Starting phenix.real_space_refine
on Sat Apr  4 23:10:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qkz_53224/04_2026/9qkz_53224.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    3560      2.51       5
     N     961      2.21       5
     O    1055      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5615
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 977
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 8, 'TRANS': 109}
    Chain: "B"
      Number of atoms: 2625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2625
          Classifications: {'peptide': 326}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 303}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 1935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1935
          Classifications: {'peptide': 236}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 226}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 25
          Classifications: {'water': 25}
          Link IDs: {None: 24}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
  Time building chain proxies: 1.48, per 1000 atoms: 0.26
  Number of scatterers: 5615
  At special positions: 0
  Unit cell: (79.632, 92.736, 81.648, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P       5     15.00
     Mg      2     11.99
     O    1055      8.00
     N     961      7.00
     C    3560      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 291.4 milliseconds
  

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1290

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 3 sheets defined
      60.4% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 128 through 146
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 4.069A  pdb=" N   LYS A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 173
      removed outlier: 4.052A  pdb=" N   LYS A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 195
    Processing helix  chain 'A' and resid 196 through 215
    Processing helix  chain 'B' and resid 434 through 436
      No H-bonds generated for 'chain 'B' and resid 434 through 436'
    Processing helix  chain 'B' and resid 479 through 492
    Processing helix  chain 'B' and resid 523 through 530
    Processing helix  chain 'B' and resid 535 through 556
    Processing helix  chain 'B' and resid 564 through 566
      No H-bonds generated for 'chain 'B' and resid 564 through 566'
    Processing helix  chain 'B' and resid 580 through 584
      removed outlier: 4.555A  pdb=" N   LEU B 583 " --> pdb=" O   ASP B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 604
    Processing helix  chain 'B' and resid 605 through 610
    Processing helix  chain 'B' and resid 617 through 634
    Processing helix  chain 'B' and resid 642 through 655
    Processing helix  chain 'B' and resid 664 through 667
    Processing helix  chain 'B' and resid 668 through 674
    Processing helix  chain 'B' and resid 683 through 689
      removed outlier: 4.231A  pdb=" N   GLY B 689 " --> pdb=" O   LYS B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 693 through 704
    Processing helix  chain 'B' and resid 713 through 719
      removed outlier: 3.607A  pdb=" N   LYS B 719 " --> pdb=" O   GLU B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 720 through 724
    Processing helix  chain 'B' and resid 731 through 735
    Processing helix  chain 'C' and resid 70 through 92
    Processing helix  chain 'C' and resid 95 through 113
      removed outlier: 3.680A  pdb=" N   MET C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   THR C 112 " --> pdb=" O   ARG C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 135
    Processing helix  chain 'C' and resid 140 through 156
    Processing helix  chain 'C' and resid 166 through 187
    Processing helix  chain 'C' and resid 196 through 207
      removed outlier: 3.664A  pdb=" N   ILE C 200 " --> pdb=" O   PRO C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 227
    Processing helix  chain 'C' and resid 230 through 235
    Processing helix  chain 'C' and resid 236 through 252
    Processing helix  chain 'C' and resid 261 through 267
      removed outlier: 3.508A  pdb=" N   GLY C 267 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 285
      removed outlier: 3.878A  pdb=" N   LEU C 283 " --> pdb=" O   LYS C 279 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   TYR C 284 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 302
    Processing sheet with id=AA1, first strand: chain 'B' and resid 438 through 446
      removed outlier: 5.410A  pdb=" N   CYS B 440 " --> pdb=" O   LYS B 456 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LYS B 456 " --> pdb=" O   CYS B 440 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN B 442 " --> pdb=" O   ARG B 454 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 452 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL B 451 " --> pdb=" O   ARG B 468 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE B 512 " --> pdb=" O   LEU B 469 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU B 502 " --> pdb=" O   VAL B 515 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ASN B 517 " --> pdb=" O   VAL B 500 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   VAL B 500 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 521 through 522
    Processing sheet with id=AA3, first strand: chain 'B' and resid 558 through 559

    287 hydrogen bonds defined for protein.
    804 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: 0.96

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1798
        1.34 -     1.46: 1166
        1.46 -     1.58: 2670
        1.58 -     1.69: 8
        1.69 -     1.81: 54
  Bond restraints: 5696
  Sorted by residual:
  bond pdb=" CB  LYS B 475 "
       pdb=" CG  LYS B 475 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.76e+00
  bond pdb=" CB  GLU B 436 "
       pdb=" CG  GLU B 436 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CA  GLU B 472 "
       pdb=" CB  GLU B 472 "
    ideal  model  delta    sigma   weight residual
    1.523  1.536 -0.013 1.21e-02 6.83e+03 1.12e+00
  bond pdb=" CB  GLN B 532 "
       pdb=" CG  GLN B 532 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.49e-01
  bond pdb=" CG1 ILE B 503 "
       pdb=" CD1 ILE B 503 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 8.16e-01
  ... (remaining 5691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 7618
        1.99 -     3.98: 72
        3.98 -     5.97: 6
        5.97 -     7.96: 0
        7.96 -     9.94: 1
  Bond angle restraints: 7697
  Sorted by residual:
  angle pdb=" CB  LYS B 475 "
        pdb=" CG  LYS B 475 "
        pdb=" CD  LYS B 475 "
      ideal   model   delta    sigma   weight residual
     111.30  121.24   -9.94 2.30e+00 1.89e-01 1.87e+01
  angle pdb=" C   ASP C 290 "
        pdb=" N   LEU C 291 "
        pdb=" CA  LEU C 291 "
      ideal   model   delta    sigma   weight residual
     121.54  126.84   -5.30 1.91e+00 2.74e-01 7.71e+00
  angle pdb=" CA  LYS B 475 "
        pdb=" CB  LYS B 475 "
        pdb=" CG  LYS B 475 "
      ideal   model   delta    sigma   weight residual
     114.10  119.24   -5.14 2.00e+00 2.50e-01 6.60e+00
  angle pdb=" CB  GLU B 436 "
        pdb=" CG  GLU B 436 "
        pdb=" CD  GLU B 436 "
      ideal   model   delta    sigma   weight residual
     112.60  116.56   -3.96 1.70e+00 3.46e-01 5.41e+00
  angle pdb=" CB  GLN B 532 "
        pdb=" CG  GLN B 532 "
        pdb=" CD  GLN B 532 "
      ideal   model   delta    sigma   weight residual
     112.60  116.05   -3.45 1.70e+00 3.46e-01 4.13e+00
  ... (remaining 7692 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 2989
       17.79 -    35.59: 371
       35.59 -    53.38: 106
       53.38 -    71.18: 31
       71.18 -    88.97: 12
  Dihedral angle restraints: 3509
    sinusoidal: 1518
      harmonic: 1991
  Sorted by residual:
  dihedral pdb=" CA  ASP B 522 "
           pdb=" CB  ASP B 522 "
           pdb=" CG  ASP B 522 "
           pdb=" OD1 ASP B 522 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.72   56.72     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CG  ARG A 108 "
           pdb=" CD  ARG A 108 "
           pdb=" NE  ARG A 108 "
           pdb=" CZ  ARG A 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.85  -44.85     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CB  GLU A 116 "
           pdb=" CG  GLU A 116 "
           pdb=" CD  GLU A 116 "
           pdb=" OE1 GLU A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.86   87.86     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 3506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 518
       0.028 -    0.056: 207
       0.056 -    0.084: 71
       0.084 -    0.113: 35
       0.113 -    0.141: 8
  Chirality restraints: 839
  Sorted by residual:
  chirality pdb=" CA  ILE A 119 "
            pdb=" N   ILE A 119 "
            pdb=" C   ILE A 119 "
            pdb=" CB  ILE A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE B 514 "
            pdb=" N   ILE B 514 "
            pdb=" C   ILE B 514 "
            pdb=" CB  ILE B 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.87e-01
  chirality pdb=" CA  ILE B 497 "
            pdb=" N   ILE B 497 "
            pdb=" C   ILE B 497 "
            pdb=" CB  ILE B 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 836 not shown)

  Planarity restraints: 975
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 494 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO B 495 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 495 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 495 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 628 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   PHE B 628 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE B 628 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY B 629 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 119 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO A 120 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 120 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 120 "    0.018 5.00e-02 4.00e+02
  ... (remaining 972 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 53
        2.54 -     3.13: 4235
        3.13 -     3.72: 9279
        3.72 -     4.31: 13114
        4.31 -     4.90: 21253
  Nonbonded interactions: 47934
  Sorted by model distance:
  nonbonded pdb=" O2B ANP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.945 2.170
  nonbonded pdb="MG    MG B 802 "
            pdb=" O   HOH B 909 "
     model   vdw
     1.959 2.170
  nonbonded pdb=" OD2 ASP B 580 "
            pdb="MG    MG B 803 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" N3B ANP B 801 "
            pdb="MG    MG B 803 "
     model   vdw
     2.061 2.250
  nonbonded pdb=" O2A ANP B 801 "
            pdb="MG    MG B 803 "
     model   vdw
     2.110 2.170
  ... (remaining 47929 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.460
  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:8.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6820
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      :  0.003   0.040   5696  Z= 0.126
  Angle     :  0.474   9.945   7697  Z= 0.242
  Chirality :  0.039   0.141    839
  Planarity :  0.004   0.041    975
  Dihedral  : 17.937  88.971   2219
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.65 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 22.99 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.33), residues: 667
  helix:  2.42 (0.28), residues: 354
  sheet: -0.60 (0.76), residues: 36
  loop :  1.23 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 250 
 TYR   0.016   0.001   TYR C 246 
 PHE   0.016   0.001   PHE A 171 
 TRP   0.005   0.001   TRP C 262 
 HIS   0.003   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5696)
  covalent geometry    : angle       0.47363 ( 7697)
  hydrogen bonds       : bond        0.13358 (  287)
  hydrogen bonds       : angle       4.92450 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  112 MET cc_start: 0.4902 (ptt) cc_final: 0.4536 (ptp)
REVERT: A  137 LYS cc_start: 0.6259 (ttmm) cc_final: 0.5803 (mttt)
REVERT: A  140 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6906 (mt-10)
REVERT: A  144 LYS cc_start: 0.6404 (mmtm) cc_final: 0.6070 (mppt)
REVERT: A  149 MET cc_start: 0.7023 (mmm) cc_final: 0.6703 (mtp)
REVERT: A  155 ARG cc_start: 0.6290 (ttp-170) cc_final: 0.5667 (ptm160)
REVERT: A  169 ILE cc_start: 0.6958 (mt) cc_final: 0.6660 (mt)
REVERT: A  193 GLU cc_start: 0.7917 (tp30) cc_final: 0.7572 (tp30)
REVERT: A  198 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6062 (pm20)
REVERT: A  202 LYS cc_start: 0.6928 (mtpt) cc_final: 0.6353 (mttm)
REVERT: A  205 LYS cc_start: 0.6751 (tttp) cc_final: 0.6160 (tptt)
REVERT: B  437 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5944 (mm-30)
REVERT: B  443 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6515 (ttt90)
REVERT: B  453 TYR cc_start: 0.6870 (m-80) cc_final: 0.6639 (m-80)
REVERT: B  454 ARG cc_start: 0.7150 (ttp80) cc_final: 0.6737 (ttp80)
REVERT: B  462 GLU cc_start: 0.6363 (pt0) cc_final: 0.6005 (tt0)
REVERT: B  468 ARG cc_start: 0.7033 (tmm-80) cc_final: 0.5984 (ttp80)
REVERT: B  470 LYS cc_start: 0.4166 (mmtm) cc_final: 0.3956 (mptt)
REVERT: B  471 MET cc_start: 0.2955 (pmm) cc_final: 0.2254 (mpp)
REVERT: B  475 LYS cc_start: 0.5670 (mppt) cc_final: 0.5028 (mttm)
REVERT: B  527 MET cc_start: 0.7588 (mtm) cc_final: 0.7052 (mtm)
REVERT: B  530 MET cc_start: 0.5852 (ptm) cc_final: 0.5630 (ptp)
REVERT: B  562 ASP cc_start: 0.7876 (t0) cc_final: 0.7663 (t0)
REVERT: B  565 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (p)
REVERT: B  592 LYS cc_start: 0.7123 (mtmm) cc_final: 0.6572 (mtmt)
REVERT: B  641 LYS cc_start: 0.7325 (mtmt) cc_final: 0.7115 (mtmm)
REVERT: B  652 LYS cc_start: 0.7229 (ptmm) cc_final: 0.6734 (ttpt)
REVERT: B  653 ASP cc_start: 0.7255 (m-30) cc_final: 0.6990 (m-30)
REVERT: B  700 MET cc_start: 0.7685 (tpp) cc_final: 0.7481 (tpp)
REVERT: B  701 ASN cc_start: 0.7961 (m-40) cc_final: 0.7632 (m110)
REVERT: B  728 LEU cc_start: 0.8051 (mm) cc_final: 0.7756 (mm)
REVERT: C   83 GLU cc_start: 0.7193 (tp30) cc_final: 0.6486 (tp30)
REVERT: C  155 ARG cc_start: 0.6779 (ttm170) cc_final: 0.6160 (ttm-80)
REVERT: C  159 LYS cc_start: 0.7485 (ttpt) cc_final: 0.7091 (tttp)
REVERT: C  182 ARG cc_start: 0.7319 (tpt-90) cc_final: 0.7075 (tpt90)
REVERT: C  190 CYS cc_start: 0.6828 (m) cc_final: 0.6530 (m)
REVERT: C  211 ARG cc_start: 0.6855 (mmp-170) cc_final: 0.5975 (mmm160)
REVERT: C  213 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6825 (tp40)
REVERT: C  253 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6773 (mt-10)
REVERT: C  271 GLU cc_start: 0.6279 (mp0) cc_final: 0.5942 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 128
  average time/residue: 0.6355
  time to fit residues: 84.4624
Evaluate side-chains
  119 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  677 SER
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  119 SER
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  219 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
B 493 GLN
B 552 HIS
B 567 ASN
B 634 GLN
B 646 GLN
B 648 ASN
B 679 HIS
C 103 GLN
C 107 GLN
C 129 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.156733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.125570 restraints weight = 5437.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.25
r_work: 0.3267 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5696  Z= 0.145
  Angle     :  0.517   6.233   7697  Z= 0.270
  Chirality :  0.041   0.145    839
  Planarity :  0.004   0.038    975
  Dihedral  :  7.221  76.161    789
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.20 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.38 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.33), residues: 667
  helix:  2.57 (0.27), residues: 349
  sheet: -0.55 (0.73), residues: 36
  loop :  1.24 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 687 
 TYR   0.022   0.002   TYR C 246 
 PHE   0.012   0.002   PHE A 186 
 TRP   0.008   0.001   TRP C 262 
 HIS   0.003   0.001   HIS B 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5696)
  covalent geometry    : angle       0.51690 ( 7697)
  hydrogen bonds       : bond        0.04538 (  287)
  hydrogen bonds       : angle       4.12415 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5351 (ptt) cc_final: 0.5089 (ptp)
REVERT: A  137 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7135 (mmpt)
REVERT: A  149 MET cc_start: 0.7798 (mmm) cc_final: 0.7585 (mtp)
REVERT: A  155 ARG cc_start: 0.6683 (ttp-170) cc_final: 0.6436 (ptm160)
REVERT: B  437 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6874 (mm-30)
REVERT: B  453 TYR cc_start: 0.7359 (m-80) cc_final: 0.7159 (m-80)
REVERT: B  468 ARG cc_start: 0.7732 (tmm-80) cc_final: 0.7161 (ttp80)
REVERT: B  471 MET cc_start: 0.3162 (pmm) cc_final: 0.2954 (mpp)
REVERT: B  475 LYS cc_start: 0.6471 (mppt) cc_final: 0.6121 (mmpt)
REVERT: B  516 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7970 (mtp)
REVERT: B  527 MET cc_start: 0.8172 (mtm) cc_final: 0.7667 (mtm)
REVERT: B  556 ASN cc_start: 0.8914 (m-40) cc_final: 0.8572 (m110)
REVERT: B  592 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7686 (mttt)
REVERT: B  660 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6844 (pttm)
REVERT: C  155 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7052 (ttm-80)
REVERT: C  163 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8133 (tp)
REVERT: C  190 CYS cc_start: 0.7249 (m) cc_final: 0.7012 (m)
REVERT: C  211 ARG cc_start: 0.6973 (mmp-170) cc_final: 0.6684 (mmm160)
REVERT: C  213 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7604 (tp40)
REVERT: C  253 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7507 (mt-10)
REVERT: C  287 LYS cc_start: 0.3157 (OUTLIER) cc_final: 0.2725 (mmtm)
  outliers start: 19
  outliers final: 8
  residues processed: 110
  average time/residue: 0.6747
  time to fit residues: 76.9688
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  287 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.8044

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

Flipped N/Q/H residues before XYZ refinement:
B 634 GLN
B 701 ASN
C  86 GLN
C 274 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.158017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.126854 restraints weight = 5298.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.25
r_work: 0.3275 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5696  Z= 0.142
  Angle     :  0.509   5.421   7697  Z= 0.267
  Chirality :  0.040   0.149    839
  Planarity :  0.004   0.039    975
  Dihedral  :  7.138  79.090    784
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.65 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.21 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.33), residues: 667
  helix:  2.48 (0.27), residues: 349
  sheet: -0.68 (0.69), residues: 36
  loop :  1.11 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 501 
 TYR   0.016   0.002   TYR C 246 
 PHE   0.013   0.002   PHE A 186 
 TRP   0.009   0.002   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5696)
  covalent geometry    : angle       0.50935 ( 7697)
  hydrogen bonds       : bond        0.04416 (  287)
  hydrogen bonds       : angle       4.08796 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5372 (ptt) cc_final: 0.5076 (ptp)
REVERT: A  137 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7101 (mmpt)
REVERT: A  155 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.6475 (ptm160)
REVERT: A  158 GLU cc_start: 0.7757 (tp30) cc_final: 0.7441 (mm-30)
REVERT: B  437 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6900 (mm-30)
REVERT: B  443 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7166 (ttt90)
REVERT: B  453 TYR cc_start: 0.7475 (m-80) cc_final: 0.7274 (m-80)
REVERT: B  468 ARG cc_start: 0.7687 (tmm-80) cc_final: 0.7295 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6454 (mppt) cc_final: 0.6108 (mmpt)
REVERT: B  510 ASP cc_start: 0.6978 (t70) cc_final: 0.6680 (t70)
REVERT: B  516 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7956 (mtp)
REVERT: B  527 MET cc_start: 0.8236 (mtm) cc_final: 0.7646 (mtm)
REVERT: B  556 ASN cc_start: 0.8919 (m-40) cc_final: 0.8576 (m110)
REVERT: B  592 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7638 (mttt)
REVERT: B  660 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6918 (pttp)
REVERT: C   83 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7550 (tp30)
REVERT: C  155 ARG cc_start: 0.7530 (ttm170) cc_final: 0.7119 (ttm-80)
REVERT: C  159 LYS cc_start: 0.7559 (ttpt) cc_final: 0.7303 (tttp)
REVERT: C  190 CYS cc_start: 0.7251 (m) cc_final: 0.7025 (m)
REVERT: C  211 ARG cc_start: 0.6957 (mmp-170) cc_final: 0.6674 (mmm160)
REVERT: C  213 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7578 (tp40)
REVERT: C  253 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7516 (mt-10)
  outliers start: 21
  outliers final: 8
  residues processed: 107
  average time/residue: 0.6697
  time to fit residues: 74.2933
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.158839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.127827 restraints weight = 5321.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.24
r_work: 0.3304 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5696  Z= 0.122
  Angle     :  0.484   5.350   7697  Z= 0.255
  Chirality :  0.040   0.147    839
  Planarity :  0.004   0.040    975
  Dihedral  :  7.015  79.916    783
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.05 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.53 (0.33), residues: 667
  helix:  2.53 (0.27), residues: 349
  sheet: -0.60 (0.68), residues: 36
  loop :  1.05 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 687 
 TYR   0.013   0.001   TYR C 246 
 PHE   0.010   0.001   PHE C 263 
 TRP   0.007   0.001   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5696)
  covalent geometry    : angle       0.48382 ( 7697)
  hydrogen bonds       : bond        0.04032 (  287)
  hydrogen bonds       : angle       4.02508 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5449 (ptt) cc_final: 0.5195 (ptp)
REVERT: A  137 LYS cc_start: 0.7361 (ttmm) cc_final: 0.7122 (mmpt)
REVERT: A  158 GLU cc_start: 0.7776 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  437 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6868 (mm-30)
REVERT: B  443 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7127 (ttt90)
REVERT: B  468 ARG cc_start: 0.7719 (tmm-80) cc_final: 0.7388 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6366 (mppt) cc_final: 0.5901 (mmtm)
REVERT: B  510 ASP cc_start: 0.6758 (t70) cc_final: 0.6552 (t70)
REVERT: B  516 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7954 (mtp)
REVERT: B  527 MET cc_start: 0.8237 (mtm) cc_final: 0.7653 (mtm)
REVERT: B  556 ASN cc_start: 0.8895 (m-40) cc_final: 0.8567 (m110)
REVERT: B  592 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7635 (mttt)
REVERT: B  700 MET cc_start: 0.8179 (tpp) cc_final: 0.7898 (tpp)
REVERT: C   83 GLU cc_start: 0.7997 (tp30) cc_final: 0.7491 (tp30)
REVERT: C  155 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7106 (ttm-80)
REVERT: C  159 LYS cc_start: 0.7549 (ttpt) cc_final: 0.7296 (tttp)
REVERT: C  190 CYS cc_start: 0.7100 (m) cc_final: 0.6873 (m)
REVERT: C  213 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7561 (tp40)
REVERT: C  253 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7493 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 101
  average time/residue: 0.6590
  time to fit residues: 69.0374
Evaluate side-chains
  100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0030
   chunk 52 optimal weight:    0.0370
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.5072

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.160715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.129913 restraints weight = 5449.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.26
r_work: 0.3337 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5696  Z= 0.090
  Angle     :  0.441   5.422   7697  Z= 0.231
  Chirality :  0.039   0.147    839
  Planarity :  0.004   0.041    975
  Dihedral  :  6.761  79.227    783
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.95 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.38 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.33), residues: 667
  helix:  2.72 (0.27), residues: 348
  sheet: -0.43 (0.68), residues: 36
  loop :  1.08 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 211 
 TYR   0.011   0.001   TYR C 246 
 PHE   0.009   0.001   PHE A 171 
 TRP   0.006   0.001   TRP C 220 
 HIS   0.002   0.000   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 5696)
  covalent geometry    : angle       0.44105 ( 7697)
  hydrogen bonds       : bond        0.03339 (  287)
  hydrogen bonds       : angle       3.86375 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5396 (ptt) cc_final: 0.5155 (ptp)
REVERT: A  137 LYS cc_start: 0.7338 (ttmm) cc_final: 0.7132 (mttt)
REVERT: A  158 GLU cc_start: 0.7680 (tp30) cc_final: 0.7459 (tp30)
REVERT: B  443 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7084 (ttt90)
REVERT: B  468 ARG cc_start: 0.7685 (tmm-80) cc_final: 0.7390 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6407 (mppt) cc_final: 0.5922 (mmtm)
REVERT: B  516 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7903 (mtp)
REVERT: B  527 MET cc_start: 0.8218 (mtm) cc_final: 0.7543 (mtm)
REVERT: B  556 ASN cc_start: 0.8836 (m-40) cc_final: 0.8523 (m110)
REVERT: B  592 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7677 (mtmt)
REVERT: B  700 MET cc_start: 0.8252 (tpp) cc_final: 0.7957 (tpp)
REVERT: C   83 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7493 (tp30)
REVERT: C  155 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7117 (ttm-80)
REVERT: C  159 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7257 (tttp)
REVERT: C  190 CYS cc_start: 0.6982 (m) cc_final: 0.6762 (m)
REVERT: C  211 ARG cc_start: 0.7202 (mmt-90) cc_final: 0.6950 (mmm160)
REVERT: C  213 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7466 (tm130)
REVERT: C  253 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7497 (mt-10)
  outliers start: 15
  outliers final: 6
  residues processed: 101
  average time/residue: 0.6467
  time to fit residues: 67.8709
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0770
   chunk 45 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 21 optimal weight:   50.0000
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
C 274 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.160759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.129348 restraints weight = 5427.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.35
r_work: 0.3309 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5696  Z= 0.096
  Angle     :  0.448   6.489   7697  Z= 0.234
  Chirality :  0.039   0.156    839
  Planarity :  0.004   0.040    975
  Dihedral  :  6.544  79.238    781
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.70 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.74 (0.33), residues: 667
  helix:  2.75 (0.27), residues: 348
  sheet: -0.46 (0.68), residues: 36
  loop :  1.09 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 211 
 TYR   0.010   0.001   TYR C 246 
 PHE   0.009   0.001   PHE C 263 
 TRP   0.007   0.001   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 5696)
  covalent geometry    : angle       0.44777 ( 7697)
  hydrogen bonds       : bond        0.03410 (  287)
  hydrogen bonds       : angle       3.83079 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5494 (ptt) cc_final: 0.5244 (ptp)
REVERT: A  137 LYS cc_start: 0.7312 (ttmm) cc_final: 0.7086 (mmpt)
REVERT: B  443 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7050 (ttt90)
REVERT: B  468 ARG cc_start: 0.7711 (tmm-80) cc_final: 0.7406 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6373 (mppt) cc_final: 0.5876 (mmtm)
REVERT: B  516 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7956 (mtp)
REVERT: B  527 MET cc_start: 0.8220 (mtm) cc_final: 0.7529 (mtm)
REVERT: B  556 ASN cc_start: 0.8845 (m-40) cc_final: 0.8529 (m110)
REVERT: B  592 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7678 (mttt)
REVERT: B  700 MET cc_start: 0.8272 (tpp) cc_final: 0.7974 (tpp)
REVERT: C   83 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7516 (tp30)
REVERT: C  155 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7114 (ttm-80)
REVERT: C  190 CYS cc_start: 0.6975 (m) cc_final: 0.6754 (m)
REVERT: C  211 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6905 (mmm160)
REVERT: C  213 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7457 (tm130)
REVERT: C  253 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7510 (mt-10)
REVERT: C  258 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7579 (m-40)
  outliers start: 12
  outliers final: 7
  residues processed: 98
  average time/residue: 0.6598
  time to fit residues: 67.1907
Evaluate side-chains
  101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 634 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.159403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127841 restraints weight = 5468.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.48
r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5696  Z= 0.121
  Angle     :  0.487   6.135   7697  Z= 0.256
  Chirality :  0.040   0.146    839
  Planarity :  0.004   0.039    975
  Dihedral  :  6.692  80.208    781
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.38 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.33), residues: 667
  helix:  2.61 (0.27), residues: 349
  sheet: -0.47 (0.68), residues: 36
  loop :  1.07 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 211 
 TYR   0.013   0.001   TYR C 246 
 PHE   0.011   0.001   PHE A 186 
 TRP   0.008   0.001   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5696)
  covalent geometry    : angle       0.48743 ( 7697)
  hydrogen bonds       : bond        0.03909 (  287)
  hydrogen bonds       : angle       3.92469 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  106 SER cc_start: 0.5929 (m) cc_final: 0.5494 (t)
REVERT: A  112 MET cc_start: 0.5448 (ptt) cc_final: 0.5202 (ptp)
REVERT: A  137 LYS cc_start: 0.7319 (ttmm) cc_final: 0.7065 (mmpt)
REVERT: B  443 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7022 (ttt90)
REVERT: B  468 ARG cc_start: 0.7726 (tmm-80) cc_final: 0.7418 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6276 (mppt) cc_final: 0.5778 (mmtm)
REVERT: B  516 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7959 (mtp)
REVERT: B  527 MET cc_start: 0.8197 (mtm) cc_final: 0.7631 (mtm)
REVERT: B  556 ASN cc_start: 0.8892 (m-40) cc_final: 0.8569 (m110)
REVERT: B  592 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7683 (mttt)
REVERT: B  700 MET cc_start: 0.8232 (tpp) cc_final: 0.7906 (tpp)
REVERT: C   83 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7537 (tp30)
REVERT: C  155 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7112 (ttm-80)
REVERT: C  190 CYS cc_start: 0.7106 (m) cc_final: 0.6882 (m)
REVERT: C  211 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6989 (mmp-170)
REVERT: C  213 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7493 (tm130)
REVERT: C  253 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7505 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 99
  average time/residue: 0.6419
  time to fit residues: 65.9713
Evaluate side-chains
  101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  211 ARG
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.9388

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.160282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.129652 restraints weight = 5391.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.25
r_work: 0.3307 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5696  Z= 0.103
  Angle     :  0.465   7.330   7697  Z= 0.242
  Chirality :  0.039   0.146    839
  Planarity :  0.004   0.040    975
  Dihedral  :  6.621  79.881    781
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.54 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.33), residues: 667
  helix:  2.67 (0.27), residues: 349
  sheet: -0.41 (0.68), residues: 36
  loop :  1.09 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 211 
 TYR   0.012   0.001   TYR C 246 
 PHE   0.009   0.001   PHE C 263 
 TRP   0.007   0.001   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5696)
  covalent geometry    : angle       0.46479 ( 7697)
  hydrogen bonds       : bond        0.03582 (  287)
  hydrogen bonds       : angle       3.86846 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  106 SER cc_start: 0.6009 (m) cc_final: 0.5589 (t)
REVERT: A  112 MET cc_start: 0.5620 (ptt) cc_final: 0.5389 (ptp)
REVERT: A  137 LYS cc_start: 0.7275 (ttmm) cc_final: 0.7038 (mmpt)
REVERT: B  443 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7059 (ttt90)
REVERT: B  468 ARG cc_start: 0.7748 (tmm-80) cc_final: 0.7431 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6315 (mppt) cc_final: 0.5831 (mmtm)
REVERT: B  516 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7926 (mtp)
REVERT: B  527 MET cc_start: 0.8167 (mtm) cc_final: 0.7472 (mtm)
REVERT: B  556 ASN cc_start: 0.8868 (m-40) cc_final: 0.8535 (m110)
REVERT: B  592 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7713 (mtmt)
REVERT: B  700 MET cc_start: 0.8258 (tpp) cc_final: 0.7919 (tpp)
REVERT: C   83 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7469 (tp30)
REVERT: C  155 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7083 (ttm-80)
REVERT: C  190 CYS cc_start: 0.7038 (m) cc_final: 0.6816 (m)
REVERT: C  211 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6889 (mmm160)
REVERT: C  213 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7497 (tm130)
REVERT: C  253 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7486 (mt-10)
  outliers start: 15
  outliers final: 9
  residues processed: 99
  average time/residue: 0.6752
  time to fit residues: 69.3496
Evaluate side-chains
  103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  124 SER
Chi-restraints excluded: chain C residue  211 ARG
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.156249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123112 restraints weight = 5514.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.34
r_work: 0.3268 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5696  Z= 0.179
  Angle     :  0.571   7.767   7697  Z= 0.298
  Chirality :  0.043   0.147    839
  Planarity :  0.005   0.044    975
  Dihedral  :  6.951  81.585    781
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.70 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.32), residues: 667
  helix:  2.36 (0.27), residues: 350
  sheet: -0.68 (0.67), residues: 36
  loop :  0.94 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 141 
 TYR   0.015   0.002   TYR B 615 
 PHE   0.020   0.002   PHE A 186 
 TRP   0.010   0.002   TRP C 262 
 HIS   0.004   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 5696)
  covalent geometry    : angle       0.57080 ( 7697)
  hydrogen bonds       : bond        0.04671 (  287)
  hydrogen bonds       : angle       4.11081 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  106 SER cc_start: 0.6104 (m) cc_final: 0.5512 (t)
REVERT: A  137 LYS cc_start: 0.7369 (ttmm) cc_final: 0.7114 (mmpt)
REVERT: B  443 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7137 (ttt90)
REVERT: B  468 ARG cc_start: 0.7758 (tmm-80) cc_final: 0.7437 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6271 (mppt) cc_final: 0.5759 (mmtm)
REVERT: B  516 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7931 (mtp)
REVERT: B  527 MET cc_start: 0.8230 (mtm) cc_final: 0.7675 (mtm)
REVERT: B  556 ASN cc_start: 0.8888 (m-40) cc_final: 0.8578 (m110)
REVERT: B  592 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7633 (mttt)
REVERT: B  700 MET cc_start: 0.8194 (tpp) cc_final: 0.7903 (tpp)
REVERT: C   83 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7507 (tp30)
REVERT: C  155 ARG cc_start: 0.7522 (ttm170) cc_final: 0.7111 (ttm-80)
REVERT: C  190 CYS cc_start: 0.7285 (m) cc_final: 0.7082 (m)
REVERT: C  213 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7576 (tp40)
REVERT: C  253 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7529 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 99
  average time/residue: 0.6780
  time to fit residues: 69.5613
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:   50.0000
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
B 634 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.158254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125238 restraints weight = 5560.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.35
r_work: 0.3281 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5696  Z= 0.113
  Angle     :  0.496   9.137   7697  Z= 0.257
  Chirality :  0.040   0.147    839
  Planarity :  0.004   0.040    975
  Dihedral  :  6.787  80.786    781
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.65 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.87 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.33), residues: 667
  helix:  2.54 (0.27), residues: 349
  sheet: -0.58 (0.67), residues: 36
  loop :  1.00 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 141 
 TYR   0.011   0.001   TYR C 246 
 PHE   0.009   0.001   PHE C 263 
 TRP   0.007   0.001   TRP C 262 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5696)
  covalent geometry    : angle       0.49634 ( 7697)
  hydrogen bonds       : bond        0.03844 (  287)
  hydrogen bonds       : angle       3.97115 (  804)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  106 SER cc_start: 0.6090 (m) cc_final: 0.5547 (t)
REVERT: A  112 MET cc_start: 0.5373 (ptt) cc_final: 0.5094 (ptp)
REVERT: A  137 LYS cc_start: 0.7321 (ttmm) cc_final: 0.7092 (mmpt)
REVERT: B  443 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7124 (ttt90)
REVERT: B  468 ARG cc_start: 0.7732 (tmm-80) cc_final: 0.7365 (ttp-170)
REVERT: B  475 LYS cc_start: 0.6238 (mppt) cc_final: 0.5748 (mmtm)
REVERT: B  511 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7812 (mtpt)
REVERT: B  516 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7903 (mtp)
REVERT: B  527 MET cc_start: 0.8180 (mtm) cc_final: 0.7500 (mtm)
REVERT: B  556 ASN cc_start: 0.8888 (m-40) cc_final: 0.8555 (m110)
REVERT: B  592 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7614 (mttt)
REVERT: B  700 MET cc_start: 0.8217 (tpp) cc_final: 0.7944 (tpp)
REVERT: C   83 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7500 (tp30)
REVERT: C  155 ARG cc_start: 0.7519 (ttm170) cc_final: 0.7099 (ttm-80)
REVERT: C  190 CYS cc_start: 0.7178 (m) cc_final: 0.6968 (m)
REVERT: C  213 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7547 (tp40)
REVERT: C  253 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7513 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 100
  average time/residue: 0.6524
  time to fit residues: 67.6485
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  449 TYR
Chi-restraints excluded: chain B residue  511 LYS
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  730 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  258 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.159751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.127431 restraints weight = 5475.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.33
r_work: 0.3315 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5696  Z= 0.099
  Angle     :  0.482   9.781   7697  Z= 0.248
  Chirality :  0.039   0.147    839
  Planarity :  0.004   0.040    975
  Dihedral  :  6.633  80.208    781
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.80 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.36 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.33), residues: 667
  helix:  2.67 (0.27), residues: 349
  sheet: -0.52 (0.68), residues: 36
  loop :  1.07 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 141 
 TYR   0.014   0.001   TYR C 246 
 PHE   0.008   0.001   PHE C 263 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.003   0.000   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 5696)
  covalent geometry    : angle       0.48173 ( 7697)
  hydrogen bonds       : bond        0.03455 (  287)
  hydrogen bonds       : angle       3.86888 (  804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2604.11 seconds
wall clock time: 44 minutes 55.03 seconds (2695.03 seconds total)