82 GLN
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 481 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.139944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117011 restraints weight = 5133.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.119602 restraints weight = 3330.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121330 restraints weight = 2493.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3345  Z= 0.265
  Angle     :  0.821   7.995   4548  Z= 0.419
  Chirality :  0.050   0.200    487
  Planarity :  0.007   0.085    581
  Dihedral  : 17.717  93.006    544
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 11.44 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 19.14 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.48 (0.36), residues: 402
  helix: -3.40 (0.78), residues: 21
  sheet: -3.11 (0.42), residues: 114
  loop : -3.03 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.027   0.002   PHE R 515 
 TYR   0.018   0.002   TYR L  49 
 ARG   0.006   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.8391 (m-80) cc_final: 0.8030 (m-10)
REVERT: L   79 GLN cc_start: 0.8421 (mp10) cc_final: 0.7707 (mp10)
REVERT: R  387 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: R  454 ARG cc_start: 0.8019 (mtp180) cc_final: 0.6649 (mtp85)
REVERT: R  462 LYS cc_start: 0.8526 (pptt) cc_final: 0.8094 (ptmm)
REVERT: R  467 ASP cc_start: 0.6022 (p0) cc_final: 0.5224 (p0)
REVERT: R  493 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7727 (tm-30)
REVERT: R  516 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7491 (pp20)
  outliers start: 25
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1772
  time to fit residues: 25.6692
Evaluate side-chains
  118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   82 GLN
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  425 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Chi-restraints excluded: chain R residue  493 GLN
Chi-restraints excluded: chain R residue  495 TYR
Chi-restraints excluded: chain R residue  516 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    0.2980
   chunk 25 optimal weight:    0.0020
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
H  82 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.142036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.117969 restraints weight = 4974.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.120744 restraints weight = 3152.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.122644 restraints weight = 2316.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3345  Z= 0.227
  Angle     :  0.742   9.194   4548  Z= 0.370
  Chirality :  0.049   0.230    487
  Planarity :  0.006   0.079    581
  Dihedral  : 14.608  80.164    536
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.20 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 18.86 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.02 (0.37), residues: 402
  helix: -3.70 (0.70), residues: 21
  sheet: -2.39 (0.47), residues: 111
  loop : -2.87 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.024   0.002   PHE R 515 
 TYR   0.022   0.002   TYR H 105 
 ARG   0.003   0.000   ARG R 408 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.8313 (m-80) cc_final: 0.8065 (m-10)
REVERT: L   79 GLN cc_start: 0.8452 (mp10) cc_final: 0.8023 (mp10)
REVERT: L  100 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: R  386 LYS cc_start: 0.4571 (pttt) cc_final: 0.3217 (pttt)
REVERT: R  387 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8292 (tt)
REVERT: R  462 LYS cc_start: 0.8488 (pptt) cc_final: 0.8095 (ptmm)
REVERT: R  493 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7458 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 123
  average time/residue: 0.1981
  time to fit residues: 29.0486
Evaluate side-chains
  120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.142678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.119338 restraints weight = 5041.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122660 restraints weight = 3839.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.123446 restraints weight = 2400.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3345  Z= 0.226
  Angle     :  0.719   8.392   4548  Z= 0.363
  Chirality :  0.047   0.239    487
  Planarity :  0.007   0.082    581
  Dihedral  : 11.844  63.666    526
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  8.46 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 21.71 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.08 (0.37), residues: 402
  helix: -3.60 (0.82), residues: 19
  sheet: -2.51 (0.44), residues: 125
  loop : -2.88 (0.34), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.019   0.002   PHE R 392 
 TYR   0.018   0.002   TYR H 105 
 ARG   0.007   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8895 (tpp) cc_final: 0.8677 (tpp)
REVERT: H   43 GLN cc_start: 0.7025 (mp10) cc_final: 0.6627 (mp10)
REVERT: H   60 TYR cc_start: 0.8361 (m-80) cc_final: 0.8106 (m-10)
REVERT: L   62 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6895 (p90)
REVERT: L   79 GLN cc_start: 0.8458 (mp10) cc_final: 0.7952 (mp10)
REVERT: L  100 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: R  386 LYS cc_start: 0.4334 (pttt) cc_final: 0.3117 (pttt)
REVERT: R  387 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8160 (tt)
REVERT: R  493 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7568 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 116
  average time/residue: 0.1700
  time to fit residues: 23.3937
Evaluate side-chains
  112 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 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 = 0.3805 r_free = 0.3805 target = 0.141534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.117935 restraints weight = 5116.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.121488 restraints weight = 4026.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.122352 restraints weight = 2550.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3345  Z= 0.250
  Angle     :  0.737  10.867   4548  Z= 0.365
  Chirality :  0.047   0.201    487
  Planarity :  0.006   0.078    581
  Dihedral  : 10.076  49.223    521
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.20 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  8.86 %
    Allowed  : 21.14 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.00 (0.37), residues: 402
  helix: -3.59 (0.80), residues: 19
  sheet: -2.47 (0.45), residues: 121
  loop : -2.80 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP H 109 
 HIS   0.001   0.000   HIS L  34 
 PHE   0.015   0.002   PHE R 515 
 TYR   0.025   0.002   TYR R 380 
 ARG   0.003   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.367 
Fit side-chains
REVERT: H   43 GLN cc_start: 0.7093 (mp10) cc_final: 0.6701 (mp10)
REVERT: H   60 TYR cc_start: 0.8434 (m-80) cc_final: 0.8138 (m-10)
REVERT: L   62 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7017 (p90)
REVERT: L   79 GLN cc_start: 0.8490 (mp10) cc_final: 0.8017 (mp10)
REVERT: L  100 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: R  386 LYS cc_start: 0.4338 (pttt) cc_final: 0.3104 (pttt)
REVERT: R  387 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8121 (tt)
REVERT: R  409 GLN cc_start: 0.8314 (mt0) cc_final: 0.7593 (mt0)
REVERT: R  466 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6237 (ptp-110)
REVERT: R  493 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7523 (tm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 113
  average time/residue: 0.1659
  time to fit residues: 22.2907
Evaluate side-chains
  113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   82 GLN
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Chi-restraints excluded: chain R residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0070
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
H  82 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 422 ASN
R 450 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119861 restraints weight = 5195.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.123526 restraints weight = 3977.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124346 restraints weight = 2441.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3345  Z= 0.242
  Angle     :  0.729   9.647   4548  Z= 0.363
  Chirality :  0.047   0.202    487
  Planarity :  0.006   0.076    581
  Dihedral  :  9.427  50.937    521
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.46 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 22.00 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.90 (0.37), residues: 402
  helix: -3.25 (0.93), residues: 19
  sheet: -2.40 (0.45), residues: 117
  loop : -2.78 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.013   0.001   PHE R 392 
 TYR   0.024   0.002   TYR H 105 
 ARG   0.004   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.367 
Fit side-chains
REVERT: H   43 GLN cc_start: 0.7078 (mp10) cc_final: 0.6613 (mp10)
REVERT: H   60 TYR cc_start: 0.8416 (m-80) cc_final: 0.8088 (m-10)
REVERT: H  102 TRP cc_start: 0.7872 (t-100) cc_final: 0.7491 (t-100)
REVERT: H  109 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7068 (p90)
REVERT: L   62 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7145 (p90)
REVERT: L   79 GLN cc_start: 0.8492 (mp10) cc_final: 0.8038 (mp10)
REVERT: L  100 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: R  386 LYS cc_start: 0.4241 (pttt) cc_final: 0.3073 (pttt)
REVERT: R  387 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8140 (tt)
REVERT: R  454 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7688 (mtp85)
REVERT: R  466 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6209 (ptp-110)
REVERT: R  467 ASP cc_start: 0.6666 (p0) cc_final: 0.6327 (p0)
REVERT: R  493 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7666 (tm-30)
REVERT: R  508 TYR cc_start: 0.5772 (m-80) cc_final: 0.5019 (m-80)
  outliers start: 28
  outliers final: 19
  residues processed: 112
  average time/residue: 0.1741
  time to fit residues: 23.1708
Evaluate side-chains
  112 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0770
   chunk 35 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.143105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119217 restraints weight = 5017.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.123004 restraints weight = 3943.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.123826 restraints weight = 2383.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3345  Z= 0.213
  Angle     :  0.714   9.068   4548  Z= 0.355
  Chirality :  0.046   0.157    487
  Planarity :  0.006   0.077    581
  Dihedral  :  8.883  52.531    521
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.71 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 22.29 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.78 (0.37), residues: 402
  helix: -3.45 (0.84), residues: 19
  sheet: -2.34 (0.44), residues: 118
  loop : -2.65 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP H 109 
 HIS   0.000   0.000   HIS L  34 
 PHE   0.012   0.001   PHE R 392 
 TYR   0.022   0.002   TYR H 105 
 ARG   0.004   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   25 SER cc_start: 0.7709 (t) cc_final: 0.7296 (m)
REVERT: H   60 TYR cc_start: 0.8378 (m-80) cc_final: 0.8025 (m-10)
REVERT: H   90 ASP cc_start: 0.7591 (m-30) cc_final: 0.7346 (m-30)
REVERT: H   95 TYR cc_start: 0.7897 (m-80) cc_final: 0.7654 (m-80)
REVERT: H  109 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.7107 (p90)
REVERT: L   62 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7065 (p90)
REVERT: L   79 GLN cc_start: 0.8481 (mp10) cc_final: 0.7958 (mp10)
REVERT: R  386 LYS cc_start: 0.4225 (pttt) cc_final: 0.2979 (pttt)
REVERT: R  387 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8074 (tt)
REVERT: R  408 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8184 (ptm160)
REVERT: R  453 TYR cc_start: 0.8606 (p90) cc_final: 0.8253 (p90)
REVERT: R  493 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7721 (tm-30)
  outliers start: 27
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1733
  time to fit residues: 23.3585
Evaluate side-chains
  111 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0770
   chunk 36 optimal weight:    0.1980
   chunk 25 optimal weight:    0.0370
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.150388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126088 restraints weight = 4897.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.129030 restraints weight = 3220.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130858 restraints weight = 2436.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3345  Z= 0.199
  Angle     :  0.720   8.418   4548  Z= 0.364
  Chirality :  0.047   0.197    487
  Planarity :  0.006   0.077    581
  Dihedral  :  8.246  53.896    519
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.46 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 23.71 %
    Favored  : 69.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.60 (0.37), residues: 402
  helix: -3.56 (0.83), residues: 19
  sheet: -2.30 (0.44), residues: 116
  loop : -2.46 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP H 109 
 HIS   0.001   0.000   HIS L  34 
 PHE   0.012   0.001   PHE R 392 
 TYR   0.021   0.002   TYR H 105 
 ARG   0.003   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   25 SER cc_start: 0.7658 (t) cc_final: 0.7241 (m)
REVERT: H   60 TYR cc_start: 0.8284 (m-80) cc_final: 0.7954 (m-10)
REVERT: H  102 TRP cc_start: 0.7600 (t-100) cc_final: 0.7150 (t-100)
REVERT: L   62 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7054 (p90)
REVERT: L   79 GLN cc_start: 0.8497 (mp10) cc_final: 0.7991 (mp10)
REVERT: R  386 LYS cc_start: 0.4190 (pttt) cc_final: 0.2937 (pttt)
REVERT: R  387 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: R  408 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (ptm-80)
REVERT: R  409 GLN cc_start: 0.7678 (mt0) cc_final: 0.7478 (mt0)
REVERT: R  453 TYR cc_start: 0.8594 (p90) cc_final: 0.8291 (p90)
REVERT: R  454 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7519 (mtp85)
REVERT: R  493 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7675 (tm-30)
  outliers start: 23
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1750
  time to fit residues: 22.1017
Evaluate side-chains
  111 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    0.0030
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0050
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4404

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.152225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.128766 restraints weight = 4916.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131526 restraints weight = 3307.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.133306 restraints weight = 2516.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3345  Z= 0.227
  Angle     :  0.733   8.101   4548  Z= 0.371
  Chirality :  0.047   0.208    487
  Planarity :  0.006   0.076    581
  Dihedral  :  8.045  57.634    519
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.21 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.43 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -3.39 (0.38), residues: 402
  helix: -3.56 (0.83), residues: 19
  sheet: -2.08 (0.46), residues: 111
  loop : -2.35 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.003   TRP H 109 
 HIS   0.000   0.000   HIS L  34 
 PHE   0.018   0.002   PHE H 106 
 TYR   0.023   0.002   TYR H 105 
 ARG   0.004   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: H   25 SER cc_start: 0.7555 (t) cc_final: 0.7166 (m)
REVERT: H   60 TYR cc_start: 0.8297 (m-80) cc_final: 0.8015 (m-10)
REVERT: H  102 TRP cc_start: 0.7500 (t-100) cc_final: 0.7073 (t-100)
REVERT: L   62 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7129 (p90)
REVERT: L   79 GLN cc_start: 0.8497 (mp10) cc_final: 0.8102 (mp10)
REVERT: R  386 LYS cc_start: 0.4402 (pttt) cc_final: 0.3140 (pttt)
REVERT: R  387 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8069 (tt)
REVERT: R  408 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8136 (ptm-80)
REVERT: R  493 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7465 (tm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1709
  time to fit residues: 20.5943
Evaluate side-chains
  108 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 15 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.1980
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.1780

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.155208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132098 restraints weight = 4865.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134908 restraints weight = 3292.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.136538 restraints weight = 2493.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3345  Z= 0.179
  Angle     :  0.753   7.917   4548  Z= 0.382
  Chirality :  0.047   0.166    487
  Planarity :  0.006   0.077    581
  Dihedral  :  7.306  52.209    513
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 26.86 %
    Favored  : 68.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -3.27 (0.39), residues: 402
  helix: -3.65 (0.80), residues: 19
  sheet: -2.06 (0.46), residues: 116
  loop : -2.21 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP H 109 
 HIS   0.001   0.000   HIS L  34 
 PHE   0.025   0.002   PHE L  83 
 TYR   0.024   0.002   TYR H 105 
 ARG   0.007   0.001   ARG R 454 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: H   25 SER cc_start: 0.7411 (t) cc_final: 0.7148 (m)
REVERT: L   79 GLN cc_start: 0.8473 (mp10) cc_final: 0.8052 (mp10)
REVERT: R  386 LYS cc_start: 0.4385 (pttt) cc_final: 0.3026 (pttt)
REVERT: R  387 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8053 (tt)
REVERT: R  408 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8080 (ptm-80)
REVERT: R  493 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7684 (tm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1608
  time to fit residues: 19.3386
Evaluate side-chains
  102 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  472 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.152387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.129216 restraints weight = 4906.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.131976 restraints weight = 3304.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133863 restraints weight = 2512.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.4461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3345  Z= 0.242
  Angle     :  0.761   7.902   4548  Z= 0.387
  Chirality :  0.048   0.180    487
  Planarity :  0.006   0.076    581
  Dihedral  :  7.287  50.763    513
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.57 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -3.29 (0.39), residues: 402
  helix: -3.53 (0.90), residues: 18
  sheet: -2.25 (0.44), residues: 122
  loop : -2.12 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.003   TRP H 109 
 HIS   0.000   0.000   HIS L  34 
 PHE   0.023   0.002   PHE H 106 
 TYR   0.026   0.002   TYR H  60 
 ARG   0.006   0.001   ARG R 454 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1812.54 seconds
wall clock time: 32 minutes 3.66 seconds (1923.66 seconds total)