Starting phenix.real_space_refine
on Wed Sep 17 07:11:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yex_39204/09_2025/8yex_39204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yex_39204/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yex_39204/09_2025/8yex_39204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yex_39204/09_2025/8yex_39204.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yex_39204/09_2025/8yex_39204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yex_39204/09_2025/8yex_39204.map"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.52, per 1000 atoms: 0.23
  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: 0.45
  Conformation dependent library (CDL) restraints added in 271.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.18
  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: 0.71

  Time building geometry restraints manager: 0.59 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: 0.01
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:             1.330
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.850
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.440
-------------------------------------------------------------------------------
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   6754  Z= 0.182
  Angle     :  0.794   9.565   9196  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (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
 ARG   0.007   0.001   ARG B 308 
 TYR   0.042   0.002   TYR B 368 
 PHE   0.024   0.002   PHE A 487 
 TRP   0.032   0.002   TRP A 607 
 HIS   0.004   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 6752)
  covalent geometry    : angle       0.79368 ( 9192)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       1.50492 (    4)
  hydrogen bonds       : bond        0.12697 (  432)
  hydrogen bonds       : angle       5.48182 ( 1293)

*********************** 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  : 0.232 
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: 0.0622
  time to fit residues: 13.1767
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  : 0.198 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0570
   overall best weight:    0.9304

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.173687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.132471 restraints weight = 13404.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.137023 restraints weight = 7108.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.139972 restraints weight = 5011.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.141698 restraints weight = 4126.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.142660 restraints weight = 3706.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6754  Z= 0.152
  Angle     :  0.647   8.503   9196  Z= 0.331
  Chirality :  0.043   0.138   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.558  38.335    868
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.31), residues: 780
  helix:  1.60 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.97 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 570 
 TYR   0.026   0.002   TYR A 524 
 PHE   0.025   0.001   PHE B 511 
 TRP   0.022   0.001   TRP B 292 
 HIS   0.004   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6752)
  covalent geometry    : angle       0.64668 ( 9192)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       1.21975 (    4)
  hydrogen bonds       : bond        0.05433 (  432)
  hydrogen bonds       : angle       4.30217 ( 1293)

*********************** 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
  175 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8278 (t80) cc_final: 0.7907 (t80)
REVERT: A  558 TYR cc_start: 0.2647 (OUTLIER) cc_final: 0.1794 (t80)
REVERT: A  615 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7818 (mm-30)
REVERT: B  308 ARG cc_start: 0.8407 (mmp80) cc_final: 0.8088 (mmp80)
REVERT: B  495 LEU cc_start: 0.9094 (mm) cc_final: 0.8809 (pp)
  outliers start: 22
  outliers final: 9
  residues processed: 170
  average time/residue: 0.0660
  time to fit residues: 15.9485
Evaluate side-chains
  150 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 55 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.4376 r_free = 0.4376 target = 0.173586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.132837 restraints weight = 13344.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.137301 restraints weight = 7088.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.140183 restraints weight = 5008.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.141899 restraints weight = 4138.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.142433 restraints weight = 3707.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6754  Z= 0.139
  Angle     :  0.618   9.003   9196  Z= 0.315
  Chirality :  0.042   0.142   1006
  Planarity :  0.004   0.036   1120
  Dihedral  :  4.270  17.080    864
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.31), residues: 780
  helix:  1.76 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.91 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 570 
 TYR   0.019   0.002   TYR A 524 
 PHE   0.016   0.001   PHE B 474 
 TRP   0.018   0.002   TRP B 514 
 HIS   0.007   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6752)
  covalent geometry    : angle       0.61742 ( 9192)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       1.21190 (    4)
  hydrogen bonds       : bond        0.05065 (  432)
  hydrogen bonds       : angle       4.13244 ( 1293)

*********************** 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
  180 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8268 (t80) cc_final: 0.7885 (t80)
REVERT: A  531 LYS cc_start: 0.7514 (tptp) cc_final: 0.7157 (tptp)
REVERT: A  532 MET cc_start: 0.7244 (mmm) cc_final: 0.6988 (mmm)
REVERT: A  558 TYR cc_start: 0.2645 (OUTLIER) cc_final: 0.1701 (t80)
REVERT: B  308 ARG cc_start: 0.8419 (mmp80) cc_final: 0.8111 (mmp80)
REVERT: B  495 LEU cc_start: 0.9144 (mm) cc_final: 0.8822 (pp)
  outliers start: 30
  outliers final: 12
  residues processed: 171
  average time/residue: 0.0568
  time to fit residues: 14.1924
Evaluate side-chains
  146 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
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  413 MET
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  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 35 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0980
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0870
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5960

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.174280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.133719 restraints weight = 13514.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.138349 restraints weight = 7172.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.141291 restraints weight = 5038.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.142619 restraints weight = 4127.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.143637 restraints weight = 3736.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6754  Z= 0.132
  Angle     :  0.632   9.172   9196  Z= 0.318
  Chirality :  0.043   0.191   1006
  Planarity :  0.004   0.037   1120
  Dihedral  :  4.237  17.035    864
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 27.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.31), residues: 780
  helix:  1.78 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.89 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 380 
 TYR   0.017   0.002   TYR B 483 
 PHE   0.025   0.001   PHE B 511 
 TRP   0.025   0.001   TRP A 607 
 HIS   0.006   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6752)
  covalent geometry    : angle       0.63183 ( 9192)
  SS BOND              : bond        0.00234 (    2)
  SS BOND              : angle       1.17997 (    4)
  hydrogen bonds       : bond        0.04828 (  432)
  hydrogen bonds       : angle       4.11700 ( 1293)

*********************** 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: 32
    poor density    : 149
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8553 (t80) cc_final: 0.8034 (t80)
REVERT: A  462 GLN cc_start: 0.8839 (mt0) cc_final: 0.8513 (mt0)
REVERT: A  531 LYS cc_start: 0.7613 (tptp) cc_final: 0.7253 (tptp)
REVERT: A  532 MET cc_start: 0.7295 (mmm) cc_final: 0.7077 (mmm)
REVERT: A  558 TYR cc_start: 0.2478 (OUTLIER) cc_final: 0.1472 (t80)
REVERT: B  308 ARG cc_start: 0.8457 (mmp80) cc_final: 0.8152 (mmp80)
REVERT: B  528 TRP cc_start: 0.8583 (t-100) cc_final: 0.8250 (t-100)
  outliers start: 32
  outliers final: 22
  residues processed: 174
  average time/residue: 0.0568
  time to fit residues: 14.4342
Evaluate side-chains
  157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  284 LEU
Chi-restraints excluded: chain A residue  349 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  278 LEU
Chi-restraints excluded: chain B residue  285 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  538 ASP
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 50 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0040
   chunk 39 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.4090

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 387 HIS
** 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 = 0.4389 r_free = 0.4389 target = 0.175534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.135156 restraints weight = 13615.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.139812 restraints weight = 7190.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.142805 restraints weight = 5047.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.144107 restraints weight = 4139.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.145344 restraints weight = 3738.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6754  Z= 0.128
  Angle     :  0.616  10.156   9196  Z= 0.311
  Chirality :  0.042   0.144   1006
  Planarity :  0.004   0.039   1120
  Dihedral  :  4.219  17.344    864
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.31), residues: 780
  helix:  1.85 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.85 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 570 
 TYR   0.018   0.001   TYR A 524 
 PHE   0.026   0.001   PHE B 357 
 TRP   0.028   0.001   TRP A 607 
 HIS   0.003   0.000   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6752)
  covalent geometry    : angle       0.61581 ( 9192)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       1.00332 (    4)
  hydrogen bonds       : bond        0.04564 (  432)
  hydrogen bonds       : angle       4.06952 ( 1293)

*********************** 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
  169 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8571 (t80) cc_final: 0.7973 (t80)
REVERT: A  398 ASP cc_start: 0.7858 (t0) cc_final: 0.7620 (t0)
REVERT: A  531 LYS cc_start: 0.7504 (tptp) cc_final: 0.6865 (tptp)
REVERT: A  532 MET cc_start: 0.7168 (mmm) cc_final: 0.6912 (mmm)
REVERT: A  558 TYR cc_start: 0.2414 (OUTLIER) cc_final: 0.1405 (t80)
REVERT: B  284 LEU cc_start: 0.8748 (mt) cc_final: 0.8484 (mt)
REVERT: B  308 ARG cc_start: 0.8456 (mmp80) cc_final: 0.8108 (mmp80)
REVERT: B  495 LEU cc_start: 0.9080 (mm) cc_final: 0.8787 (pp)
REVERT: B  615 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7803 (mm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 163
  average time/residue: 0.0617
  time to fit residues: 14.4764
Evaluate side-chains
  148 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  349 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  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  310 ASN
Chi-restraints excluded: chain B residue  417 TYR
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 72 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0270
   chunk 11 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6642

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.175425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.134912 restraints weight = 13809.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.139457 restraints weight = 7316.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.142301 restraints weight = 5176.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.144104 restraints weight = 4271.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.144478 restraints weight = 3832.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6754  Z= 0.129
  Angle     :  0.625  10.276   9196  Z= 0.312
  Chirality :  0.042   0.166   1006
  Planarity :  0.004   0.040   1120
  Dihedral  :  4.192  17.359    864
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 26.93 %
    Favored  : 68.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.31), residues: 780
  helix:  1.94 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.84 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 548 
 TYR   0.015   0.001   TYR A 524 
 PHE   0.028   0.001   PHE B 511 
 TRP   0.019   0.001   TRP A 607 
 HIS   0.003   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6752)
  covalent geometry    : angle       0.62488 ( 9192)
  SS BOND              : bond        0.00414 (    2)
  SS BOND              : angle       1.00268 (    4)
  hydrogen bonds       : bond        0.04557 (  432)
  hydrogen bonds       : angle       4.00138 ( 1293)

*********************** 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
  171 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8546 (t80) cc_final: 0.8032 (t80)
REVERT: A  531 LYS cc_start: 0.7508 (tptp) cc_final: 0.6924 (tptp)
REVERT: A  532 MET cc_start: 0.7193 (mmm) cc_final: 0.6977 (mmm)
REVERT: A  558 TYR cc_start: 0.2427 (OUTLIER) cc_final: 0.1498 (t80)
REVERT: B  308 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8110 (mmp80)
REVERT: B  495 LEU cc_start: 0.9037 (mm) cc_final: 0.8754 (pp)
  outliers start: 32
  outliers final: 23
  residues processed: 161
  average time/residue: 0.0576
  time to fit residues: 13.6524
Evaluate side-chains
  153 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  284 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  349 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  396 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0370
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.0062

-------------------------------------------------------------------------------
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 462 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.174606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.133858 restraints weight = 13590.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.138403 restraints weight = 7235.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.141208 restraints weight = 5141.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.142391 restraints weight = 4247.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.143759 restraints weight = 3865.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6754  Z= 0.141
  Angle     :  0.637  10.769   9196  Z= 0.316
  Chirality :  0.043   0.171   1006
  Planarity :  0.004   0.041   1120
  Dihedral  :  4.197  17.520    864
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 28.22 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.31), residues: 780
  helix:  1.89 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.66 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 548 
 TYR   0.014   0.001   TYR A 524 
 PHE   0.024   0.001   PHE B 357 
 TRP   0.020   0.002   TRP A 607 
 HIS   0.003   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6752)
  covalent geometry    : angle       0.63674 ( 9192)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       1.07123 (    4)
  hydrogen bonds       : bond        0.04780 (  432)
  hydrogen bonds       : angle       4.04575 ( 1293)

*********************** 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
  163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8585 (t80) cc_final: 0.8090 (t80)
REVERT: A  531 LYS cc_start: 0.7519 (tptp) cc_final: 0.6964 (tptp)
REVERT: A  558 TYR cc_start: 0.2692 (OUTLIER) cc_final: 0.1710 (t80)
REVERT: B  308 ARG cc_start: 0.8426 (mmp80) cc_final: 0.8038 (mmp80)
REVERT: B  495 LEU cc_start: 0.9048 (mm) cc_final: 0.8757 (pp)
  outliers start: 28
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0646
  time to fit residues: 14.2411
Evaluate side-chains
  152 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  349 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
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 58 optimal weight:    0.3980
   chunk 45 optimal weight:    0.2980
   chunk 70 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0980
   chunk 17 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0980
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
** B 476 HIS ** 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 = 0.4401 r_free = 0.4401 target = 0.176190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.136140 restraints weight = 13549.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.140648 restraints weight = 7120.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.143408 restraints weight = 5030.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.145290 restraints weight = 4153.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.146052 restraints weight = 3714.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6754  Z= 0.123
  Angle     :  0.621  10.476   9196  Z= 0.309
  Chirality :  0.043   0.224   1006
  Planarity :  0.004   0.041   1120
  Dihedral  :  4.153  17.557    864
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.23 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.31), residues: 780
  helix:  1.93 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.65 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 548 
 TYR   0.018   0.001   TYR B 290 
 PHE   0.028   0.001   PHE B 511 
 TRP   0.036   0.002   TRP A 607 
 HIS   0.003   0.000   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6752)
  covalent geometry    : angle       0.62090 ( 9192)
  SS BOND              : bond        0.00353 (    2)
  SS BOND              : angle       1.06533 (    4)
  hydrogen bonds       : bond        0.04343 (  432)
  hydrogen bonds       : angle       3.95115 ( 1293)

*********************** 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
  158 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8535 (t80) cc_final: 0.8001 (t80)
REVERT: A  462 GLN cc_start: 0.8779 (mt0) cc_final: 0.8494 (mt0)
REVERT: A  531 LYS cc_start: 0.7472 (tptp) cc_final: 0.7270 (tptp)
REVERT: A  558 TYR cc_start: 0.2412 (OUTLIER) cc_final: 0.1343 (t80)
REVERT: B  308 ARG cc_start: 0.8480 (mmp80) cc_final: 0.8094 (mmp80)
REVERT: B  495 LEU cc_start: 0.9045 (mm) cc_final: 0.8749 (pp)
  outliers start: 20
  outliers final: 16
  residues processed: 153
  average time/residue: 0.0604
  time to fit residues: 13.5106
Evaluate side-chains
  151 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  349 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
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0270
   chunk 64 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
B 288 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
** B 476 HIS ** 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 = 0.4397 r_free = 0.4397 target = 0.175228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.133838 restraints weight = 13650.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.138484 restraints weight = 7280.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.141409 restraints weight = 5155.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.143186 restraints weight = 4251.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.143888 restraints weight = 3823.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6754  Z= 0.130
  Angle     :  0.611  10.258   9196  Z= 0.308
  Chirality :  0.042   0.164   1006
  Planarity :  0.004   0.047   1120
  Dihedral  :  4.124  17.815    864
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.37 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.31), residues: 780
  helix:  1.93 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.60 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 308 
 TYR   0.015   0.001   TYR A 496 
 PHE   0.026   0.001   PHE A 416 
 TRP   0.032   0.002   TRP A 607 
 HIS   0.003   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6752)
  covalent geometry    : angle       0.61098 ( 9192)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       1.11362 (    4)
  hydrogen bonds       : bond        0.04448 (  432)
  hydrogen bonds       : angle       3.97676 ( 1293)

*********************** 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
  149 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8558 (t80) cc_final: 0.8051 (t80)
REVERT: A  462 GLN cc_start: 0.8789 (mt0) cc_final: 0.8503 (mt0)
REVERT: A  531 LYS cc_start: 0.7392 (tptp) cc_final: 0.7035 (tptp)
REVERT: A  532 MET cc_start: 0.6905 (mmm) cc_final: 0.6424 (mmm)
REVERT: A  558 TYR cc_start: 0.2533 (OUTLIER) cc_final: 0.1473 (t80)
REVERT: B  308 ARG cc_start: 0.8490 (mmp80) cc_final: 0.8049 (mmp80)
  outliers start: 20
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0592
  time to fit residues: 12.3205
Evaluate side-chains
  144 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  349 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  394 PHE
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 62 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0670
   chunk 14 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0070
   chunk 59 optimal weight:    0.0020
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.2944

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
B 310 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
** B 476 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 = 0.4411 r_free = 0.4411 target = 0.176653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135800 restraints weight = 13376.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.140285 restraints weight = 7519.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.143027 restraints weight = 5473.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.144533 restraints weight = 4582.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.145672 restraints weight = 4155.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6754  Z= 0.125
  Angle     :  0.628  10.431   9196  Z= 0.317
  Chirality :  0.042   0.163   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.097  18.005    864
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.94 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.31), residues: 780
  helix:  2.00 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.58 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 548 
 TYR   0.018   0.001   TYR B 290 
 PHE   0.026   0.001   PHE B 511 
 TRP   0.030   0.002   TRP A 607 
 HIS   0.003   0.000   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6752)
  covalent geometry    : angle       0.62805 ( 9192)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       1.18843 (    4)
  hydrogen bonds       : bond        0.04111 (  432)
  hydrogen bonds       : angle       3.90947 ( 1293)

********************** 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
  160 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 PHE cc_start: 0.8564 (t80) cc_final: 0.7872 (t80)
REVERT: A  458 LEU cc_start: 0.9224 (mt) cc_final: 0.8966 (mt)
REVERT: A  462 GLN cc_start: 0.8762 (mt0) cc_final: 0.8487 (mt0)
REVERT: A  482 LYS cc_start: 0.9517 (ttpp) cc_final: 0.8959 (ttpp)
REVERT: A  558 TYR cc_start: 0.2188 (OUTLIER) cc_final: 0.1113 (t80)
REVERT: B  308 ARG cc_start: 0.8456 (mmp80) cc_final: 0.8039 (mmp80)
REVERT: B  495 LEU cc_start: 0.9053 (mm) cc_final: 0.8760 (pp)
  outliers start: 20
  outliers final: 18
  residues processed: 155
  average time/residue: 0.0626
  time to fit residues: 14.1076
Evaluate side-chains
  153 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  396 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  394 PHE
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 43 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:    0.3980
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 452 GLN
B 462 GLN
** B 476 HIS ** 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 = 0.4392 r_free = 0.4392 target = 0.175952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134954 restraints weight = 13965.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.139490 restraints weight = 7668.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.142366 restraints weight = 5506.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.144100 restraints weight = 4548.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.144809 restraints weight = 4092.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
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      :  0.003   0.032   6754  Z= 0.138
  Angle     :  0.648  10.215   9196  Z= 0.326
  Chirality :  0.045   0.276   1006
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.083  18.405    864
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 30.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.31), residues: 780
  helix:  1.95 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.49 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 548 
 TYR   0.016   0.001   TYR B 272 
 PHE   0.027   0.001   PHE A 416 
 TRP   0.048   0.002   TRP A 607 
 HIS   0.003   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6752)
  covalent geometry    : angle       0.64787 ( 9192)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       1.13902 (    4)
  hydrogen bonds       : bond        0.04388 (  432)
  hydrogen bonds       : angle       3.98642 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1339.73 seconds
wall clock time: 23 minutes 49.46 seconds (1429.46 seconds total)