Starting phenix.real_space_refine
on Wed Sep 17 08:45:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rs6_54211/09_2025/9rs6_54211.cif"
  }
  resolution = 3.0
  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=   0.005
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      20      5.16       5
     C    4460      2.51       5
     N    1213      2.21       5
     O    1279      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6972
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3410
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 437, 3400
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 21, 'TRANS': 415}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 437, 3400
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 21, 'TRANS': 415}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3456
    Chain: "B"
      Number of atoms: 3562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3562
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 427}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 409 " occ=0.43
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 409 " occ=0.57
  Time building chain proxies: 2.41, per 1000 atoms: 0.35
  Number of scatterers: 6972
  At special positions: 0
  Unit cell: (68, 82.96, 123.76, 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      20     16.00
     O    1279      8.00
     N    1213      7.00
     C    4460      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: 0.49
  Conformation dependent library (CDL) restraints added in 460.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1634

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 7 sheets defined
      43.4% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 210 through 220
    Processing helix  chain 'A' and resid 241 through 262
      removed outlier: 4.635A  pdb=" N   SER A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   THR A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
    Processing helix  chain 'A' and resid 315 through 323
      removed outlier: 3.630A  pdb=" N   PHE A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 4.245A  pdb=" N   LEU A 341 " --> pdb=" O   GLY A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 367 through 381
      removed outlier: 3.750A  pdb=" N   SER A 381 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 421
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 3.562A  pdb=" N   ARG A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN A 513 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 529
    Processing helix  chain 'A' and resid 533 through 538
    Processing helix  chain 'A' and resid 570 through 593
    Processing helix  chain 'A' and resid 635 through 653
      removed outlier: 3.573A  pdb=" N   MET A 639 " --> pdb=" O   GLY A 635 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLU A 642 " --> pdb=" O   GLY A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 658
    Processing helix  chain 'B' and resid 25 through 28
    Processing helix  chain 'B' and resid 33 through 36
    Processing helix  chain 'B' and resid 44 through 54
      removed outlier: 4.640A  pdb=" N   GLN B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 120
      removed outlier: 4.227A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   PHE B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 211
    Processing helix  chain 'B' and resid 214 through 223
    Processing helix  chain 'B' and resid 223 through 242
    Processing helix  chain 'B' and resid 249 through 255
      removed outlier: 3.994A  pdb=" N   PHE B 255 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 275
    Processing helix  chain 'B' and resid 276 through 290
      removed outlier: 3.958A  pdb=" N   VAL B 287 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU B 288 " --> pdb=" O   GLU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 354
    Processing helix  chain 'B' and resid 553 through 555
      No H-bonds generated for 'chain 'B' and resid 553 through 555'
    Processing helix  chain 'B' and resid 556 through 569
      removed outlier: 3.557A  pdb=" N   GLU B 562 " --> pdb=" O   PRO B 558 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER B 569 " --> pdb=" O   HIS B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 580
    Processing helix  chain 'B' and resid 648 through 666
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237
      removed outlier: 3.709A  pdb=" N   ILE A 278 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU A 267 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA B 132 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   TRP B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   ASP B 150 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   LEU B  17 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 396 through 401
      removed outlier: 6.649A  pdb=" N   LEU A 391 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL A 400 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   GLY A 389 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558
      removed outlier: 3.883A  pdb=" N   VAL A 601 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 154
    Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259
      removed outlier: 5.898A  pdb=" N   ILE B 258 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   SER B 616 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 330
      removed outlier: 5.383A  pdb=" N   ALA B 328 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ARG B 300 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASP B 295 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY B 299 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 601 through 602
      removed outlier: 4.059A  pdb=" N   GLN B 601 " --> pdb=" O   SER B 739 " (cutoff:3.500A)

    370 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.70 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: 2274
        1.34 -     1.46: 1549
        1.46 -     1.58: 3270
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 7124
  Sorted by residual:
  bond pdb=" CA  ARG A 263 "
       pdb=" C   ARG A 263 "
    ideal  model  delta    sigma   weight residual
    1.522  1.536 -0.014 1.33e-02 5.65e+03 1.10e+00
  bond pdb=" CA  LYS A 540 "
       pdb=" CB  LYS A 540 "
    ideal  model  delta    sigma   weight residual
    1.529  1.545 -0.016 1.58e-02 4.01e+03 1.03e+00
  bond pdb=" CB  LYS A 540 "
       pdb=" CG  LYS A 540 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.62e-01
  bond pdb=" C   THR B 551 "
       pdb=" N   PRO B 552 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.27e-01
  bond pdb=" CB  LYS A 580 "
       pdb=" CG  LYS A 580 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.20e-01
  ... (remaining 7119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 9348
        1.62 -     3.24: 250
        3.24 -     4.86: 41
        4.86 -     6.48: 16
        6.48 -     8.11: 6
  Bond angle restraints: 9661
  Sorted by residual:
  angle pdb=" CA  LYS A 540 "
        pdb=" CB  LYS A 540 "
        pdb=" CG  LYS A 540 "
      ideal   model   delta    sigma   weight residual
     114.10  120.18   -6.08 2.00e+00 2.50e-01 9.25e+00
  angle pdb=" C   ASN A 553 "
        pdb=" N   VAL A 554 "
        pdb=" CA  VAL A 554 "
      ideal   model   delta    sigma   weight residual
     121.97  127.05   -5.08 1.80e+00 3.09e-01 7.97e+00
  angle pdb=" C   THR B 551 "
        pdb=" N   PRO B 552 "
        pdb=" CA  PRO B 552 "
      ideal   model   delta    sigma   weight residual
     119.84  116.33    3.51 1.25e+00 6.40e-01 7.88e+00
  angle pdb=" C   GLY B 317 "
        pdb=" N   LEU B 318 "
        pdb=" CA  LEU B 318 "
      ideal   model   delta    sigma   weight residual
     121.54  126.28   -4.74 1.91e+00 2.74e-01 6.16e+00
  angle pdb=" CB  MET B 348 "
        pdb=" CG  MET B 348 "
        pdb=" SD  MET B 348 "
      ideal   model   delta    sigma   weight residual
     112.70  105.45    7.25 3.00e+00 1.11e-01 5.84e+00
  ... (remaining 9656 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 3849
       17.06 -    34.12: 308
       34.12 -    51.19: 62
       51.19 -    68.25: 12
       68.25 -    85.31: 11
  Dihedral angle restraints: 4242
    sinusoidal: 1701
      harmonic: 2541
  Sorted by residual:
  dihedral pdb=" CA  VAL B 537 "
           pdb=" C   VAL B 537 "
           pdb=" N   SER B 538 "
           pdb=" CA  SER B 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.78   20.22     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  MET A 506 "
           pdb=" C   MET A 506 "
           pdb=" N   ARG A 507 "
           pdb=" CA  ARG A 507 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.58  -17.42     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  MET A 639 "
           pdb=" C   MET A 639 "
           pdb=" N   ALA A 640 "
           pdb=" CA  ALA A 640 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.94   16.06     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4239 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 768
       0.037 -    0.074: 221
       0.074 -    0.111: 79
       0.111 -    0.148: 23
       0.148 -    0.185: 6
  Chirality restraints: 1097
  Sorted by residual:
  chirality pdb=" CB  VAL A 554 "
            pdb=" CA  VAL A 554 "
            pdb=" CG1 VAL A 554 "
            pdb=" CG2 VAL A 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  ILE A 280 "
            pdb=" N   ILE A 280 "
            pdb=" C   ILE A 280 "
            pdb=" CB  ILE A 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" CA  ILE B  22 "
            pdb=" N   ILE B  22 "
            pdb=" C   ILE B  22 "
            pdb=" CB  ILE B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 1094 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 249 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO B 250 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 250 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 250 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 565 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO A 566 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 209 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A 210 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1139
        2.77 -     3.30: 6960
        3.30 -     3.83: 12152
        3.83 -     4.37: 13909
        4.37 -     4.90: 24389
  Nonbonded interactions: 58549
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 432 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OH  TYR A 225 "
            pdb=" OE1 GLN A 302 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER B 119 "
            pdb=" O   GLU B 122 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ALA A 502 "
            pdb=" OG  SER A 505 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OE2 GLU B 279 "
            pdb=" OG  SER B 578 "
     model   vdw
     2.281 3.040
  ... (remaining 58544 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 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:             6.100
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.020
  Find NCS groups from input model:        0.050
  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:7.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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   0.029   7124  Z= 0.148
  Angle     :  0.684   8.106   9661  Z= 0.352
  Chirality :  0.044   0.185   1097
  Planarity :  0.005   0.049   1225
  Dihedral  : 13.764  85.310   2608
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.81 (0.28), residues: 868
  helix:  0.66 (0.26), residues: 363
  sheet: -1.15 (0.40), residues: 165
  loop : -1.45 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 338 
 TYR   0.019   0.002   TYR A 447 
 PHE   0.016   0.002   PHE A 378 
 TRP   0.023   0.001   TRP B 695 
 HIS   0.006   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7124)
  covalent geometry    : angle       0.68369 ( 9661)
  hydrogen bonds       : bond        0.15554 (  370)
  hydrogen bonds       : angle       6.78741 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8146 (mmm160)
REVERT: A  422 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: A  595 ARG cc_start: 0.8040 (tpm170) cc_final: 0.7786 (tpm-80)
REVERT: B  125 ASP cc_start: 0.8613 (m-30) cc_final: 0.8363 (m-30)
REVERT: B  253 ASP cc_start: 0.8740 (m-30) cc_final: 0.8483 (m-30)
REVERT: B  339 LYS cc_start: 0.9195 (tppp) cc_final: 0.8881 (mmmt)
REVERT: B  496 GLU cc_start: 0.7930 (tp30) cc_final: 0.7723 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.4587
  time to fit residues: 48.0925
Evaluate side-chains
  54 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 346 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 = 0.3641 r_free = 0.3641 target = 0.098232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.079202 restraints weight = 42411.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 5.79
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7124  Z= 0.186
  Angle     :  0.651   9.899   9661  Z= 0.319
  Chirality :  0.044   0.170   1097
  Planarity :  0.005   0.055   1225
  Dihedral  :  4.201  20.227    967
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 10.24 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.28), residues: 868
  helix:  1.17 (0.27), residues: 362
  sheet: -1.44 (0.38), residues: 179
  loop : -1.18 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 263 
 TYR   0.018   0.002   TYR A 449 
 PHE   0.021   0.002   PHE A 378 
 TRP   0.015   0.001   TRP B 695 
 HIS   0.004   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7124)
  covalent geometry    : angle       0.65122 ( 9661)
  hydrogen bonds       : bond        0.04482 (  370)
  hydrogen bonds       : angle       5.52967 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8262 (mmm160)
REVERT: A  422 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7814 (mm-30)
REVERT: A  447 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7651 (t80)
REVERT: A  506 MET cc_start: 0.8586 (tpp) cc_final: 0.7833 (tpp)
REVERT: B  125 ASP cc_start: 0.8604 (m-30) cc_final: 0.8328 (m-30)
REVERT: B  253 ASP cc_start: 0.8780 (m-30) cc_final: 0.8488 (m-30)
REVERT: B  339 LYS cc_start: 0.9183 (tppp) cc_final: 0.8947 (mmmt)
REVERT: B  496 GLU cc_start: 0.8041 (tp30) cc_final: 0.7613 (tp30)
REVERT: B  600 HIS cc_start: 0.7182 (m170) cc_final: 0.6954 (m-70)
  outliers start: 17
  outliers final: 6
  residues processed: 74
  average time/residue: 0.5221
  time to fit residues: 41.1689
Evaluate side-chains
  57 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  550 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0070
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 593 HIS
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 656 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.098891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.079802 restraints weight = 41414.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 5.76
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7124  Z= 0.149
  Angle     :  0.608   9.468   9661  Z= 0.296
  Chirality :  0.043   0.153   1097
  Planarity :  0.005   0.060   1225
  Dihedral  :  4.091  20.063    967
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.77 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.36 (0.28), residues: 868
  helix:  1.28 (0.26), residues: 368
  sheet: -1.57 (0.37), residues: 181
  loop : -1.14 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 263 
 TYR   0.016   0.001   TYR A 449 
 PHE   0.018   0.002   PHE A 378 
 TRP   0.014   0.001   TRP B 698 
 HIS   0.003   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7124)
  covalent geometry    : angle       0.60807 ( 9661)
  hydrogen bonds       : bond        0.03877 (  370)
  hydrogen bonds       : angle       5.21193 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8247 (mmm160)
REVERT: A  422 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7752 (mp0)
REVERT: A  447 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7532 (t80)
REVERT: A  506 MET cc_start: 0.8627 (tpp) cc_final: 0.7665 (tpp)
REVERT: A  657 LEU cc_start: 0.8393 (mt) cc_final: 0.8169 (mp)
REVERT: B  125 ASP cc_start: 0.8622 (m-30) cc_final: 0.8361 (m-30)
REVERT: B  253 ASP cc_start: 0.8827 (m-30) cc_final: 0.8513 (m-30)
REVERT: B  496 GLU cc_start: 0.8048 (tp30) cc_final: 0.7622 (tp30)
REVERT: B  698 TRP cc_start: 0.5926 (t60) cc_final: 0.5708 (t60)
  outliers start: 17
  outliers final: 5
  residues processed: 72
  average time/residue: 0.5083
  time to fit residues: 39.1560
Evaluate side-chains
  62 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  639 MET
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  550 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 210 HIS
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 656 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.097257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.078553 restraints weight = 33608.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 5.20
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7124  Z= 0.194
  Angle     :  0.628   9.359   9661  Z= 0.306
  Chirality :  0.043   0.154   1097
  Planarity :  0.004   0.039   1225
  Dihedral  :  4.107  20.498    967
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.03 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.34 (0.28), residues: 868
  helix:  1.34 (0.26), residues: 368
  sheet: -1.68 (0.37), residues: 180
  loop : -1.10 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 531 
 TYR   0.019   0.002   TYR B 185 
 PHE   0.020   0.002   PHE A 378 
 TRP   0.017   0.001   TRP B 695 
 HIS   0.004   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 7124)
  covalent geometry    : angle       0.62798 ( 9661)
  hydrogen bonds       : bond        0.03751 (  370)
  hydrogen bonds       : angle       5.16055 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.8643 (mmm160) cc_final: 0.8237 (mmm160)
REVERT: A  422 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7796 (mp0)
REVERT: A  447 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7392 (t80)
REVERT: A  506 MET cc_start: 0.8694 (tpp) cc_final: 0.7638 (tpp)
REVERT: A  657 LEU cc_start: 0.8476 (mt) cc_final: 0.8270 (mt)
REVERT: B  125 ASP cc_start: 0.8577 (m-30) cc_final: 0.8303 (m-30)
REVERT: B  253 ASP cc_start: 0.8796 (m-30) cc_final: 0.8455 (m-30)
REVERT: B  473 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: B  496 GLU cc_start: 0.8043 (tp30) cc_final: 0.7575 (tp30)
REVERT: B  698 TRP cc_start: 0.5948 (t60) cc_final: 0.5691 (t60)
  outliers start: 20
  outliers final: 6
  residues processed: 77
  average time/residue: 0.5637
  time to fit residues: 45.9600
Evaluate side-chains
  56 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  550 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 656 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.097348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.079640 restraints weight = 26224.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 4.61
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7124  Z= 0.154
  Angle     :  0.637  10.872   9661  Z= 0.305
  Chirality :  0.043   0.200   1097
  Planarity :  0.005   0.066   1225
  Dihedral  :  4.104  20.624    967
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.16 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.29), residues: 868
  helix:  1.45 (0.27), residues: 368
  sheet: -1.68 (0.37), residues: 179
  loop : -1.11 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 263 
 TYR   0.023   0.002   TYR B 185 
 PHE   0.017   0.002   PHE A 378 
 TRP   0.017   0.001   TRP B 695 
 HIS   0.002   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7124)
  covalent geometry    : angle       0.63653 ( 9661)
  hydrogen bonds       : bond        0.03632 (  370)
  hydrogen bonds       : angle       5.05995 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8793 (pm20)
REVERT: A  293 ARG cc_start: 0.8595 (mmm160) cc_final: 0.8188 (mmm160)
REVERT: A  338 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8379 (p)
REVERT: A  422 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7802 (mp0)
REVERT: A  447 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7438 (t80)
REVERT: A  506 MET cc_start: 0.8712 (tpp) cc_final: 0.7626 (tpp)
REVERT: A  595 ARG cc_start: 0.7836 (tpm170) cc_final: 0.7355 (tpm-80)
REVERT: A  657 LEU cc_start: 0.8457 (mt) cc_final: 0.8246 (mt)
REVERT: B   38 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8267 (pp)
REVERT: B  125 ASP cc_start: 0.8522 (m-30) cc_final: 0.8243 (m-30)
REVERT: B  253 ASP cc_start: 0.8744 (m-30) cc_final: 0.8380 (m-30)
REVERT: B  339 LYS cc_start: 0.9196 (tppp) cc_final: 0.8950 (mmmt)
REVERT: B  496 GLU cc_start: 0.8037 (tp30) cc_final: 0.7569 (tp30)
REVERT: B  698 TRP cc_start: 0.5944 (t60) cc_final: 0.5452 (t60)
  outliers start: 25
  outliers final: 6
  residues processed: 77
  average time/residue: 0.4820
  time to fit residues: 39.7355
Evaluate side-chains
  60 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  550 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.096794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.077460 restraints weight = 41231.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 5.73
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7124  Z= 0.181
  Angle     :  0.642  11.095   9661  Z= 0.308
  Chirality :  0.043   0.166   1097
  Planarity :  0.004   0.038   1225
  Dihedral  :  4.095  20.960    967
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.96 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.29), residues: 868
  helix:  1.48 (0.27), residues: 367
  sheet: -1.70 (0.37), residues: 178
  loop : -1.10 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 578 
 TYR   0.026   0.002   TYR B 185 
 PHE   0.019   0.002   PHE A 258 
 TRP   0.021   0.001   TRP B 695 
 HIS   0.003   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7124)
  covalent geometry    : angle       0.64238 ( 9661)
  hydrogen bonds       : bond        0.03664 (  370)
  hydrogen bonds       : angle       5.05060 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (pm20)
REVERT: A  293 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8223 (mmm160)
REVERT: A  338 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (p)
REVERT: A  422 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7802 (mp0)
REVERT: A  447 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7371 (t80)
REVERT: A  506 MET cc_start: 0.8714 (tpp) cc_final: 0.7667 (tpp)
REVERT: A  657 LEU cc_start: 0.8504 (mt) cc_final: 0.8290 (mt)
REVERT: B  125 ASP cc_start: 0.8532 (m-30) cc_final: 0.8234 (m-30)
REVERT: B  339 LYS cc_start: 0.9235 (tppp) cc_final: 0.8862 (mmmm)
REVERT: B  496 GLU cc_start: 0.8008 (tp30) cc_final: 0.7508 (tp30)
REVERT: B  600 HIS cc_start: 0.7313 (m170) cc_final: 0.7075 (m-70)
  outliers start: 21
  outliers final: 9
  residues processed: 71
  average time/residue: 0.4745
  time to fit residues: 36.0176
Evaluate side-chains
  62 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   99 HIS
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0970
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.096790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.077563 restraints weight = 41374.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 5.73
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7124  Z= 0.167
  Angle     :  0.637  11.203   9661  Z= 0.303
  Chirality :  0.043   0.149   1097
  Planarity :  0.005   0.071   1225
  Dihedral  :  4.076  21.089    967
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.09 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.29), residues: 868
  helix:  1.53 (0.27), residues: 368
  sheet: -1.73 (0.37), residues: 179
  loop : -1.06 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 263 
 TYR   0.023   0.002   TYR B 185 
 PHE   0.017   0.002   PHE A 378 
 TRP   0.021   0.001   TRP B 695 
 HIS   0.002   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7124)
  covalent geometry    : angle       0.63689 ( 9661)
  hydrogen bonds       : bond        0.03612 (  370)
  hydrogen bonds       : angle       5.00739 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8819 (pm20)
REVERT: A  293 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8211 (mmm160)
REVERT: A  338 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8353 (p)
REVERT: A  422 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7758 (mp0)
REVERT: A  447 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7267 (t80)
REVERT: A  506 MET cc_start: 0.8712 (tpp) cc_final: 0.7635 (tpp)
REVERT: A  657 LEU cc_start: 0.8525 (mt) cc_final: 0.8310 (mt)
REVERT: B   38 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8306 (pp)
REVERT: B  125 ASP cc_start: 0.8546 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  339 LYS cc_start: 0.9228 (tppp) cc_final: 0.8887 (mmmm)
REVERT: B  496 GLU cc_start: 0.8016 (tp30) cc_final: 0.7605 (tp30)
REVERT: B  600 HIS cc_start: 0.7285 (m170) cc_final: 0.6965 (m-70)
REVERT: B  698 TRP cc_start: 0.6016 (t60) cc_final: 0.5711 (t60)
  outliers start: 20
  outliers final: 7
  residues processed: 68
  average time/residue: 0.4921
  time to fit residues: 35.6327
Evaluate side-chains
  60 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.097417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.079134 restraints weight = 28617.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 4.85
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7124  Z= 0.157
  Angle     :  0.638  12.173   9661  Z= 0.303
  Chirality :  0.043   0.173   1097
  Planarity :  0.004   0.062   1225
  Dihedral  :  4.051  21.074    967
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.15 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.20 (0.29), residues: 868
  helix:  1.53 (0.27), residues: 368
  sheet: -1.71 (0.37), residues: 179
  loop : -1.05 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 263 
 TYR   0.022   0.002   TYR B 185 
 PHE   0.016   0.002   PHE A 378 
 TRP   0.022   0.001   TRP B 695 
 HIS   0.003   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7124)
  covalent geometry    : angle       0.63787 ( 9661)
  hydrogen bonds       : bond        0.03578 (  370)
  hydrogen bonds       : angle       5.01364 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8797 (pm20)
REVERT: A  293 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8172 (mmm160)
REVERT: A  338 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8371 (p)
REVERT: A  422 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7780 (mp0)
REVERT: A  447 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7230 (t80)
REVERT: A  506 MET cc_start: 0.8719 (tpp) cc_final: 0.7601 (tpp)
REVERT: A  595 ARG cc_start: 0.7844 (tpm170) cc_final: 0.7350 (tpm-80)
REVERT: A  657 LEU cc_start: 0.8510 (mt) cc_final: 0.8300 (mt)
REVERT: B   38 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8301 (pp)
REVERT: B  125 ASP cc_start: 0.8536 (m-30) cc_final: 0.8254 (m-30)
REVERT: B  339 LYS cc_start: 0.9219 (tppp) cc_final: 0.8878 (mmmm)
REVERT: B  496 GLU cc_start: 0.8024 (tp30) cc_final: 0.7525 (tp30)
REVERT: B  600 HIS cc_start: 0.7239 (m170) cc_final: 0.6954 (m-70)
REVERT: B  698 TRP cc_start: 0.5996 (t60) cc_final: 0.5686 (t60)
  outliers start: 17
  outliers final: 7
  residues processed: 69
  average time/residue: 0.4844
  time to fit residues: 35.7411
Evaluate side-chains
  64 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.097071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.079159 restraints weight = 26837.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 4.67
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7124  Z= 0.156
  Angle     :  0.641  12.222   9661  Z= 0.305
  Chirality :  0.043   0.163   1097
  Planarity :  0.004   0.066   1225
  Dihedral  :  4.047  21.060    967
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.42 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.25 (0.29), residues: 868
  helix:  1.48 (0.27), residues: 370
  sheet: -1.74 (0.37), residues: 179
  loop : -1.08 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 263 
 TYR   0.024   0.002   TYR B 185 
 PHE   0.015   0.002   PHE A 378 
 TRP   0.026   0.002   TRP B 695 
 HIS   0.003   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7124)
  covalent geometry    : angle       0.64144 ( 9661)
  hydrogen bonds       : bond        0.03561 (  370)
  hydrogen bonds       : angle       4.98724 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8790 (pm20)
REVERT: A  293 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8163 (mmm160)
REVERT: A  338 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8366 (p)
REVERT: A  422 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7784 (mp0)
REVERT: A  447 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7213 (t80)
REVERT: A  506 MET cc_start: 0.8723 (tpp) cc_final: 0.7592 (tpp)
REVERT: A  595 ARG cc_start: 0.7819 (tpm170) cc_final: 0.7313 (tpm-80)
REVERT: A  657 LEU cc_start: 0.8510 (mt) cc_final: 0.8306 (mt)
REVERT: B   38 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8303 (pp)
REVERT: B  125 ASP cc_start: 0.8531 (m-30) cc_final: 0.8251 (m-30)
REVERT: B  339 LYS cc_start: 0.9201 (tppp) cc_final: 0.8854 (mmmm)
REVERT: B  496 GLU cc_start: 0.8027 (tp30) cc_final: 0.7527 (tp30)
REVERT: B  600 HIS cc_start: 0.7209 (m170) cc_final: 0.6933 (m-70)
REVERT: B  695 TRP cc_start: 0.4946 (m100) cc_final: 0.4670 (m100)
REVERT: B  698 TRP cc_start: 0.6037 (t60) cc_final: 0.5423 (t60)
  outliers start: 18
  outliers final: 8
  residues processed: 67
  average time/residue: 0.5360
  time to fit residues: 38.2626
Evaluate side-chains
  65 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
** B 346 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 = 0.3645 r_free = 0.3645 target = 0.098997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.079690 restraints weight = 41625.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 5.84
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3307
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7124  Z= 0.125
  Angle     :  0.637  14.557   9661  Z= 0.301
  Chirality :  0.042   0.148   1097
  Planarity :  0.004   0.068   1225
  Dihedral  :  3.982  20.775    967
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.22 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.24 (0.29), residues: 868
  helix:  1.47 (0.27), residues: 369
  sheet: -1.70 (0.37), residues: 179
  loop : -1.08 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 263 
 TYR   0.024   0.002   TYR A 585 
 PHE   0.013   0.002   PHE A 378 
 TRP   0.026   0.001   TRP B 694 
 HIS   0.003   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7124)
  covalent geometry    : angle       0.63736 ( 9661)
  hydrogen bonds       : bond        0.03501 (  370)
  hydrogen bonds       : angle       4.92404 ( 1053)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8840 (pm20)
REVERT: A  293 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8156 (mmm160)
REVERT: A  338 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8327 (p)
REVERT: A  422 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7775 (mp0)
REVERT: A  447 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7256 (t80)
REVERT: A  506 MET cc_start: 0.8699 (tpp) cc_final: 0.7580 (tpp)
REVERT: A  595 ARG cc_start: 0.7800 (tpm170) cc_final: 0.7282 (tpm-80)
REVERT: A  657 LEU cc_start: 0.8470 (mt) cc_final: 0.8260 (mt)
REVERT: B   38 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8270 (pp)
REVERT: B  125 ASP cc_start: 0.8540 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  339 LYS cc_start: 0.9215 (tppp) cc_final: 0.8869 (mmmm)
REVERT: B  496 GLU cc_start: 0.8047 (tp30) cc_final: 0.7627 (tp30)
REVERT: B  600 HIS cc_start: 0.7212 (m170) cc_final: 0.6950 (m-70)
REVERT: B  695 TRP cc_start: 0.4861 (m100) cc_final: 0.4609 (m100)
REVERT: B  698 TRP cc_start: 0.6060 (t60) cc_final: 0.5511 (t60)
  outliers start: 12
  outliers final: 5
  residues processed: 69
  average time/residue: 0.5806
  time to fit residues: 42.6944
Evaluate side-chains
  63 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  447 TYR
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0270
   chunk 56 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** B 346 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 = 0.3636 r_free = 0.3636 target = 0.098361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.079852 restraints weight = 33817.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 5.23
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7124  Z= 0.142
  Angle     :  0.637  14.242   9661  Z= 0.302
  Chirality :  0.042   0.166   1097
  Planarity :  0.004   0.070   1225
  Dihedral  :  3.971  20.600    967
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.75 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.22 (0.29), residues: 868
  helix:  1.50 (0.27), residues: 368
  sheet: -1.67 (0.37), residues: 179
  loop : -1.08 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 263 
 TYR   0.026   0.002   TYR A 585 
 PHE   0.015   0.002   PHE A 378 
 TRP   0.026   0.002   TRP B 694 
 HIS   0.003   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7124)
  covalent geometry    : angle       0.63733 ( 9661)
  hydrogen bonds       : bond        0.03486 (  370)
  hydrogen bonds       : angle       4.89432 ( 1053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1941.24 seconds
wall clock time: 34 minutes 8.48 seconds (2048.48 seconds total)