Starting phenix.real_space_refine
on Tue Mar 11 19:17:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yex_39204/03_2025/8yex_39204.cif"
  }
  resolution = 3.68
  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=  -0.001 sd=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4384      2.51       5
     N    1044      2.21       5
     O    1074      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 6532
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3266
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 14, 'TRANS': 377}
    Chain: "B"
      Number of atoms: 3266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3266
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 14, 'TRANS': 377}
  Time building chain proxies: 4.59, per 1000 atoms: 0.70
  Number of scatterers: 6532
  At special positions: 0
  Unit cell: (78.1, 68.2, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1074      8.00
     N    1044      7.00
     C    4384      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 1.45
  Conformation dependent library (CDL) restraints added in 863.2 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      76.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 259
      removed outlier: 3.768A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 3.816A  pdb=" N   ILE A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.726A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
      removed outlier: 3.526A  pdb=" N   ALA A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 383
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 390 through 402
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.854A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 4.392A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.254A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 532
      removed outlier: 3.799A  pdb=" N   PHE A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET A 532 " --> pdb=" O   TRP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 583
      removed outlier: 3.802A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 574 " --> pdb=" O   ARG A 570 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 619
      removed outlier: 4.404A  pdb=" N   ASP A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 4.446A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 259
      removed outlier: 3.902A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 3.513A  pdb=" N   ILE B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
      removed outlier: 3.679A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.812A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.063A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 503
      removed outlier: 3.903A  pdb=" N   ALA B 480 " --> pdb=" O   HIS B 476 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 530
      removed outlier: 3.959A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 583
      removed outlier: 3.838A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER B 581 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 597
    Processing helix  chain 'B' and resid 599 through 619
      removed outlier: 4.013A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1932
        1.34 -     1.46: 1951
        1.46 -     1.58: 2826
        1.58 -     1.70: 1
        1.70 -     1.83: 42
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CB  PRO B 338 "
       pdb=" CG  PRO B 338 "
    ideal  model  delta    sigma   weight residual
    1.492  1.592 -0.100 5.00e-02 4.00e+02 4.03e+00
  bond pdb=" C   PHE A 474 "
       pdb=" N   PRO A 475 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.15e+00
  bond pdb=" CG  LEU A 284 "
       pdb=" CD1 LEU A 284 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.97e+00
  bond pdb=" CB  PHE B 354 "
       pdb=" CG  PHE B 354 "
    ideal  model  delta    sigma   weight residual
    1.502  1.532 -0.030 2.30e-02 1.89e+03 1.67e+00
  bond pdb=" CB  TRP B 423 "
       pdb=" CG  TRP B 423 "
    ideal  model  delta    sigma   weight residual
    1.498  1.537 -0.039 3.10e-02 1.04e+03 1.59e+00
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 8914
        1.91 -     3.83: 216
        3.83 -     5.74: 45
        5.74 -     7.65: 11
        7.65 -     9.57: 6
  Bond angle restraints: 9192
  Sorted by residual:
  angle pdb=" CA  PRO B 338 "
        pdb=" N   PRO B 338 "
        pdb=" CD  PRO B 338 "
      ideal   model   delta    sigma   weight residual
     112.00  107.08    4.92 1.40e+00 5.10e-01 1.24e+01
  angle pdb=" N   VAL A 346 "
        pdb=" CA  VAL A 346 "
        pdb=" C   VAL A 346 "
      ideal   model   delta    sigma   weight residual
     112.96  110.03    2.93 1.00e+00 1.00e+00 8.57e+00
  angle pdb=" N   VAL B 341 "
        pdb=" CA  VAL B 341 "
        pdb=" C   VAL B 341 "
      ideal   model   delta    sigma   weight residual
     111.67  108.97    2.70 9.50e-01 1.11e+00 8.11e+00
  angle pdb=" CA  GLU A 304 "
        pdb=" CB  GLU A 304 "
        pdb=" CG  GLU A 304 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.97e+00
  angle pdb=" CA  PRO B 598 "
        pdb=" C   PRO B 598 "
        pdb=" O   PRO B 598 "
      ideal   model   delta    sigma   weight residual
     121.38  119.21    2.17 7.70e-01 1.69e+00 7.96e+00
  ... (remaining 9187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3243
       17.86 -    35.72: 453
       35.72 -    53.57: 121
       53.57 -    71.43: 9
       71.43 -    89.29: 8
  Dihedral angle restraints: 3834
    sinusoidal: 1518
      harmonic: 2316
  Sorted by residual:
  dihedral pdb=" CB  CYS B 415 "
           pdb=" SG  CYS B 415 "
           pdb=" SG  CYS B 440 "
           pdb=" CB  CYS B 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.38  -64.38     1      1.00e+01 1.00e-02 5.45e+01
  dihedral pdb=" CA  PHE B 517 "
           pdb=" C   PHE B 517 "
           pdb=" N   TYR B 518 "
           pdb=" CA  TYR B 518 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.99   18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ALA A 473 "
           pdb=" C   ALA A 473 "
           pdb=" N   PHE A 474 "
           pdb=" CA  PHE A 474 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.06  -16.94     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 3831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 719
       0.044 -    0.087: 224
       0.087 -    0.130: 54
       0.130 -    0.174: 8
       0.174 -    0.217: 1
  Chirality restraints: 1006
  Sorted by residual:
  chirality pdb=" CB  ILE A 461 "
            pdb=" CA  ILE A 461 "
            pdb=" CG1 ILE A 461 "
            pdb=" CG2 ILE A 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CG  LEU B 536 "
            pdb=" CB  LEU B 536 "
            pdb=" CD1 LEU B 536 "
            pdb=" CD2 LEU B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CG  LEU A 284 "
            pdb=" CB  LEU A 284 "
            pdb=" CD1 LEU A 284 "
            pdb=" CD2 LEU A 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.41e-01
  ... (remaining 1003 not shown)

  Planarity restraints: 1120
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 337 "   -0.064 5.00e-02 4.00e+02   9.49e-02 1.44e+01
        pdb=" N   PRO B 338 "    0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO B 338 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 338 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 368 "   -0.012 2.00e-02 2.50e+03   1.75e-02 6.12e+00
        pdb=" CG  TYR B 368 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 368 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 368 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 368 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 368 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 368 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 368 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 540 "    0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   ASN A 540 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASN A 540 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 541 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1117 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 137
        2.69 -     3.24: 6951
        3.24 -     3.80: 10704
        3.80 -     4.35: 12674
        4.35 -     4.90: 20693
  Nonbonded interactions: 51159
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 478 "
            pdb=" OH  TYR B 524 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OH  TYR A 443 "
            pdb=" O   THR A 580 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OD2 ASP B 529 "
            pdb=" NH2 ARG B 570 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" O   SER A 578 "
            pdb=" OG1 THR A 582 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   CYS B 440 "
            pdb=" NH2 ARG B 448 "
     model   vdw
     2.220 3.120
  ... (remaining 51154 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             1.420
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.470
  Find NCS groups from input model:        0.190
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
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      :  0.004   0.100   6752  Z= 0.266
  Angle     :  0.794   9.565   9192  Z= 0.427
  Chirality :  0.045   0.217   1006
  Planarity :  0.005   0.095   1120
  Dihedral  : 17.185  89.290   2336
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 32.23 %
    Favored  : 67.05 %
  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:  0.80 (0.31), residues: 780
  helix:  1.42 (0.22), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.89 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 607 
 HIS   0.004   0.001   HIS A 504 
 PHE   0.024   0.002   PHE A 487 
 TYR   0.042   0.002   TYR B 368 
 ARG   0.007   0.001   ARG B 308 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  284 LEU cc_start: 0.8820 (mt) cc_final: 0.8481 (mt)
REVERT: B  308 ARG cc_start: 0.8362 (mmp80) cc_final: 0.7995 (mmp80)
  outliers start: 5
  outliers final: 2
  residues processed: 150
  average time/residue: 0.1626
  time to fit residues: 33.7017
Evaluate side-chains
  144 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  590 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.173938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.132955 restraints weight = 13326.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.137541 restraints weight = 7107.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.140390 restraints weight = 5023.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6752  Z= 0.228
  Angle     :  0.651   8.474   9192  Z= 0.335
  Chirality :  0.043   0.138   1006
  Planarity :  0.004   0.047   1120
  Dihedral  :  4.564  38.288    868
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 26.65 %
    Favored  : 70.06 %
  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:  0.99 (0.31), residues: 780
  helix:  1.59 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.97 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 292 
 HIS   0.004   0.001   HIS A 504 
 PHE   0.025   0.001   PHE B 511 
 TYR   0.025   0.002   TYR A 524 
 ARG   0.007   0.001   ARG B 570 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8301 (t80) cc_final: 0.7930 (t80)
REVERT: A  558 TYR cc_start: 0.2664 (OUTLIER) cc_final: 0.1819 (t80)
REVERT: A  615 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: B  308 ARG cc_start: 0.8432 (mmp80) cc_final: 0.8107 (mmp80)
  outliers start: 23
  outliers final: 9
  residues processed: 169
  average time/residue: 0.1519
  time to fit residues: 36.2984
Evaluate side-chains
  149 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  486 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.173134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.132244 restraints weight = 13472.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.136737 restraints weight = 7126.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.139572 restraints weight = 5035.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6752  Z= 0.208
  Angle     :  0.628   8.763   9192  Z= 0.319
  Chirality :  0.042   0.144   1006
  Planarity :  0.004   0.036   1120
  Dihedral  :  4.284  17.073    864
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.64 %
    Favored  : 69.34 %
  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:  1.19 (0.31), residues: 780
  helix:  1.72 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.92 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 514 
 HIS   0.007   0.001   HIS B 499 
 PHE   0.016   0.001   PHE B 474 
 TYR   0.020   0.002   TYR A 524 
 ARG   0.006   0.001   ARG B 570 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8293 (t80) cc_final: 0.7866 (t80)
REVERT: A  398 ASP cc_start: 0.7796 (t0) cc_final: 0.7592 (t0)
REVERT: A  531 LYS cc_start: 0.7665 (tptp) cc_final: 0.7300 (tptp)
REVERT: A  532 MET cc_start: 0.7389 (mmm) cc_final: 0.7150 (mmm)
REVERT: A  558 TYR cc_start: 0.2549 (OUTLIER) cc_final: 0.1663 (t80)
REVERT: B  308 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8131 (mmp80)
REVERT: B  495 LEU cc_start: 0.9141 (mm) cc_final: 0.8820 (pp)
  outliers start: 35
  outliers final: 15
  residues processed: 175
  average time/residue: 0.1386
  time to fit residues: 34.4146
Evaluate side-chains
  155 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 ASN
B 452 GLN
** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.174367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.133919 restraints weight = 13665.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.138472 restraints weight = 7135.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.141265 restraints weight = 5006.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6752  Z= 0.183
  Angle     :  0.633   9.147   9192  Z= 0.318
  Chirality :  0.043   0.168   1006
  Planarity :  0.004   0.036   1120
  Dihedral  :  4.257  16.751    864
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 26.93 %
    Favored  : 68.62 %
  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:  1.26 (0.31), residues: 780
  helix:  1.74 (0.22), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.79 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 607 
 HIS   0.006   0.001   HIS B 499 
 PHE   0.026   0.001   PHE B 511 
 TYR   0.017   0.002   TYR B 483 
 ARG   0.004   0.001   ARG A 380 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8527 (t80) cc_final: 0.7991 (t80)
REVERT: A  462 GLN cc_start: 0.8826 (mt0) cc_final: 0.8498 (mt0)
REVERT: A  531 LYS cc_start: 0.7641 (tptp) cc_final: 0.7062 (tptp)
REVERT: A  532 MET cc_start: 0.7311 (mmm) cc_final: 0.7008 (mmm)
REVERT: A  558 TYR cc_start: 0.2549 (OUTLIER) cc_final: 0.1550 (t80)
REVERT: A  615 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7800 (mm-30)
REVERT: B  308 ARG cc_start: 0.8451 (mmp80) cc_final: 0.8149 (mmp80)
  outliers start: 31
  outliers final: 19
  residues processed: 171
  average time/residue: 0.1389
  time to fit residues: 33.5780
Evaluate side-chains
  157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 69 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    0.1980
   chunk 14 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.174005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.133699 restraints weight = 13460.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.138060 restraints weight = 7425.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.140836 restraints weight = 5344.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6752  Z= 0.178
  Angle     :  0.618   9.928   9192  Z= 0.310
  Chirality :  0.042   0.143   1006
  Planarity :  0.004   0.037   1120
  Dihedral  :  4.222  17.120    864
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 27.51 %
    Favored  : 68.05 %
  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:  1.32 (0.31), residues: 780
  helix:  1.82 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.84 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.021   0.001   PHE A 416 
 TYR   0.019   0.002   TYR A 524 
 ARG   0.004   0.000   ARG B 570 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8594 (t80) cc_final: 0.8076 (t80)
REVERT: A  531 LYS cc_start: 0.7516 (tptp) cc_final: 0.7138 (tptp)
REVERT: A  532 MET cc_start: 0.7207 (mmm) cc_final: 0.6982 (mmm)
REVERT: A  558 TYR cc_start: 0.2551 (OUTLIER) cc_final: 0.1542 (t80)
REVERT: B  308 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8104 (mmp80)
REVERT: B  495 LEU cc_start: 0.9083 (mm) cc_final: 0.8791 (pp)
REVERT: B  615 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7816 (mm-30)
  outliers start: 31
  outliers final: 17
  residues processed: 171
  average time/residue: 0.1400
  time to fit residues: 34.3031
Evaluate side-chains
  150 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0000
   chunk 67 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0070
   chunk 55 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4804

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 310 ASN
B 452 GLN
B 476 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.176349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.135982 restraints weight = 13533.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.140556 restraints weight = 7227.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.143361 restraints weight = 5107.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6752  Z= 0.172
  Angle     :  0.634  10.153   9192  Z= 0.312
  Chirality :  0.043   0.163   1006
  Planarity :  0.004   0.040   1120
  Dihedral  :  4.191  17.251    864
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 27.51 %
    Favored  : 68.34 %
  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:  1.38 (0.31), residues: 780
  helix:  1.85 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.77 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.030   0.001   PHE B 357 
 TYR   0.015   0.002   TYR A 524 
 ARG   0.003   0.000   ARG A 604 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8593 (t80) cc_final: 0.8083 (t80)
REVERT: A  531 LYS cc_start: 0.7523 (tptp) cc_final: 0.6945 (tptp)
REVERT: A  532 MET cc_start: 0.7168 (mmm) cc_final: 0.6968 (mmm)
REVERT: A  558 TYR cc_start: 0.2499 (OUTLIER) cc_final: 0.1551 (t80)
REVERT: B  308 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8103 (mmp80)
REVERT: B  495 LEU cc_start: 0.9034 (mm) cc_final: 0.8752 (pp)
  outliers start: 29
  outliers final: 16
  residues processed: 160
  average time/residue: 0.1372
  time to fit residues: 31.4737
Evaluate side-chains
  145 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0070
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.175611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.135081 restraints weight = 13507.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.139634 restraints weight = 7229.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.142522 restraints weight = 5128.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6752  Z= 0.178
  Angle     :  0.620  10.976   9192  Z= 0.310
  Chirality :  0.043   0.181   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.177  17.372    864
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 29.66 %
    Favored  : 66.76 %
  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:  1.46 (0.31), residues: 780
  helix:  1.88 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.67 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.014   0.001   PHE B 354 
 TYR   0.014   0.001   TYR A 524 
 ARG   0.003   0.000   ARG B 308 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8570 (t80) cc_final: 0.8030 (t80)
REVERT: A  531 LYS cc_start: 0.7502 (tptp) cc_final: 0.6936 (tptp)
REVERT: A  558 TYR cc_start: 0.2517 (OUTLIER) cc_final: 0.1443 (t80)
REVERT: B  308 ARG cc_start: 0.8495 (mmp80) cc_final: 0.8105 (mmp80)
REVERT: B  495 LEU cc_start: 0.9043 (mm) cc_final: 0.8750 (pp)
  outliers start: 25
  outliers final: 19
  residues processed: 149
  average time/residue: 0.1310
  time to fit residues: 28.3490
Evaluate side-chains
  152 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 288 ASN
B 310 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.173384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.132407 restraints weight = 13477.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.136928 restraints weight = 7173.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.139799 restraints weight = 5077.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6752  Z= 0.228
  Angle     :  0.641  10.559   9192  Z= 0.319
  Chirality :  0.043   0.180   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.191  17.796    864
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.94 %
    Favored  : 67.34 %
  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:  1.45 (0.31), residues: 780
  helix:  1.84 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.57 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.028   0.001   PHE B 511 
 TYR   0.017   0.002   TYR B 560 
 ARG   0.004   0.000   ARG A 548 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8604 (t80) cc_final: 0.8118 (t80)
REVERT: A  462 GLN cc_start: 0.8825 (mt0) cc_final: 0.8532 (mt0)
REVERT: A  558 TYR cc_start: 0.2708 (OUTLIER) cc_final: 0.1763 (t80)
REVERT: B  308 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8102 (mmp80)
  outliers start: 26
  outliers final: 18
  residues processed: 160
  average time/residue: 0.1357
  time to fit residues: 31.4033
Evaluate side-chains
  151 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
B 288 ASN
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.173605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.132749 restraints weight = 13411.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.137047 restraints weight = 7504.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.139827 restraints weight = 5441.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6752  Z= 0.197
  Angle     :  0.663  11.180   9192  Z= 0.326
  Chirality :  0.045   0.265   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.173  17.674    864
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 29.94 %
    Favored  : 67.05 %
  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:  1.43 (0.31), residues: 780
  helix:  1.81 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.53 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 607 
 HIS   0.003   0.001   HIS B 499 
 PHE   0.018   0.001   PHE B 322 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A 548 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8591 (t80) cc_final: 0.8127 (t80)
REVERT: A  462 GLN cc_start: 0.8823 (mt0) cc_final: 0.8529 (mt0)
REVERT: A  558 TYR cc_start: 0.2629 (OUTLIER) cc_final: 0.1584 (t80)
REVERT: B  308 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8139 (mmp80)
  outliers start: 21
  outliers final: 18
  residues processed: 149
  average time/residue: 0.1371
  time to fit residues: 29.3883
Evaluate side-chains
  154 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    0.2980
   chunk 77 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0020
   chunk 14 optimal weight:    0.1980
   chunk 34 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 310 ASN
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.176283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.134010 restraints weight = 13677.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.138655 restraints weight = 7378.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.141527 restraints weight = 5296.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6752  Z= 0.171
  Angle     :  0.654  10.943   9192  Z= 0.321
  Chirality :  0.044   0.193   1006
  Planarity :  0.004   0.045   1120
  Dihedral  :  4.161  17.849    864
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 30.95 %
    Favored  : 66.76 %
  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:  1.45 (0.31), residues: 780
  helix:  1.85 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.55 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.028   0.001   PHE B 511 
 TYR   0.017   0.001   TYR A 496 
 ARG   0.004   0.000   ARG A 548 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8616 (t80) cc_final: 0.7950 (t80)
REVERT: A  462 GLN cc_start: 0.8756 (mt0) cc_final: 0.8493 (mt0)
REVERT: A  558 TYR cc_start: 0.2549 (OUTLIER) cc_final: 0.1524 (t80)
REVERT: B  308 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8128 (mmp80)
  outliers start: 16
  outliers final: 14
  residues processed: 148
  average time/residue: 0.1393
  time to fit residues: 29.6180
Evaluate side-chains
  150 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  492 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  558 TYR
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  419 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0060
   chunk 49 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
B 288 ASN
B 310 ASN
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.175552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.134482 restraints weight = 13655.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.139080 restraints weight = 7277.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.142086 restraints weight = 5126.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.147   6752  Z= 0.343
  Angle     :  1.059  59.200   9192  Z= 0.612
  Chirality :  0.048   0.587   1006
  Planarity :  0.004   0.051   1120
  Dihedral  :  4.178  17.847    864
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 31.52 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.13 %
  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:  1.45 (0.31), residues: 780
  helix:  1.84 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.54 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 607 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.022   0.001   PHE B 354 
 TYR   0.017   0.001   TYR A 352 
 ARG   0.004   0.000   ARG A 548 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2328.79 seconds
wall clock time: 40 minutes 59.49 seconds (2459.49 seconds total)