Starting phenix.real_space_refine
on Sat May  2 13:12:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qkt_53221/05_2026/9qkt_53221.map"
  }
  resolution = 2.4
  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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      33      5.16       5
     C    3575      2.51       5
     N     958      2.21       5
     O    1081      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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5649
  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: "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: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2629
          Classifications: {'peptide': 327}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 304}
          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: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'NK3': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "C"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 35
          Classifications: {'water': 35}
          Link IDs: {None: 34}
  Time building chain proxies: 1.63, per 1000 atoms: 0.29
  Number of scatterers: 5649
  At special positions: 0
  Unit cell: (78.54, 93.84, 81.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P       2     15.00
     O    1081      8.00
     N     958      7.00
     C    3575      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: 0.60
  Conformation dependent library (CDL) restraints added in 380.5 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:
      33 helices and 3 sheets defined
      58.3% alpha, 5.3% 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
      removed outlier: 3.619A  pdb=" N   VAL A 102 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
    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: 4.142A  pdb=" N   LYS A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 173
      removed outlier: 4.035A  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 'C' and resid 70 through 92
    Processing helix  chain 'C' and resid 95 through 112
      removed outlier: 3.593A  pdb=" N   MET C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
      removed outlier: 4.326A  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: 3.647A  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: 3.501A  pdb=" N   GLY C 267 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 285
      removed outlier: 3.911A  pdb=" N   LEU C 283 " --> pdb=" O   LYS C 279 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   TYR C 284 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 302
    Processing helix  chain 'B' and resid 479 through 492
    Processing helix  chain 'B' and resid 523 through 529
    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 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 668 through 674
    Processing helix  chain 'B' and resid 683 through 689
      removed outlier: 4.168A  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: 3.710A  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 sheet with id=AA1, first strand: chain 'B' and resid 433 through 434
      removed outlier: 6.749A  pdb=" N   ARG B 433 " --> pdb=" O   VAL B 505 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   VAL B 500 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASN B 517 " --> pdb=" O   VAL B 500 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU B 502 " --> pdb=" O   VAL B 515 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 451 " --> pdb=" O   ARG B 468 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL B 452 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   LYS B 456 " --> pdb=" O   CYS B 440 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   CYS B 440 " --> pdb=" O   LYS B 456 " (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

    282 hydrogen bonds defined for protein.
    795 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: 0.84

  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:
        1.18 -     1.31: 908
        1.31 -     1.44: 1448
        1.44 -     1.56: 3283
        1.56 -     1.69: 4
        1.69 -     1.82: 55
  Bond restraints: 5698
  Sorted by residual:
  bond pdb=" C09 NK3 B 801 "
       pdb=" C11 NK3 B 801 "
    ideal  model  delta    sigma   weight residual
    1.434  1.506 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C07 NK3 B 801 "
       pdb=" N08 NK3 B 801 "
    ideal  model  delta    sigma   weight residual
    1.420  1.474 -0.054 2.00e-02 2.50e+03 7.37e+00
  bond pdb=" C09 NK3 B 801 "
       pdb=" O10 NK3 B 801 "
    ideal  model  delta    sigma   weight residual
    1.238  1.184  0.054 2.00e-02 2.50e+03 7.20e+00
  bond pdb=" C27 NK3 B 801 "
       pdb=" N25 NK3 B 801 "
    ideal  model  delta    sigma   weight residual
    1.497  1.451  0.046 2.00e-02 2.50e+03 5.23e+00
  bond pdb=" C01 NK3 B 801 "
       pdb=" C02 NK3 B 801 "
    ideal  model  delta    sigma   weight residual
    1.492  1.536 -0.044 2.00e-02 2.50e+03 4.88e+00
  ... (remaining 5693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 7587
        1.76 -     3.52: 86
        3.52 -     5.28: 18
        5.28 -     7.04: 3
        7.04 -     8.81: 2
  Bond angle restraints: 7696
  Sorted by residual:
  angle pdb=" C09 NK3 B 801 "
        pdb=" C11 NK3 B 801 "
        pdb=" S15 NK3 B 801 "
      ideal   model   delta    sigma   weight residual
     123.31  132.12   -8.81 3.00e+00 1.11e-01 8.62e+00
  angle pdb=" CB  MET B 621 "
        pdb=" CG  MET B 621 "
        pdb=" SD  MET B 621 "
      ideal   model   delta    sigma   weight residual
     112.70  120.85   -8.15 3.00e+00 1.11e-01 7.37e+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  116.98   -4.38 1.70e+00 3.46e-01 6.64e+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  119.05   -4.95 2.00e+00 2.50e-01 6.14e+00
  angle pdb=" CA  TYR C 246 "
        pdb=" CB  TYR C 246 "
        pdb=" CG  TYR C 246 "
      ideal   model   delta    sigma   weight residual
     113.90  118.27   -4.37 1.80e+00 3.09e-01 5.89e+00
  ... (remaining 7691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 2937
       17.60 -    35.21: 397
       35.21 -    52.81: 115
       52.81 -    70.41: 32
       70.41 -    88.01: 11
  Dihedral angle restraints: 3492
    sinusoidal: 1500
      harmonic: 1992
  Sorted by residual:
  dihedral pdb=" CA  HIS B 521 "
           pdb=" C   HIS B 521 "
           pdb=" N   ASP B 522 "
           pdb=" CA  ASP B 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.44   16.56     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASP A 184 "
           pdb=" CB  ASP A 184 "
           pdb=" CG  ASP A 184 "
           pdb=" OD1 ASP A 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.13   55.13     1      2.00e+01 2.50e-03 1.03e+01
  dihedral pdb=" CA  TYR B 453 "
           pdb=" C   TYR B 453 "
           pdb=" N   ARG B 454 "
           pdb=" CA  ARG B 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 530
       0.029 -    0.059: 200
       0.059 -    0.088: 67
       0.088 -    0.117: 32
       0.117 -    0.146: 7
  Chirality restraints: 836
  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    2.58   -0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  PRO C 196 "
            pdb=" N   PRO C 196 "
            pdb=" C   PRO C 196 "
            pdb=" CB  PRO C 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE B 503 "
            pdb=" N   ILE B 503 "
            pdb=" C   ILE B 503 "
            pdb=" CB  ILE B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 833 not shown)

  Planarity restraints: 979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 494 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO B 495 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 495 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 495 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 436 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" CD  GLU B 436 "   -0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 436 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 436 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 246 "   -0.014 2.00e-02 2.50e+03   8.60e-03 1.48e+00
        pdb=" CG  TYR C 246 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 246 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 246 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 246 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 976 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 256
        2.72 -     3.27: 5547
        3.27 -     3.81: 9805
        3.81 -     4.36: 11973
        4.36 -     4.90: 19944
  Nonbonded interactions: 47525
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 449 "
            pdb=" O   PRO B 755 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" N   GLN B 532 "
            pdb=" OE1 GLN B 532 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" N   GLU C 271 "
            pdb=" OE1 GLU C 271 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   ARG B 484 "
            pdb=" OG1 THR B 488 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ALA B 584 "
            pdb=" O   HOH B 901 "
     model   vdw
     2.296 3.040
  ... (remaining 47520 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:             0.530
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.710
  Find NCS groups from input model:        0.020
  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:9.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
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   0.072   5698  Z= 0.153
  Angle     :  0.504   8.806   7696  Z= 0.244
  Chirality :  0.038   0.146    836
  Planarity :  0.004   0.047    979
  Dihedral  : 18.304  88.014   2202
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.20 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.87 %
    Favored  : 76.85 %
  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:  2.64 (0.33), residues: 667
  helix:  2.66 (0.28), residues: 344
  sheet:  0.03 (1.14), residues: 26
  loop :  0.96 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 259 
 TYR   0.020   0.001   TYR C 246 
 PHE   0.009   0.001   PHE C 106 
 TRP   0.006   0.001   TRP C 220 
 HIS   0.003   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5698)
  covalent geometry    : angle       0.50421 ( 7696)
  hydrogen bonds       : bond        0.14164 (  282)
  hydrogen bonds       : angle       4.93895 (  795)

*********************** 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
  103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  112 MET cc_start: 0.4609 (ptt) cc_final: 0.4385 (ptt)
REVERT: A  136 GLN cc_start: 0.6813 (tm-30) cc_final: 0.6605 (tp40)
REVERT: A  148 ASP cc_start: 0.7442 (t0) cc_final: 0.7160 (t70)
REVERT: A  151 TYR cc_start: 0.7494 (t80) cc_final: 0.7293 (t80)
REVERT: A  154 GLN cc_start: 0.7736 (mt0) cc_final: 0.7532 (mp10)
REVERT: A  192 SER cc_start: 0.7476 (OUTLIER) cc_final: 0.6929 (p)
REVERT: A  210 LYS cc_start: 0.5766 (OUTLIER) cc_final: 0.5258 (tttp)
REVERT: C   76 ASP cc_start: 0.6915 (t0) cc_final: 0.5795 (m-30)
REVERT: C  152 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7579 (ttt90)
REVERT: C  158 LYS cc_start: 0.7387 (mttm) cc_final: 0.7183 (mttt)
REVERT: C  159 LYS cc_start: 0.7706 (tttt) cc_final: 0.7335 (tttp)
REVERT: C  186 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (mm-30)
REVERT: C  211 ARG cc_start: 0.7207 (mmp80) cc_final: 0.6893 (mmp80)
REVERT: C  274 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7215 (mm-40)
REVERT: B  437 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7532 (mm-30)
REVERT: B  483 LEU cc_start: 0.7911 (mt) cc_final: 0.7478 (tp)
REVERT: B  512 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: B  643 GLU cc_start: 0.6833 (mp0) cc_final: 0.6257 (tt0)
REVERT: B  661 ILE cc_start: 0.7848 (pt) cc_final: 0.7632 (pt)
  outliers start: 20
  outliers final: 10
  residues processed: 98
  average time/residue: 0.7728
  time to fit residues: 78.2657
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  512 ILE
Chi-restraints excluded: chain B residue  565 THR
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  616 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.3764

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
A 150 ASN
C 103 GLN
C 107 GLN
C 129 HIS
C 205 GLN
C 282 GLN
B 493 GLN
B 567 ASN
B 646 GLN
B 648 ASN
B 682 ASN
B 695 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.108795 restraints weight = 6010.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.63
r_work: 0.3016 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5698  Z= 0.163
  Angle     :  0.538   4.794   7696  Z= 0.286
  Chirality :  0.042   0.173    836
  Planarity :  0.005   0.044    979
  Dihedral  :  7.778  68.942    785
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.06 %
    Favored  : 78.98 %
  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:  2.21 (0.33), residues: 667
  helix:  2.22 (0.28), residues: 352
  sheet: -0.48 (0.93), residues: 34
  loop :  0.89 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 259 
 TYR   0.023   0.002   TYR A 151 
 PHE   0.010   0.002   PHE C 106 
 TRP   0.005   0.001   TRP C 220 
 HIS   0.005   0.001   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 5698)
  covalent geometry    : angle       0.53751 ( 7696)
  hydrogen bonds       : bond        0.05386 (  282)
  hydrogen bonds       : angle       4.21806 (  795)

*********************** 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
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5111 (ptt) cc_final: 0.4838 (ptt)
REVERT: A  113 SER cc_start: 0.4579 (OUTLIER) cc_final: 0.3759 (m)
REVERT: A  192 SER cc_start: 0.8112 (p) cc_final: 0.7795 (p)
REVERT: C   76 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6590 (m-30)
REVERT: C  155 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7069 (ttp-110)
REVERT: C  158 LYS cc_start: 0.7770 (mttm) cc_final: 0.7543 (mttt)
REVERT: C  159 LYS cc_start: 0.7938 (tttt) cc_final: 0.7637 (tttp)
REVERT: C  211 ARG cc_start: 0.7315 (mmp80) cc_final: 0.7110 (mmp80)
REVERT: C  270 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7453 (tp30)
REVERT: B  443 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7486 (ttp80)
REVERT: B  572 HIS cc_start: 0.7664 (m-70) cc_final: 0.7425 (m-70)
REVERT: B  726 THR cc_start: 0.8260 (t) cc_final: 0.8040 (m)
  outliers start: 18
  outliers final: 6
  residues processed: 87
  average time/residue: 0.7882
  time to fit residues: 70.8693
Evaluate side-chains
  82 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  715 GLU
Chi-restraints excluded: chain B residue  751 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 35 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 282 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.143612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.112652 restraints weight = 5937.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.61
r_work: 0.3115 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5698  Z= 0.093
  Angle     :  0.442   4.445   7696  Z= 0.235
  Chirality :  0.039   0.145    836
  Planarity :  0.004   0.046    979
  Dihedral  :  6.131  67.962    764
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.91 %
    Favored  : 79.80 %
  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:  2.45 (0.33), residues: 667
  helix:  2.54 (0.28), residues: 347
  sheet: -0.45 (0.94), residues: 34
  loop :  0.88 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.018   0.001   TYR C 246 
 PHE   0.009   0.001   PHE C 106 
 TRP   0.005   0.001   TRP C 220 
 HIS   0.003   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 5698)
  covalent geometry    : angle       0.44190 ( 7696)
  hydrogen bonds       : bond        0.03819 (  282)
  hydrogen bonds       : angle       3.92827 (  795)

*********************** 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
  93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5500 (ptt) cc_final: 0.5224 (ptt)
REVERT: A  137 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (mttt)
REVERT: A  158 GLU cc_start: 0.8057 (mp0) cc_final: 0.7845 (mp0)
REVERT: A  192 SER cc_start: 0.8061 (p) cc_final: 0.7687 (p)
REVERT: C   76 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6723 (m-30)
REVERT: C  155 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7212 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7935 (tttt) cc_final: 0.7630 (tttp)
REVERT: C  211 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6865 (mmp80)
REVERT: C  258 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6822 (m110)
REVERT: C  270 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7695 (tp30)
REVERT: B  443 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7453 (ttp80)
REVERT: B  471 MET cc_start: 0.7725 (mtp) cc_final: 0.7465 (mtp)
REVERT: B  512 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (mp)
REVERT: B  572 HIS cc_start: 0.7579 (m-70) cc_final: 0.7364 (m-70)
REVERT: B  726 THR cc_start: 0.8241 (t) cc_final: 0.8036 (m)
  outliers start: 20
  outliers final: 11
  residues processed: 85
  average time/residue: 0.7706
  time to fit residues: 67.7704
Evaluate side-chains
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  192 HIS
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  512 ILE
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  715 GLU
Chi-restraints excluded: chain B residue  751 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 258 ASN
C 282 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.142471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110839 restraints weight = 6001.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.66
r_work: 0.3094 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5698  Z= 0.114
  Angle     :  0.463   5.058   7696  Z= 0.246
  Chirality :  0.040   0.152    836
  Planarity :  0.004   0.045    979
  Dihedral  :  5.633  68.183    760
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.75 %
    Favored  : 80.13 %
  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:  2.40 (0.33), residues: 667
  helix:  2.49 (0.28), residues: 347
  sheet: -0.51 (0.94), residues: 34
  loop :  0.85 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.020   0.002   TYR C 246 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.006   0.001   TRP C 220 
 HIS   0.003   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5698)
  covalent geometry    : angle       0.46296 ( 7696)
  hydrogen bonds       : bond        0.04214 (  282)
  hydrogen bonds       : angle       3.93433 (  795)

*********************** 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
  92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5423 (ptt) cc_final: 0.5212 (ptt)
REVERT: A  137 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (mttt)
REVERT: C   76 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6706 (m-30)
REVERT: C  155 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7243 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7918 (tttt) cc_final: 0.7620 (tttp)
REVERT: C  186 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7789 (mm-30)
REVERT: C  211 ARG cc_start: 0.7266 (mtp85) cc_final: 0.6960 (mmp80)
REVERT: C  258 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6910 (m-40)
REVERT: C  270 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7668 (tp30)
REVERT: B  443 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7471 (ttp80)
REVERT: B  471 MET cc_start: 0.7755 (mtp) cc_final: 0.7499 (mtp)
REVERT: B  572 HIS cc_start: 0.7620 (m-70) cc_final: 0.7374 (m-70)
REVERT: B  726 THR cc_start: 0.8265 (t) cc_final: 0.8055 (m)
  outliers start: 19
  outliers final: 10
  residues processed: 84
  average time/residue: 0.8103
  time to fit residues: 70.2830
Evaluate side-chains
  89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  715 GLU
Chi-restraints excluded: chain B residue  751 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0870
   chunk 50 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 282 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111973 restraints weight = 6064.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.69
r_work: 0.3080 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5698  Z= 0.102
  Angle     :  0.453   5.159   7696  Z= 0.240
  Chirality :  0.039   0.142    836
  Planarity :  0.004   0.045    979
  Dihedral  :  5.441  67.945    760
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.91 %
    Favored  : 80.30 %
  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:  2.42 (0.33), residues: 667
  helix:  2.51 (0.28), residues: 347
  sheet: -0.46 (0.95), residues: 34
  loop :  0.86 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 259 
 TYR   0.019   0.001   TYR C 246 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.006   0.001   TRP C 220 
 HIS   0.002   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5698)
  covalent geometry    : angle       0.45298 ( 7696)
  hydrogen bonds       : bond        0.03930 (  282)
  hydrogen bonds       : angle       3.88380 (  795)

*********************** 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
  93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5345 (ptt) cc_final: 0.5105 (ptt)
REVERT: A  137 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7822 (mttt)
REVERT: C   76 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6682 (m-30)
REVERT: C  155 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7233 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7909 (tttt) cc_final: 0.7602 (tttp)
REVERT: C  186 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7817 (mm-30)
REVERT: C  211 ARG cc_start: 0.7312 (mtp85) cc_final: 0.6997 (mmp80)
REVERT: C  258 ASN cc_start: 0.7519 (m110) cc_final: 0.7229 (m-40)
REVERT: C  259 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6949 (ptp-110)
REVERT: C  270 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7672 (tp30)
REVERT: B  443 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7376 (ttp80)
REVERT: B  471 MET cc_start: 0.7737 (mtp) cc_final: 0.7487 (mtp)
REVERT: B  572 HIS cc_start: 0.7628 (m-70) cc_final: 0.7388 (m-70)
REVERT: B  726 THR cc_start: 0.8255 (t) cc_final: 0.8047 (m)
  outliers start: 17
  outliers final: 9
  residues processed: 85
  average time/residue: 0.7838
  time to fit residues: 68.7746
Evaluate side-chains
  87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  259 ARG
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  715 GLU
Chi-restraints excluded: chain B residue  751 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 149 HIS
C 192 HIS
C 282 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.140771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.108142 restraints weight = 5921.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.65
r_work: 0.3055 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5698  Z= 0.194
  Angle     :  0.562   6.128   7696  Z= 0.299
  Chirality :  0.044   0.173    836
  Planarity :  0.005   0.046    979
  Dihedral  :  5.555  69.263    760
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.91 %
    Favored  : 80.13 %
  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:  1.99 (0.33), residues: 667
  helix:  2.02 (0.27), residues: 352
  sheet: -0.58 (0.93), residues: 34
  loop :  0.82 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 152 
 TYR   0.023   0.002   TYR C 246 
 PHE   0.011   0.002   PHE C 263 
 TRP   0.006   0.002   TRP C 220 
 HIS   0.005   0.001   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 5698)
  covalent geometry    : angle       0.56236 ( 7696)
  hydrogen bonds       : bond        0.05572 (  282)
  hydrogen bonds       : angle       4.20511 (  795)

*********************** 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
  91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  137 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7863 (mttt)
REVERT: A  154 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7852 (mt0)
REVERT: A  192 SER cc_start: 0.8183 (p) cc_final: 0.7790 (p)
REVERT: C   76 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: C  155 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7206 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7884 (tttt) cc_final: 0.7571 (tttp)
REVERT: C  211 ARG cc_start: 0.7325 (mtp85) cc_final: 0.7027 (mmp80)
REVERT: C  259 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7148 (ptp-110)
REVERT: C  270 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7724 (tp30)
REVERT: B  443 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7508 (ttp80)
REVERT: B  531 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6285 (mptp)
REVERT: B  726 THR cc_start: 0.8349 (t) cc_final: 0.8095 (m)
  outliers start: 18
  outliers final: 8
  residues processed: 85
  average time/residue: 0.7760
  time to fit residues: 68.1110
Evaluate side-chains
  90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  259 ARG
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  531 LYS
Chi-restraints excluded: chain B residue  715 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 50 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 282 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111941 restraints weight = 6109.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.70
r_work: 0.3063 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5698  Z= 0.112
  Angle     :  0.470   5.823   7696  Z= 0.250
  Chirality :  0.040   0.147    836
  Planarity :  0.004   0.046    979
  Dihedral  :  5.361  68.741    760
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.24 %
    Favored  : 79.97 %
  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:  2.26 (0.33), residues: 667
  helix:  2.34 (0.28), residues: 347
  sheet: -0.47 (0.94), residues: 34
  loop :  0.83 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.022   0.002   TYR A 151 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.003   0.001   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5698)
  covalent geometry    : angle       0.47017 ( 7696)
  hydrogen bonds       : bond        0.04173 (  282)
  hydrogen bonds       : angle       3.98668 (  795)

*********************** 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
  89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  137 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7894 (mttt)
REVERT: A  154 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7403 (mp10)
REVERT: C   76 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6661 (m-30)
REVERT: C  155 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7150 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7857 (tttt) cc_final: 0.7541 (tttp)
REVERT: C  211 ARG cc_start: 0.7347 (mtp85) cc_final: 0.7118 (mmp80)
REVERT: C  259 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7094 (ptp-110)
REVERT: C  270 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7569 (tp30)
REVERT: B  443 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7486 (ttp80)
REVERT: B  471 MET cc_start: 0.7763 (mtp) cc_final: 0.7444 (mtp)
REVERT: B  531 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6262 (mptp)
REVERT: B  726 THR cc_start: 0.8342 (t) cc_final: 0.8105 (m)
  outliers start: 17
  outliers final: 7
  residues processed: 82
  average time/residue: 0.8173
  time to fit residues: 69.2315
Evaluate side-chains
  87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  259 ARG
Chi-restraints excluded: chain C residue  270 GLU
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  531 LYS
Chi-restraints excluded: chain B residue  715 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 205 GLN
C 282 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.114881 restraints weight = 5990.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.60
r_work: 0.3114 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5698  Z= 0.095
  Angle     :  0.454   7.240   7696  Z= 0.239
  Chirality :  0.039   0.142    836
  Planarity :  0.004   0.045    979
  Dihedral  :  5.167  68.166    760
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.65 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.57 %
    Favored  : 80.13 %
  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:  2.43 (0.33), residues: 667
  helix:  2.51 (0.28), residues: 346
  sheet: -0.43 (0.96), residues: 34
  loop :  0.88 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.019   0.001   TYR C 246 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.003   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 5698)
  covalent geometry    : angle       0.45394 ( 7696)
  hydrogen bonds       : bond        0.03716 (  282)
  hydrogen bonds       : angle       3.86853 (  795)

*********************** 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
  87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  137 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7878 (mttt)
REVERT: A  154 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7382 (mp10)
REVERT: A  155 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6744 (mmm160)
REVERT: C   76 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6623 (m-30)
REVERT: C  155 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7095 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7849 (tttt) cc_final: 0.7536 (tttp)
REVERT: C  186 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7829 (mm-30)
REVERT: C  211 ARG cc_start: 0.7313 (mtp85) cc_final: 0.7087 (mmp80)
REVERT: C  259 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7214 (ptp-110)
REVERT: B  443 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7402 (ttp80)
REVERT: B  471 MET cc_start: 0.7694 (mtp) cc_final: 0.7366 (mtp)
REVERT: B  726 THR cc_start: 0.8311 (t) cc_final: 0.8084 (m)
  outliers start: 14
  outliers final: 7
  residues processed: 80
  average time/residue: 0.8429
  time to fit residues: 69.5825
Evaluate side-chains
  89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  259 ARG
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  616 SER
Chi-restraints excluded: chain B residue  715 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0040
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0370
   chunk 47 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.5674

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
C 192 HIS
C 205 GLN
C 282 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.112505 restraints weight = 6028.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.63
r_work: 0.3084 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5698  Z= 0.122
  Angle     :  0.484   7.193   7696  Z= 0.255
  Chirality :  0.040   0.154    836
  Planarity :  0.004   0.046    979
  Dihedral  :  5.238  68.693    760
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.23 %
    Favored  : 79.47 %
  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:  2.31 (0.33), residues: 667
  helix:  2.29 (0.28), residues: 352
  sheet: -0.45 (0.95), residues: 34
  loop :  0.96 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.020   0.002   TYR C 246 
 PHE   0.011   0.001   PHE C 106 
 TRP   0.006   0.001   TRP C 220 
 HIS   0.004   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5698)
  covalent geometry    : angle       0.48412 ( 7696)
  hydrogen bonds       : bond        0.04319 (  282)
  hydrogen bonds       : angle       3.95255 (  795)

*********************** 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
  87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5902 (ptt) cc_final: 0.5579 (ptt)
REVERT: A  137 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7902 (mttt)
REVERT: A  150 ASN cc_start: 0.8296 (m-40) cc_final: 0.8091 (OUTLIER)
REVERT: A  154 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7336 (mp10)
REVERT: C   76 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6661 (m-30)
REVERT: C  155 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.7115 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7854 (tttt) cc_final: 0.7541 (tttp)
REVERT: C  211 ARG cc_start: 0.7301 (mtp85) cc_final: 0.7068 (mmp80)
REVERT: B  443 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7444 (ttp80)
REVERT: B  471 MET cc_start: 0.7780 (mtp) cc_final: 0.7463 (mtp)
REVERT: B  531 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6347 (mptp)
REVERT: B  726 THR cc_start: 0.8337 (t) cc_final: 0.8099 (m)
  outliers start: 14
  outliers final: 7
  residues processed: 80
  average time/residue: 0.8596
  time to fit residues: 70.9420
Evaluate side-chains
  82 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  137 LYS
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  531 LYS
Chi-restraints excluded: chain B residue  616 SER
Chi-restraints excluded: chain B residue  715 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C 192 HIS
C 205 GLN
C 282 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.145130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.113474 restraints weight = 6107.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.46
r_work: 0.3119 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5698  Z= 0.097
  Angle     :  0.455   8.089   7696  Z= 0.238
  Chirality :  0.039   0.141    836
  Planarity :  0.004   0.046    979
  Dihedral  :  5.102  68.072    760
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.39 %
    Favored  : 79.31 %
  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:  2.44 (0.34), residues: 667
  helix:  2.42 (0.28), residues: 352
  sheet: -0.41 (0.96), residues: 34
  loop :  1.01 (0.40), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.023   0.001   TYR A 151 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.003   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 5698)
  covalent geometry    : angle       0.45526 ( 7696)
  hydrogen bonds       : bond        0.03679 (  282)
  hydrogen bonds       : angle       3.84680 (  795)

********************** 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
  84 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  140 GLU cc_start: 0.7733 (tp30) cc_final: 0.7170 (mm-30)
REVERT: A  154 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7316 (mp10)
REVERT: C   76 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6605 (m-30)
REVERT: C  155 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7064 (ttp-110)
REVERT: C  159 LYS cc_start: 0.7950 (tttt) cc_final: 0.7650 (tttp)
REVERT: C  186 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7817 (mm-30)
REVERT: C  211 ARG cc_start: 0.7292 (mtp85) cc_final: 0.7073 (mmp80)
REVERT: B  443 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7369 (ttp80)
REVERT: B  471 MET cc_start: 0.7760 (mtp) cc_final: 0.7448 (mtp)
REVERT: B  531 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6358 (mptp)
REVERT: B  726 THR cc_start: 0.8306 (t) cc_final: 0.8078 (m)
  outliers start: 14
  outliers final: 7
  residues processed: 78
  average time/residue: 0.8923
  time to fit residues: 71.6998
Evaluate side-chains
  84 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  117 LYS
Chi-restraints excluded: chain C residue  158 LYS
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain B residue  443 ARG
Chi-restraints excluded: chain B residue  531 LYS
Chi-restraints excluded: chain B residue  715 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
C 192 HIS
C 205 GLN
C 282 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.113372 restraints weight = 5996.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.63
r_work: 0.3089 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5698  Z= 0.112
  Angle     :  0.476   8.700   7696  Z= 0.249
  Chirality :  0.039   0.146    836
  Planarity :  0.004   0.046    979
  Dihedral  :  5.134  68.351    760
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.50 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.90 %
    Favored  : 79.64 %
  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:  2.38 (0.33), residues: 667
  helix:  2.35 (0.28), residues: 352
  sheet: -0.41 (0.96), residues: 34
  loop :  1.00 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 259 
 TYR   0.019   0.002   TYR C 246 
 PHE   0.010   0.001   PHE C 106 
 TRP   0.007   0.001   TRP C 220 
 HIS   0.004   0.001   HIS B 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5698)
  covalent geometry    : angle       0.47563 ( 7696)
  hydrogen bonds       : bond        0.03991 (  282)
  hydrogen bonds       : angle       3.88983 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2525.41 seconds
wall clock time: 43 minutes 46.43 seconds (2626.43 seconds total)