Starting phenix.real_space_refine
on Wed Mar 12 19:18:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zgo_14709/03_2025/7zgo_14709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zgo_14709/03_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_14709/03_2025/7zgo_14709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2025/7zgo_14709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2025/7zgo_14709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_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-5624/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: 5.32, per 1000 atoms: 0.69
  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: 2.36
  Conformation dependent library (CDL) restraints added in 900.1 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: 0.63
  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: 2.09

  Time building geometry restraints manager: 2.71 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:             1.510
  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:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.400
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.020
  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:12.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.600
-------------------------------------------------------------------------------
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  : 0.809 
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: 1.3242
  time to fit residues: 154.1687
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  : 2.529 
-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.142310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.107334 restraints weight = 8301.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.71
r_work: 0.3088 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1137

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   6.027  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  : 0.746 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7472 (mtp85)
REVERT: A  296 MET cc_start: 0.8550 (mtm) cc_final: 0.7975 (mtp)
REVERT: A  433 LYS cc_start: 0.6812 (mmmm) cc_final: 0.6470 (mttp)
REVERT: A  480 ASP cc_start: 0.8431 (t0) cc_final: 0.8136 (t0)
REVERT: A  513 ASP cc_start: 0.7451 (t0) cc_final: 0.7237 (t0)
REVERT: A  515 GLN cc_start: 0.7885 (mt0) cc_final: 0.7551 (mt0)
REVERT: A  670 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7023 (tt0)
REVERT: A  705 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6655 (ttm110)
REVERT: B  296 MET cc_start: 0.8509 (mtm) cc_final: 0.7985 (mtp)
REVERT: B  428 MET cc_start: 0.5300 (mmm) cc_final: 0.5040 (tpt)
REVERT: B  433 LYS cc_start: 0.6770 (mmmm) cc_final: 0.6417 (mttp)
REVERT: B  480 ASP cc_start: 0.8608 (t0) cc_final: 0.8261 (t0)
REVERT: B  513 ASP cc_start: 0.7469 (t0) cc_final: 0.6901 (t70)
REVERT: B  624 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7517 (mtmm)
REVERT: B  705 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6686 (ttm110)
REVERT: B  727 MET cc_start: 0.8661 (ptm) cc_final: 0.8384 (ptm)
  outliers start: 8
  outliers final: 3
  residues processed: 89
  average time/residue: 1.2093
  time to fit residues: 114.4548
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  : 0.840 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 506 ASN
B 571 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.108510 restraints weight = 8500.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.74
r_work: 0.3107 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1375

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= 0.160
  Angle     :  0.442   5.103  10707  Z= 0.235
  Chirality :  0.038   0.133   1247
  Planarity :  0.003   0.041   1249
  Dihedral  : 15.918 131.222   1715
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.79 %
    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:  2.17 (0.27), residues: 936
  helix:  2.34 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.75 (0.38), residues: 284

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   0.014   0.001   PHE B 681 
 TYR   0.012   0.001   TYR A 739 
 ARG   0.001   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
  92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7457 (mtp85)
REVERT: A  296 MET cc_start: 0.8567 (mtm) cc_final: 0.8038 (mtp)
REVERT: A  433 LYS cc_start: 0.6880 (mmmm) cc_final: 0.6542 (mttp)
REVERT: A  515 GLN cc_start: 0.7919 (mt0) cc_final: 0.7605 (mt0)
REVERT: A  631 LYS cc_start: 0.7598 (mmtm) cc_final: 0.6871 (ttmt)
REVERT: A  670 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6923 (tt0)
REVERT: A  705 ARG cc_start: 0.7032 (mtm110) cc_final: 0.6653 (ttm110)
REVERT: B  296 MET cc_start: 0.8531 (mtm) cc_final: 0.7993 (mtp)
REVERT: B  433 LYS cc_start: 0.6787 (mmmm) cc_final: 0.6466 (mttp)
REVERT: B  480 ASP cc_start: 0.8534 (t0) cc_final: 0.8232 (t0)
REVERT: B  513 ASP cc_start: 0.7465 (t0) cc_final: 0.6912 (t70)
REVERT: B  624 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7553 (mtmm)
REVERT: B  631 LYS cc_start: 0.7469 (mmtm) cc_final: 0.6770 (ttmt)
REVERT: B  667 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7811 (mm)
REVERT: B  705 ARG cc_start: 0.7246 (mtm110) cc_final: 0.6744 (ttm110)
  outliers start: 9
  outliers final: 3
  residues processed: 86
  average time/residue: 1.2513
  time to fit residues: 114.1854
Evaluate side-chains
  86 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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  667 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0570
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 80 optimal weight:    0.3980
   chunk 92 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.6100

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.145411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.110672 restraints weight = 8483.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.73
r_work: 0.3135 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1567

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= 0.132
  Angle     :  0.414   5.061  10707  Z= 0.221
  Chirality :  0.038   0.121   1247
  Planarity :  0.003   0.040   1249
  Dihedral  : 15.258 125.772   1715
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.58 %
    Favored  : 88.98 %
  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:  2.33 (0.27), residues: 936
  helix:  2.50 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.83 (0.38), residues: 282

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   0.012   0.001   PHE A 681 
 TYR   0.012   0.001   TYR A 739 
 ARG   0.002   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
  101 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7446 (mtp85)
REVERT: A  296 MET cc_start: 0.8519 (mtm) cc_final: 0.7970 (mtp)
REVERT: A  433 LYS cc_start: 0.6858 (mmmm) cc_final: 0.6510 (mttp)
REVERT: A  506 ASN cc_start: 0.7058 (m-40) cc_final: 0.6806 (m-40)
REVERT: A  515 GLN cc_start: 0.7808 (mt0) cc_final: 0.7528 (mt0)
REVERT: A  631 LYS cc_start: 0.7500 (mmtm) cc_final: 0.6778 (ttmt)
REVERT: A  667 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7784 (mm)
REVERT: A  705 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6626 (ttm110)
REVERT: B  296 MET cc_start: 0.8508 (mtm) cc_final: 0.7959 (mtp)
REVERT: B  433 LYS cc_start: 0.6771 (mmmm) cc_final: 0.6421 (mttp)
REVERT: B  480 ASP cc_start: 0.8390 (t0) cc_final: 0.8052 (t0)
REVERT: B  513 ASP cc_start: 0.7492 (t0) cc_final: 0.6890 (t70)
REVERT: B  624 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7549 (mtmm)
REVERT: B  631 LYS cc_start: 0.7443 (mmtm) cc_final: 0.6727 (ttmt)
REVERT: B  705 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6727 (ttm110)
  outliers start: 11
  outliers final: 3
  residues processed: 94
  average time/residue: 1.0663
  time to fit residues: 107.1757
Evaluate side-chains
  87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
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:    0.0170
   chunk 66 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.145864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.110705 restraints weight = 8400.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.75
r_work: 0.3147 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7899  Z= 0.126
  Angle     :  0.410   5.043  10707  Z= 0.218
  Chirality :  0.037   0.117   1247
  Planarity :  0.004   0.071   1249
  Dihedral  : 14.816 123.965   1715
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.89 %
    Favored  : 87.40 %
  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:  2.42 (0.27), residues: 936
  helix:  2.57 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.80 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 733 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.012   0.001   PHE B 681 
 TYR   0.018   0.001   TYR A 739 
 ARG   0.002   0.000   ARG B 294 

*********************** 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
  100 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7433 (mtp85)
REVERT: A  296 MET cc_start: 0.8516 (mtm) cc_final: 0.7951 (mtp)
REVERT: A  433 LYS cc_start: 0.6861 (mmmm) cc_final: 0.6491 (mttp)
REVERT: A  515 GLN cc_start: 0.7741 (mt0) cc_final: 0.7471 (mt0)
REVERT: A  631 LYS cc_start: 0.7487 (mmtm) cc_final: 0.6831 (ttmt)
REVERT: A  667 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7771 (mm)
REVERT: A  705 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6640 (ttm110)
REVERT: B  296 MET cc_start: 0.8504 (mtm) cc_final: 0.7960 (mtp)
REVERT: B  433 LYS cc_start: 0.6708 (mmmm) cc_final: 0.6366 (mttp)
REVERT: B  480 ASP cc_start: 0.8402 (t0) cc_final: 0.8080 (t0)
REVERT: B  513 ASP cc_start: 0.7477 (t0) cc_final: 0.6870 (t70)
REVERT: B  515 GLN cc_start: 0.8030 (mt0) cc_final: 0.7810 (mt0)
REVERT: B  624 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7505 (mtpt)
REVERT: B  631 LYS cc_start: 0.7454 (mmtm) cc_final: 0.6762 (ttmt)
REVERT: B  667 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7668 (mm)
REVERT: B  673 VAL cc_start: 0.7941 (m) cc_final: 0.7722 (p)
REVERT: B  705 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6716 (ttm110)
  outliers start: 13
  outliers final: 3
  residues processed: 92
  average time/residue: 1.1034
  time to fit residues: 108.2188
Evaluate side-chains
  88 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 LEU
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  667 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   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:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 55 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 591 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.108431 restraints weight = 8460.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.73
r_work: 0.3098 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7899  Z= 0.192
  Angle     :  0.469   5.125  10707  Z= 0.248
  Chirality :  0.039   0.126   1247
  Planarity :  0.004   0.076   1249
  Dihedral  : 14.796 128.265   1715
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.68 %
    Favored  : 86.22 %
  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:  2.08 (0.27), residues: 936
  helix:  2.24 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.84 (0.38), residues: 272

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   0.014   0.002   PHE A 681 
 TYR   0.021   0.001   TYR A 739 
 ARG   0.002   0.000   ARG A 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: 16
    poor density    : 82
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7458 (mtp85)
REVERT: A  296 MET cc_start: 0.8527 (mtm) cc_final: 0.7980 (mtp)
REVERT: A  360 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7281 (pp)
REVERT: A  433 LYS cc_start: 0.6967 (mmmm) cc_final: 0.6615 (mttp)
REVERT: A  515 GLN cc_start: 0.7698 (mt0) cc_final: 0.7471 (mt0)
REVERT: A  631 LYS cc_start: 0.7558 (mmtm) cc_final: 0.6909 (ttmt)
REVERT: A  667 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7774 (mm)
REVERT: A  705 ARG cc_start: 0.6982 (mtm110) cc_final: 0.6582 (ttm110)
REVERT: A  710 TYR cc_start: 0.8398 (m-80) cc_final: 0.8148 (m-80)
REVERT: B  296 MET cc_start: 0.8510 (mtm) cc_final: 0.7959 (mtp)
REVERT: B  319 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: B  433 LYS cc_start: 0.6766 (mmmm) cc_final: 0.6458 (mttp)
REVERT: B  480 ASP cc_start: 0.8433 (t0) cc_final: 0.8100 (t0)
REVERT: B  513 ASP cc_start: 0.7442 (t0) cc_final: 0.6907 (t70)
REVERT: B  624 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7577 (mtmm)
REVERT: B  631 LYS cc_start: 0.7577 (mmtm) cc_final: 0.6808 (ttmt)
REVERT: B  667 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7730 (mm)
REVERT: B  705 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6721 (ttm110)
  outliers start: 16
  outliers final: 5
  residues processed: 89
  average time/residue: 1.1921
  time to fit residues: 112.9794
Evaluate side-chains
  89 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0010
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.6186

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.144627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108863 restraints weight = 8470.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.80
r_work: 0.3130 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7899  Z= 0.132
  Angle     :  0.416   5.075  10707  Z= 0.221
  Chirality :  0.037   0.116   1247
  Planarity :  0.004   0.076   1249
  Dihedral  : 14.143 124.932   1715
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.12 %
    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:  2.34 (0.27), residues: 936
  helix:  2.44 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.70 (0.39), 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   0.012   0.001   PHE B 681 
 TYR   0.016   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
  97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7432 (mtp85)
REVERT: A  296 MET cc_start: 0.8521 (mtm) cc_final: 0.7977 (mtp)
REVERT: A  360 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7228 (pp)
REVERT: A  433 LYS cc_start: 0.7032 (mmmm) cc_final: 0.6659 (mttp)
REVERT: A  515 GLN cc_start: 0.7711 (mt0) cc_final: 0.7468 (mt0)
REVERT: A  631 LYS cc_start: 0.7570 (mmtm) cc_final: 0.6895 (ttmt)
REVERT: A  660 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7650 (tp)
REVERT: A  667 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7781 (mm)
REVERT: A  705 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6755 (mtp85)
REVERT: B  296 MET cc_start: 0.8521 (mtm) cc_final: 0.7960 (mtp)
REVERT: B  433 LYS cc_start: 0.6753 (mmmm) cc_final: 0.6417 (mttp)
REVERT: B  480 ASP cc_start: 0.8423 (t0) cc_final: 0.8091 (t0)
REVERT: B  513 ASP cc_start: 0.7498 (t0) cc_final: 0.6886 (t70)
REVERT: B  515 GLN cc_start: 0.7949 (mt0) cc_final: 0.7415 (mt0)
REVERT: B  624 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7599 (mtpt)
REVERT: B  631 LYS cc_start: 0.7553 (mmtm) cc_final: 0.6793 (ttmt)
REVERT: B  667 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7726 (mm)
REVERT: B  705 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6704 (ttm110)
  outliers start: 11
  outliers final: 1
  residues processed: 90
  average time/residue: 1.1116
  time to fit residues: 106.7808
Evaluate side-chains
  90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  667 LEU
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:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   chunk 57 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.144207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109287 restraints weight = 8515.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.74
r_work: 0.3125 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1836

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     :  0.430   5.092  10707  Z= 0.227
  Chirality :  0.038   0.118   1247
  Planarity :  0.004   0.075   1249
  Dihedral  : 13.951 125.419   1715
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.25 %
    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:  2.30 (0.27), residues: 936
  helix:  2.41 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.71 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 733 
 HIS   0.002   0.001   HIS A 695 
 PHE   0.013   0.001   PHE B 681 
 TYR   0.016   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
  97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7431 (mtp85)
REVERT: A  296 MET cc_start: 0.8525 (mtm) cc_final: 0.7961 (mtp)
REVERT: A  360 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7235 (pp)
REVERT: A  433 LYS cc_start: 0.6995 (mmmm) cc_final: 0.6633 (mttp)
REVERT: A  515 GLN cc_start: 0.7733 (mt0) cc_final: 0.7498 (mt0)
REVERT: A  631 LYS cc_start: 0.7542 (mmtm) cc_final: 0.6926 (ttmt)
REVERT: A  660 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7752 (tp)
REVERT: A  667 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7764 (mm)
REVERT: A  705 ARG cc_start: 0.7050 (mtm110) cc_final: 0.6653 (ttm110)
REVERT: B  296 MET cc_start: 0.8492 (mtm) cc_final: 0.7947 (mtp)
REVERT: B  433 LYS cc_start: 0.6752 (mmmm) cc_final: 0.6419 (mttp)
REVERT: B  480 ASP cc_start: 0.8405 (t0) cc_final: 0.8081 (t0)
REVERT: B  513 ASP cc_start: 0.7429 (t0) cc_final: 0.6873 (t70)
REVERT: B  624 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7580 (mtpt)
REVERT: B  631 LYS cc_start: 0.7559 (mmtm) cc_final: 0.6831 (ttmt)
REVERT: B  667 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7749 (mm)
REVERT: B  673 VAL cc_start: 0.7889 (m) cc_final: 0.7654 (p)
REVERT: B  705 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6704 (ttm110)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 1.0867
  time to fit residues: 104.8064
Evaluate side-chains
  93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  593 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0030
   chunk 52 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.9192

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.143849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108587 restraints weight = 8620.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.76
r_work: 0.3128 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7899  Z= 0.153
  Angle     :  0.438   5.898  10707  Z= 0.231
  Chirality :  0.038   0.118   1247
  Planarity :  0.004   0.073   1249
  Dihedral  : 13.882 126.253   1715
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.52 %
    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:  2.35 (0.27), residues: 936
  helix:  2.50 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.76 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 733 
 HIS   0.002   0.001   HIS B 695 
 PHE   0.013   0.001   PHE B 681 
 TYR   0.016   0.001   TYR A 739 
 ARG   0.002   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
  97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7437 (mtp85)
REVERT: A  296 MET cc_start: 0.8524 (mtm) cc_final: 0.7974 (mtp)
REVERT: A  360 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7200 (pp)
REVERT: A  433 LYS cc_start: 0.7001 (mmmm) cc_final: 0.6641 (mttp)
REVERT: A  515 GLN cc_start: 0.7775 (mt0) cc_final: 0.7545 (mt0)
REVERT: A  631 LYS cc_start: 0.7543 (mmtm) cc_final: 0.6915 (ttmt)
REVERT: A  660 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: A  667 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7784 (mm)
REVERT: A  705 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6579 (ttm110)
REVERT: B  296 MET cc_start: 0.8535 (mtm) cc_final: 0.7968 (mtp)
REVERT: B  319 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7585 (mp)
REVERT: B  433 LYS cc_start: 0.6829 (mmmm) cc_final: 0.6496 (mttp)
REVERT: B  480 ASP cc_start: 0.8411 (t0) cc_final: 0.8086 (t0)
REVERT: B  513 ASP cc_start: 0.7435 (t0) cc_final: 0.6883 (t70)
REVERT: B  515 GLN cc_start: 0.7984 (mt0) cc_final: 0.7432 (mt0)
REVERT: B  624 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7588 (mtpt)
REVERT: B  631 LYS cc_start: 0.7576 (mmtm) cc_final: 0.6899 (ttmt)
REVERT: B  667 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (mm)
REVERT: B  673 VAL cc_start: 0.7894 (m) cc_final: 0.7654 (p)
REVERT: B  705 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6712 (ttm110)
  outliers start: 11
  outliers final: 4
  residues processed: 91
  average time/residue: 1.0528
  time to fit residues: 102.5961
Evaluate side-chains
  93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  593 MET
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:    6.9990
   chunk 77 optimal weight:    0.3980
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.143516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108565 restraints weight = 8550.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.75
r_work: 0.3108 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7899  Z= 0.173
  Angle     :  0.462   7.311  10707  Z= 0.242
  Chirality :  0.039   0.123   1247
  Planarity :  0.004   0.075   1249
  Dihedral  : 13.903 128.453   1715
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.65 %
    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:  2.18 (0.27), residues: 936
  helix:  2.38 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.87 (0.37), residues: 282

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   0.014   0.001   PHE A 681 
 TYR   0.017   0.001   TYR A 739 
 ARG   0.001   0.000   ARG A 358 

********************** 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
  96 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  294 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7449 (mtp85)
REVERT: A  296 MET cc_start: 0.8534 (mtm) cc_final: 0.7996 (mtp)
REVERT: A  360 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7253 (pp)
REVERT: A  433 LYS cc_start: 0.6996 (mmmm) cc_final: 0.6643 (mttp)
REVERT: A  506 ASN cc_start: 0.7143 (m-40) cc_final: 0.6552 (m-40)
REVERT: A  515 GLN cc_start: 0.7770 (mt0) cc_final: 0.7544 (mt0)
REVERT: A  631 LYS cc_start: 0.7593 (mmtm) cc_final: 0.6983 (ttmt)
REVERT: A  660 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (tp)
REVERT: A  667 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: A  705 ARG cc_start: 0.6977 (mtm110) cc_final: 0.6677 (mtp85)
REVERT: B  296 MET cc_start: 0.8519 (mtm) cc_final: 0.7968 (mtp)
REVERT: B  319 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7604 (mp)
REVERT: B  433 LYS cc_start: 0.6835 (mmmm) cc_final: 0.6496 (mttp)
REVERT: B  480 ASP cc_start: 0.8416 (t0) cc_final: 0.8096 (t0)
REVERT: B  513 ASP cc_start: 0.7440 (t0) cc_final: 0.6894 (t70)
REVERT: B  515 GLN cc_start: 0.7999 (mt0) cc_final: 0.7445 (mt0)
REVERT: B  624 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7588 (mtmm)
REVERT: B  631 LYS cc_start: 0.7598 (mmtm) cc_final: 0.6935 (ttmt)
REVERT: B  667 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7786 (mm)
REVERT: B  705 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6705 (ttm110)
  outliers start: 10
  outliers final: 4
  residues processed: 91
  average time/residue: 1.0535
  time to fit residues: 102.8378
Evaluate side-chains
  94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  593 MET
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:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.142820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.106978 restraints weight = 8537.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.80
r_work: 0.3112 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1999

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= 0.177
  Angle     :  0.464   7.206  10707  Z= 0.243
  Chirality :  0.039   0.134   1247
  Planarity :  0.004   0.078   1249
  Dihedral  : 13.881 127.493   1715
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.65 %
    Favored  : 84.91 %
  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:  2.37 (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   0.009   0.001   TRP B 733 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.014   0.001   PHE A 681 
 TYR   0.016   0.001   TYR A 739 
 ARG   0.002   0.000   ARG A 307 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6081.33 seconds
wall clock time: 106 minutes 44.42 seconds (6404.42 seconds total)