Starting phenix.real_space_refine
on Wed Feb 12 18:36:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zgo_14709/02_2025/7zgo_14709.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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: 8
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       7      5.49       5
     S      44      5.16       5
     Cl      4      4.86       5
     Na      2      4.78       5
     C    5224      2.51       5
     N    1115      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7754
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3574
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 15, 'TRANS': 454}
    Chain: "B"
      Number of atoms: 3574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3574
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 15, 'TRANS': 454}
    Chain: "A"
      Number of atoms: 317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 317
          Unusual residues: {'  K': 1, ' CL': 2, ' NA': 1, 'POV': 4, 'Y01': 3}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 265
          Unusual residues: {'  K': 1, ' CL': 2, ' NA': 1, 'POV': 3, 'Y01': 3}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 5.00, per 1000 atoms: 0.64
  Number of scatterers: 7754
  At special positions: 0
  Unit cell: (80.106, 114.582, 91.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     K       2     19.00
     Cl      4     17.00
     S      44     16.00
     P       7     15.00
     Na      2     11.00
     O    1356      8.00
     N    1115      7.00
     C    5224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 582 " distance=2.03

  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: 2.15
  Conformation dependent library (CDL) restraints added in 911.4 milliseconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      80.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 286 through 291
    Processing helix  chain 'A' and resid 291 through 300
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 3.502A  pdb=" N   ILE A 306 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A 307 " --> pdb=" O   MET A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 302 through 307'
    Processing helix  chain 'A' and resid 307 through 315
    Processing helix  chain 'A' and resid 316 through 343
    Processing helix  chain 'A' and resid 351 through 360
    Processing helix  chain 'A' and resid 361 through 398
      removed outlier: 3.639A  pdb=" N   ALA A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   HIS A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 427
    Processing helix  chain 'A' and resid 430 through 454
      removed outlier: 4.314A  pdb=" N   ILE A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 464
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 486 through 499
      Proline residue:  A 496  - end of helix
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.993A  pdb=" N   ILE A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 513 through 544
      Proline residue:  A 519  - end of helix
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 574 through 580
      removed outlier: 3.871A  pdb=" N   GLU A 578 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   SER A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   SER A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 574 through 580'
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 599 through 632
      removed outlier: 3.860A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 635 through 643
      removed outlier: 4.611A  pdb=" N   MET A 640 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LYS A 643 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 668
      removed outlier: 3.957A  pdb=" N   ILE A 668 " --> pdb=" O   GLY A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 700
      Proline residue:  A 676  - end of helix
    Processing helix  chain 'A' and resid 712 through 731
    Processing helix  chain 'A' and resid 731 through 751
    Processing helix  chain 'B' and resid 286 through 291
    Processing helix  chain 'B' and resid 291 through 300
    Processing helix  chain 'B' and resid 302 through 307
    Processing helix  chain 'B' and resid 307 through 315
    Processing helix  chain 'B' and resid 316 through 344
    Processing helix  chain 'B' and resid 351 through 360
    Processing helix  chain 'B' and resid 362 through 398
      removed outlier: 3.663A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   HIS B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 427
    Processing helix  chain 'B' and resid 429 through 454
      removed outlier: 4.533A  pdb=" N   LYS B 433 " --> pdb=" O   GLU B 429 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ILE B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL B 437 " --> pdb=" O   LYS B 433 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 469 through 477
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 504 through 511
      removed outlier: 3.703A  pdb=" N   ILE B 507 " --> pdb=" O   GLY B 504 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   GLY B 509 " --> pdb=" O   ASN B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 544
      Proline residue:  B 519  - end of helix
    Processing helix  chain 'B' and resid 565 through 570
    Processing helix  chain 'B' and resid 574 through 578
    Processing helix  chain 'B' and resid 591 through 597
    Processing helix  chain 'B' and resid 599 through 632
      removed outlier: 3.626A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
    Processing helix  chain 'B' and resid 635 through 643
      removed outlier: 4.635A  pdb=" N   MET B 640 " --> pdb=" O   ALA B 637 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LYS B 643 " --> pdb=" O   MET B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 668
      removed outlier: 3.879A  pdb=" N   ILE B 668 " --> pdb=" O   GLY B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 700
      Proline residue:  B 676  - end of helix
    Processing helix  chain 'B' and resid 712 through 731
    Processing helix  chain 'B' and resid 731 through 751

    520 hydrogen bonds defined for protein.
    1506 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: 2.21

  Time building geometry restraints manager: 2.44 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: 1134
        1.31 -     1.44: 2049
        1.44 -     1.56: 4632
        1.56 -     1.69: 14
        1.69 -     1.82: 70
  Bond restraints: 7899
  Sorted by residual:
  bond pdb=" CAX Y01 A1311 "
       pdb=" OAH Y01 A1311 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" CAX Y01 B1308 "
       pdb=" OAH Y01 B1308 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" CAX Y01 A1310 "
       pdb=" OAH Y01 A1310 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" CAX Y01 B1309 "
       pdb=" OAH Y01 B1309 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.19e+01
  bond pdb=" CAX Y01 A1309 "
       pdb=" OAH Y01 A1309 "
    ideal  model  delta    sigma   weight residual
    1.248  1.341 -0.093 2.00e-02 2.50e+03 2.18e+01
  ... (remaining 7894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.62: 10422
        3.62 -     7.24: 222
        7.24 -    10.85: 42
       10.85 -    14.47: 14
       14.47 -    18.09: 7
  Bond angle restraints: 10707
  Sorted by residual:
  angle pdb=" C35 POV A1305 "
        pdb=" C36 POV A1305 "
        pdb=" C37 POV A1305 "
      ideal   model   delta    sigma   weight residual
     113.93  132.02  -18.09 3.00e+00 1.11e-01 3.64e+01
  angle pdb=" C35 POV A1306 "
        pdb=" C36 POV A1306 "
        pdb=" C37 POV A1306 "
      ideal   model   delta    sigma   weight residual
     113.93  131.80  -17.87 3.00e+00 1.11e-01 3.55e+01
  angle pdb=" C35 POV B1305 "
        pdb=" C36 POV B1305 "
        pdb=" C37 POV B1305 "
      ideal   model   delta    sigma   weight residual
     113.93  131.45  -17.52 3.00e+00 1.11e-01 3.41e+01
  angle pdb=" C35 POV B1307 "
        pdb=" C36 POV B1307 "
        pdb=" C37 POV B1307 "
      ideal   model   delta    sigma   weight residual
     113.93  131.38  -17.45 3.00e+00 1.11e-01 3.38e+01
  angle pdb=" C35 POV A1308 "
        pdb=" C36 POV A1308 "
        pdb=" C37 POV A1308 "
      ideal   model   delta    sigma   weight residual
     113.93  131.36  -17.43 3.00e+00 1.11e-01 3.38e+01
  ... (remaining 10702 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.28: 4683
       28.28 -    56.56: 229
       56.56 -    84.84: 36
       84.84 -   113.12: 12
      113.12 -   141.40: 1
  Dihedral angle restraints: 4961
    sinusoidal: 2275
      harmonic: 2686
  Sorted by residual:
  dihedral pdb=" CB  CYS A 577 "
           pdb=" SG  CYS A 577 "
           pdb=" SG  CYS A 582 "
           pdb=" CB  CYS A 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.93   85.93     1      1.00e+01 1.00e-02 8.92e+01
  dihedral pdb=" CB  CYS B 577 "
           pdb=" SG  CYS B 577 "
           pdb=" SG  CYS B 582 "
           pdb=" CB  CYS B 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -169.56   83.56     1      1.00e+01 1.00e-02 8.52e+01
  dihedral pdb=" C3  POV A1306 "
           pdb=" C31 POV A1306 "
           pdb=" O31 POV A1306 "
           pdb=" C32 POV A1306 "
      ideal   model   delta sinusoidal    sigma   weight residual
     172.61  -45.99 -141.40     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 4958 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1162
       0.094 -    0.188: 59
       0.188 -    0.282: 14
       0.282 -    0.376: 6
       0.376 -    0.470: 6
  Chirality restraints: 1247
  Sorted by residual:
  chirality pdb=" CBG Y01 A1309 "
            pdb=" CAQ Y01 A1309 "
            pdb=" CBD Y01 A1309 "
            pdb=" CBI Y01 A1309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.80    0.47 2.00e-01 2.50e+01 5.51e+00
  chirality pdb=" CBG Y01 A1310 "
            pdb=" CAQ Y01 A1310 "
            pdb=" CBD Y01 A1310 "
            pdb=" CBI Y01 A1310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.80    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CBG Y01 B1310 "
            pdb=" CAQ Y01 B1310 "
            pdb=" CBD Y01 B1310 "
            pdb=" CBI Y01 B1310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.80    0.47 2.00e-01 2.50e+01 5.42e+00
  ... (remaining 1244 not shown)

  Planarity restraints: 1249
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 361 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.95e+00
        pdb=" N   PRO B 362 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 362 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 362 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 361 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.28e+00
        pdb=" N   PRO A 362 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 580 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.77e+00
        pdb=" N   PRO A 581 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1246 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.76: 1377
        2.76 -     3.36: 8988
        3.36 -     3.95: 15567
        3.95 -     4.55: 22083
        4.55 -     5.14: 32006
  Nonbonded interactions: 80021
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 431 "
            pdb=" O   HOH A1401 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OH  TYR B 468 "
            pdb=" OG  SER B 539 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OH  TYR A 468 "
            pdb=" OG  SER A 539 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   GLY A 478 "
            pdb=" NH2 ARG A 546 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   LEU A 297 "
            pdb="NA    NA A1301 "
     model   vdw
     2.246 2.470
  ... (remaining 80016 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 284 through 753 or resid 1301 through 1307 or resid 1309 t \ 
hrough 1310))
  selection = (chain 'B' and (resid 284 through 753 or resid 1301 through 1307 or resid 1309 t \ 
hrough 1310))
}

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:             0.550
  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:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.790
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:13.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
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      :  0.008   0.094   7899  Z= 0.514
  Angle     :  1.241  18.089  10707  Z= 0.464
  Chirality :  0.063   0.470   1247
  Planarity :  0.003   0.043   1249
  Dihedral  : 16.937 141.402   3233
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 936
  helix:  1.80 (0.19), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.56 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 733 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.016   0.002   PHE A 681 
 TYR   0.014   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A 358 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6951 (mtp85)
REVERT: A  325 MET cc_start: 0.7995 (mmt) cc_final: 0.7780 (mmp)
REVERT: A  433 LYS cc_start: 0.6613 (mmmm) cc_final: 0.6213 (mttp)
REVERT: A  475 GLU cc_start: 0.7618 (tt0) cc_final: 0.6977 (tt0)
REVERT: A  480 ASP cc_start: 0.8135 (t0) cc_final: 0.7790 (t0)
REVERT: A  513 ASP cc_start: 0.7392 (t0) cc_final: 0.6879 (t0)
REVERT: A  515 GLN cc_start: 0.7795 (mt0) cc_final: 0.7399 (mt0)
REVERT: A  625 ILE cc_start: 0.8148 (mt) cc_final: 0.7764 (mt)
REVERT: A  727 MET cc_start: 0.8174 (ptm) cc_final: 0.7891 (ptm)
REVERT: B  325 MET cc_start: 0.7947 (mmp) cc_final: 0.7733 (mmm)
REVERT: B  428 MET cc_start: 0.5128 (mmm) cc_final: 0.4856 (tpt)
REVERT: B  433 LYS cc_start: 0.6557 (mmmm) cc_final: 0.6205 (mttp)
REVERT: B  475 GLU cc_start: 0.7503 (tt0) cc_final: 0.6848 (tt0)
REVERT: B  480 ASP cc_start: 0.8271 (t0) cc_final: 0.7923 (t0)
REVERT: B  513 ASP cc_start: 0.7110 (t0) cc_final: 0.6639 (t70)
REVERT: B  624 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7170 (mtpt)
REVERT: B  688 LEU cc_start: 0.8160 (mm) cc_final: 0.7938 (mt)
REVERT: B  713 MET cc_start: 0.8387 (ptm) cc_final: 0.8181 (ptm)
REVERT: B  727 MET cc_start: 0.8121 (ptm) cc_final: 0.7775 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 1.0718
  time to fit residues: 124.9142
Evaluate side-chains
  81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 571 ASN
A 591 GLN
B 435 GLN
B 571 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.142850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108096 restraints weight = 8292.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.71
r_work: 0.3089 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7899  Z= 0.206
  Angle     :  0.501   6.026  10707  Z= 0.262
  Chirality :  0.040   0.128   1247
  Planarity :  0.004   0.045   1249
  Dihedral  : 16.704 137.543   1715
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.35 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.27), residues: 936
  helix:  2.14 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.89 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.018   0.002   PHE B 681 
 TYR   0.009   0.001   TYR A 739 
 ARG   0.003   0.000   ARG A 307 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7471 (mtp85)
REVERT: A  296 MET cc_start: 0.8550 (mtm) cc_final: 0.7975 (mtp)
REVERT: A  433 LYS cc_start: 0.6811 (mmmm) cc_final: 0.6468 (mttp)
REVERT: A  480 ASP cc_start: 0.8432 (t0) cc_final: 0.8137 (t0)
REVERT: A  513 ASP cc_start: 0.7452 (t0) cc_final: 0.7239 (t0)
REVERT: A  515 GLN cc_start: 0.7886 (mt0) cc_final: 0.7552 (mt0)
REVERT: A  670 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7021 (tt0)
REVERT: A  705 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6658 (ttm110)
REVERT: B  296 MET cc_start: 0.8509 (mtm) cc_final: 0.7983 (mtp)
REVERT: B  428 MET cc_start: 0.5299 (mmm) cc_final: 0.5039 (tpt)
REVERT: B  433 LYS cc_start: 0.6768 (mmmm) cc_final: 0.6416 (mttp)
REVERT: B  480 ASP cc_start: 0.8608 (t0) cc_final: 0.8260 (t0)
REVERT: B  513 ASP cc_start: 0.7470 (t0) cc_final: 0.6901 (t70)
REVERT: B  624 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7519 (mtmm)
REVERT: B  705 ARG cc_start: 0.7161 (mtm110) cc_final: 0.6690 (ttm110)
REVERT: B  727 MET cc_start: 0.8660 (ptm) cc_final: 0.8384 (ptm)
  outliers start: 8
  outliers final: 3
  residues processed: 89
  average time/residue: 1.2799
  time to fit residues: 121.0594
Evaluate side-chains
  82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue  508 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 571 ASN
B 435 GLN
B 571 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.107006 restraints weight = 8507.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.75
r_work: 0.3095 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7899  Z= 0.169
  Angle     :  0.450   5.120  10707  Z= 0.239
  Chirality :  0.039   0.128   1247
  Planarity :  0.004   0.042   1249
  Dihedral  : 16.047 131.898   1715
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.53 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 936
  helix:  2.26 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.85 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 287 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.015   0.001   PHE B 681 
 TYR   0.012   0.001   TYR A 739 
 ARG   0.002   0.000   ARG B 307 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7451 (mtp85)
REVERT: A  296 MET cc_start: 0.8553 (mtm) cc_final: 0.8024 (mtp)
REVERT: A  428 MET cc_start: 0.5602 (tpt) cc_final: 0.5278 (tpt)
REVERT: A  433 LYS cc_start: 0.6892 (mmmm) cc_final: 0.6550 (mttp)
REVERT: A  515 GLN cc_start: 0.7918 (mt0) cc_final: 0.7606 (mt0)
REVERT: A  631 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6866 (ttmt)
REVERT: A  670 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6952 (tt0)
REVERT: A  705 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6651 (ttm110)
REVERT: B  296 MET cc_start: 0.8534 (mtm) cc_final: 0.8007 (mtp)
REVERT: B  433 LYS cc_start: 0.6749 (mmmm) cc_final: 0.6425 (mttp)
REVERT: B  480 ASP cc_start: 0.8521 (t0) cc_final: 0.8209 (t0)
REVERT: B  513 ASP cc_start: 0.7470 (t0) cc_final: 0.6919 (t70)
REVERT: B  624 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7553 (mtmm)
REVERT: B  631 LYS cc_start: 0.7496 (mmtm) cc_final: 0.6775 (ttmt)
REVERT: B  667 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7825 (mm)
REVERT: B  705 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6746 (ttm110)
  outliers start: 11
  outliers final: 4
  residues processed: 85
  average time/residue: 1.2460
  time to fit residues: 112.4975
Evaluate side-chains
  87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 81 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.145993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.111151 restraints weight = 8474.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.75
r_work: 0.3120 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7899  Z= 0.146
  Angle     :  0.425   5.099  10707  Z= 0.227
  Chirality :  0.038   0.120   1247
  Planarity :  0.003   0.041   1249
  Dihedral  : 15.396 127.161   1715
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.97 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 936
  helix:  2.44 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.80 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 287 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.013   0.001   PHE B 681 
 TYR   0.013   0.001   TYR A 739 
 ARG   0.001   0.000   ARG B 294 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7455 (mtp85)
REVERT: A  296 MET cc_start: 0.8522 (mtm) cc_final: 0.7974 (mtp)
REVERT: A  433 LYS cc_start: 0.6952 (mmmm) cc_final: 0.6578 (mttp)
REVERT: A  506 ASN cc_start: 0.7072 (m-40) cc_final: 0.6846 (m-40)
REVERT: A  515 GLN cc_start: 0.7742 (mt0) cc_final: 0.7485 (mt0)
REVERT: A  631 LYS cc_start: 0.7535 (mmtm) cc_final: 0.6848 (ttmt)
REVERT: A  667 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7791 (mm)
REVERT: A  705 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6636 (ttm110)
REVERT: B  296 MET cc_start: 0.8511 (mtm) cc_final: 0.7944 (mtp)
REVERT: B  433 LYS cc_start: 0.6709 (mmmm) cc_final: 0.6373 (mttp)
REVERT: B  480 ASP cc_start: 0.8392 (t0) cc_final: 0.8057 (t0)
REVERT: B  513 ASP cc_start: 0.7475 (t0) cc_final: 0.6928 (t70)
REVERT: B  624 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7560 (mtmm)
REVERT: B  631 LYS cc_start: 0.7444 (mmtm) cc_final: 0.6737 (ttmt)
REVERT: B  705 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6729 (ttm110)
  outliers start: 9
  outliers final: 2
  residues processed: 89
  average time/residue: 1.1089
  time to fit residues: 105.4964
Evaluate side-chains
  85 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  394 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.143488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.108380 restraints weight = 8441.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.74
r_work: 0.3118 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7899  Z= 0.149
  Angle     :  0.429   5.100  10707  Z= 0.228
  Chirality :  0.038   0.120   1247
  Planarity :  0.003   0.042   1249
  Dihedral  : 15.024 125.627   1715
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.29 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 936
  helix:  2.47 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.79 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 287 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.013   0.001   PHE B 681 
 TYR   0.018   0.001   TYR A 739 
 ARG   0.002   0.000   ARG A 307 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7487 (mtp85)
REVERT: A  296 MET cc_start: 0.8531 (mtm) cc_final: 0.7980 (mtp)
REVERT: A  433 LYS cc_start: 0.6920 (mmmm) cc_final: 0.6545 (mttp)
REVERT: A  506 ASN cc_start: 0.7084 (m-40) cc_final: 0.6860 (m-40)
REVERT: A  631 LYS cc_start: 0.7559 (mmtm) cc_final: 0.6899 (ttmt)
REVERT: A  667 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7790 (mm)
REVERT: A  705 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6701 (ttm110)
REVERT: B  296 MET cc_start: 0.8528 (mtm) cc_final: 0.7978 (mtp)
REVERT: B  433 LYS cc_start: 0.6719 (mmmm) cc_final: 0.6378 (mttp)
REVERT: B  480 ASP cc_start: 0.8419 (t0) cc_final: 0.8100 (t0)
REVERT: B  513 ASP cc_start: 0.7459 (t0) cc_final: 0.6910 (t70)
REVERT: B  624 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7580 (mtmm)
REVERT: B  631 LYS cc_start: 0.7534 (mmtm) cc_final: 0.6776 (ttmt)
REVERT: B  667 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7721 (mm)
REVERT: B  705 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6726 (ttm110)
  outliers start: 14
  outliers final: 5
  residues processed: 91
  average time/residue: 1.1565
  time to fit residues: 112.2520
Evaluate side-chains
  88 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.143697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108837 restraints weight = 8458.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.74
r_work: 0.3120 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7899  Z= 0.172
  Angle     :  0.447   5.117  10707  Z= 0.237
  Chirality :  0.038   0.121   1247
  Planarity :  0.004   0.041   1249
  Dihedral  : 14.591 127.208   1715
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.68 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.27), residues: 936
  helix:  2.36 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.86 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 287 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.013   0.001   PHE A 681 
 TYR   0.021   0.001   TYR A 739 
 ARG   0.001   0.000   ARG B 546 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7461 (mtp85)
REVERT: A  296 MET cc_start: 0.8516 (mtm) cc_final: 0.7974 (mtp)
REVERT: A  360 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7285 (pp)
REVERT: A  433 LYS cc_start: 0.6990 (mmmm) cc_final: 0.6635 (mttp)
REVERT: A  631 LYS cc_start: 0.7572 (mmtm) cc_final: 0.6910 (ttmt)
REVERT: A  667 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: A  705 ARG cc_start: 0.7072 (mtm110) cc_final: 0.6686 (ttm110)
REVERT: B  296 MET cc_start: 0.8510 (mtm) cc_final: 0.7958 (mtp)
REVERT: B  319 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7743 (mp)
REVERT: B  433 LYS cc_start: 0.6725 (mmmm) cc_final: 0.6429 (mttp)
REVERT: B  480 ASP cc_start: 0.8406 (t0) cc_final: 0.8077 (t0)
REVERT: B  513 ASP cc_start: 0.7440 (t0) cc_final: 0.6891 (t70)
REVERT: B  624 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7589 (mtmm)
REVERT: B  631 LYS cc_start: 0.7550 (mmtm) cc_final: 0.6784 (ttmt)
REVERT: B  667 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7774 (mm)
REVERT: B  705 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6731 (ttm110)
REVERT: B  710 TYR cc_start: 0.8389 (m-80) cc_final: 0.8117 (m-80)
  outliers start: 17
  outliers final: 6
  residues processed: 88
  average time/residue: 1.1293
  time to fit residues: 105.8821
Evaluate side-chains
  91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 86 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.109362 restraints weight = 8471.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.74
r_work: 0.3122 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7899  Z= 0.145
  Angle     :  0.426   5.087  10707  Z= 0.227
  Chirality :  0.038   0.118   1247
  Planarity :  0.003   0.041   1249
  Dihedral  : 14.194 125.678   1715
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.34 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.27), residues: 936
  helix:  2.41 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.74 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 733 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.013   0.001   PHE A 681 
 TYR   0.017   0.001   TYR A 739 
 ARG   0.002   0.000   ARG B 294 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7454 (mtp85)
REVERT: A  296 MET cc_start: 0.8536 (mtm) cc_final: 0.7991 (mtp)
REVERT: A  360 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7211 (pp)
REVERT: A  433 LYS cc_start: 0.6990 (mmmm) cc_final: 0.6634 (mttp)
REVERT: A  631 LYS cc_start: 0.7571 (mmtm) cc_final: 0.6924 (ttmt)
REVERT: A  660 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: A  667 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7792 (mm)
REVERT: A  705 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6702 (ttm110)
REVERT: B  296 MET cc_start: 0.8545 (mtm) cc_final: 0.7991 (mtp)
REVERT: B  319 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: B  433 LYS cc_start: 0.6797 (mmmm) cc_final: 0.6495 (mttp)
REVERT: B  480 ASP cc_start: 0.8427 (t0) cc_final: 0.8099 (t0)
REVERT: B  513 ASP cc_start: 0.7438 (t0) cc_final: 0.6874 (t70)
REVERT: B  624 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7607 (mtpt)
REVERT: B  631 LYS cc_start: 0.7557 (mmtm) cc_final: 0.6833 (ttmt)
REVERT: B  667 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7755 (mm)
REVERT: B  705 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6719 (ttm110)
  outliers start: 16
  outliers final: 5
  residues processed: 88
  average time/residue: 1.1356
  time to fit residues: 106.8963
Evaluate side-chains
  92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 90 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108526 restraints weight = 8539.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.76
r_work: 0.3127 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7899  Z= 0.153
  Angle     :  0.438   5.110  10707  Z= 0.231
  Chirality :  0.038   0.119   1247
  Planarity :  0.004   0.082   1249
  Dihedral  : 14.012 126.545   1715
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.34 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.27), residues: 936
  helix:  2.36 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.81 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 733 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.013   0.001   PHE B 681 
 TYR   0.017   0.001   TYR A 739 
 ARG   0.001   0.000   ARG B 546 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7441 (mtp85)
REVERT: A  296 MET cc_start: 0.8536 (mtm) cc_final: 0.7981 (mtp)
REVERT: A  360 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7265 (pp)
REVERT: A  433 LYS cc_start: 0.6997 (mmmm) cc_final: 0.6640 (mttp)
REVERT: A  631 LYS cc_start: 0.7542 (mmtm) cc_final: 0.6959 (ttmt)
REVERT: A  660 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7753 (tp)
REVERT: A  667 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: A  705 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6694 (ttm110)
REVERT: B  296 MET cc_start: 0.8524 (mtm) cc_final: 0.7962 (mtp)
REVERT: B  319 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7732 (mp)
REVERT: B  433 LYS cc_start: 0.6798 (mmmm) cc_final: 0.6492 (mttp)
REVERT: B  480 ASP cc_start: 0.8413 (t0) cc_final: 0.8094 (t0)
REVERT: B  513 ASP cc_start: 0.7434 (t0) cc_final: 0.6884 (t70)
REVERT: B  515 GLN cc_start: 0.8033 (mt0) cc_final: 0.7557 (mt0)
REVERT: B  624 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7596 (mtpt)
REVERT: B  631 LYS cc_start: 0.7590 (mmtm) cc_final: 0.6894 (ttmt)
REVERT: B  667 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7748 (mm)
REVERT: B  705 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6717 (ttm110)
  outliers start: 17
  outliers final: 5
  residues processed: 90
  average time/residue: 1.1071
  time to fit residues: 106.6940
Evaluate side-chains
  92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.1560

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.143854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109113 restraints weight = 8573.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.74
r_work: 0.3109 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7899  Z= 0.172
  Angle     :  0.457   5.797  10707  Z= 0.240
  Chirality :  0.039   0.121   1247
  Planarity :  0.004   0.083   1249
  Dihedral  : 14.000 128.238   1715
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.86 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.27), residues: 936
  helix:  2.38 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.88 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 287 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.014   0.001   PHE B 681 
 TYR   0.018   0.001   TYR A 739 
 ARG   0.001   0.000   ARG B 294 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7442 (mtp85)
REVERT: A  296 MET cc_start: 0.8551 (mtm) cc_final: 0.8006 (mtp)
REVERT: A  360 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7211 (pp)
REVERT: A  433 LYS cc_start: 0.6994 (mmmm) cc_final: 0.6640 (mttp)
REVERT: A  631 LYS cc_start: 0.7595 (mmtm) cc_final: 0.6985 (ttmt)
REVERT: A  660 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7739 (tp)
REVERT: A  667 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (mm)
REVERT: A  705 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6666 (ttm110)
REVERT: B  296 MET cc_start: 0.8530 (mtm) cc_final: 0.7967 (mtp)
REVERT: B  319 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7730 (mp)
REVERT: B  433 LYS cc_start: 0.6816 (mmmm) cc_final: 0.6505 (mttp)
REVERT: B  480 ASP cc_start: 0.8418 (t0) cc_final: 0.8095 (t0)
REVERT: B  513 ASP cc_start: 0.7442 (t0) cc_final: 0.6897 (t70)
REVERT: B  515 GLN cc_start: 0.8043 (mt0) cc_final: 0.7566 (mt0)
REVERT: B  624 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7591 (mtmm)
REVERT: B  631 LYS cc_start: 0.7605 (mmtm) cc_final: 0.6919 (ttmt)
REVERT: B  667 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: B  705 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6713 (ttm110)
  outliers start: 14
  outliers final: 5
  residues processed: 90
  average time/residue: 1.0807
  time to fit residues: 104.2205
Evaluate side-chains
  92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.108635 restraints weight = 8554.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.74
r_work: 0.3106 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7899  Z= 0.180
  Angle     :  0.467   7.415  10707  Z= 0.244
  Chirality :  0.039   0.124   1247
  Planarity :  0.004   0.079   1249
  Dihedral  : 13.939 127.262   1715
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.39 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 936
  helix:  2.34 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.89 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 733 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.014   0.001   PHE A 681 
 TYR   0.016   0.001   TYR A 739 
 ARG   0.002   0.000   ARG B 307 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7437 (mtp85)
REVERT: A  296 MET cc_start: 0.8534 (mtm) cc_final: 0.7983 (mtp)
REVERT: A  360 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7262 (pp)
REVERT: A  433 LYS cc_start: 0.6980 (mmmm) cc_final: 0.6635 (mttp)
REVERT: A  631 LYS cc_start: 0.7586 (mmtm) cc_final: 0.7152 (mtmp)
REVERT: A  660 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7730 (tp)
REVERT: A  667 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: A  705 ARG cc_start: 0.7058 (mtm110) cc_final: 0.6761 (mtp85)
REVERT: B  296 MET cc_start: 0.8532 (mtm) cc_final: 0.7968 (mtp)
REVERT: B  319 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (mp)
REVERT: B  433 LYS cc_start: 0.6813 (mmmm) cc_final: 0.6502 (mttp)
REVERT: B  480 ASP cc_start: 0.8415 (t0) cc_final: 0.8088 (t0)
REVERT: B  513 ASP cc_start: 0.7472 (t0) cc_final: 0.6917 (t70)
REVERT: B  515 GLN cc_start: 0.8041 (mt0) cc_final: 0.7565 (mt0)
REVERT: B  624 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7583 (mtmm)
REVERT: B  631 LYS cc_start: 0.7564 (mmtm) cc_final: 0.6940 (ttmt)
REVERT: B  667 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7756 (mm)
REVERT: B  705 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6705 (ttm110)
  outliers start: 12
  outliers final: 5
  residues processed: 88
  average time/residue: 1.1043
  time to fit residues: 103.9481
Evaluate side-chains
  93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  667 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.141777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107025 restraints weight = 8529.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.73
r_work: 0.3080 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7899  Z= 0.262
  Angle     :  0.537   7.990  10707  Z= 0.278
  Chirality :  0.041   0.141   1247
  Planarity :  0.004   0.078   1249
  Dihedral  : 14.353 129.405   1715
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.91 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.27), residues: 936
  helix:  2.11 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.89 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.018   0.002   PHE A 681 
 TYR   0.018   0.002   TYR A 739 
 ARG   0.004   0.001   ARG B 307 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5695.39 seconds
wall clock time: 101 minutes 8.58 seconds (6068.58 seconds total)