Starting phenix.real_space_refine
on Tue Nov 18 06:41:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oyb_3860/11_2025/5oyb_3860.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      74      5.16       5
     C    7684      2.51       5
     N    1936      2.21       5
     O    2072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11770
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5883
          Classifications: {'peptide': 718}
          Link IDs: {'PTRANS': 31, 'TRANS': 686}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.98, per 1000 atoms: 0.42
  Number of scatterers: 11770
  At special positions: 0
  Unit cell: (87.075, 125.775, 121.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      74     16.00
     O    2072      8.00
     N    1936      7.00
     C    7684      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=1.97
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=1.97

  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: 0.97
  Conformation dependent library (CDL) restraints added in 582.8 milliseconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      62.1% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 175 through 182
      removed outlier: 4.299A  pdb=" N   TYR A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.626A  pdb=" N   THR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 275
      removed outlier: 4.341A  pdb=" N   GLY A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 316 through 325
      removed outlier: 3.781A  pdb=" N   LYS A 322 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 359
      removed outlier: 3.554A  pdb=" N   PHE A 332 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.725A  pdb=" N   THR A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.754A  pdb=" N   ASN A 363 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 408 through 438
      removed outlier: 3.553A  pdb=" N   TRP A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 466
    Processing helix  chain 'A' and resid 490 through 519
      removed outlier: 3.691A  pdb=" N   VAL A 511 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 569
      removed outlier: 4.422A  pdb=" N   GLU A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 569 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 601
      removed outlier: 3.877A  pdb=" N   LEU A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 617 through 619
      No H-bonds generated for 'chain 'A' and resid 617 through 619'
    Processing helix  chain 'A' and resid 630 through 644
      removed outlier: 3.502A  pdb=" N   LEU A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 667
      Proline residue:  A 658  - end of helix
    Processing helix  chain 'A' and resid 685 through 692
      removed outlier: 4.082A  pdb=" N   ASN A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 715
      removed outlier: 4.030A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   MET A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 744
      removed outlier: 3.846A  pdb=" N   ILE A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 782
      removed outlier: 4.277A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 774 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
      removed outlier: 3.643A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 854 through 885
      removed outlier: 4.110A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASP A 883 " --> pdb=" O   SER A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 909
      removed outlier: 3.645A  pdb=" N   SER A 894 " --> pdb=" O   PRO A 890 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
    Processing helix  chain 'B' and resid 175 through 182
      removed outlier: 4.299A  pdb=" N   TYR B 182 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 204
      No H-bonds generated for 'chain 'B' and resid 202 through 204'
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 242 through 257
      removed outlier: 3.625A  pdb=" N   THR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 275
      removed outlier: 4.341A  pdb=" N   GLY B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 316 through 325
      removed outlier: 3.781A  pdb=" N   LYS B 322 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 359
      removed outlier: 3.554A  pdb=" N   PHE B 332 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
      removed outlier: 3.725A  pdb=" N   THR B 359 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 363
      removed outlier: 3.754A  pdb=" N   ASN B 363 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 360 through 363'
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 395 through 405
    Processing helix  chain 'B' and resid 408 through 438
      removed outlier: 3.553A  pdb=" N   TRP B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 466
    Processing helix  chain 'B' and resid 490 through 519
      removed outlier: 3.691A  pdb=" N   VAL B 511 " --> pdb=" O   ILE B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 569
      removed outlier: 4.423A  pdb=" N   GLU B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL B 569 " --> pdb=" O   THR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 601
      removed outlier: 3.878A  pdb=" N   LEU B 587 " --> pdb=" O   LYS B 583 " (cutoff:3.500A)
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 617 through 619
      No H-bonds generated for 'chain 'B' and resid 617 through 619'
    Processing helix  chain 'B' and resid 630 through 644
      removed outlier: 3.502A  pdb=" N   LEU B 634 " --> pdb=" O   CYS B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 667
      Proline residue:  B 658  - end of helix
    Processing helix  chain 'B' and resid 685 through 692
      removed outlier: 4.082A  pdb=" N   ASN B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 715
      removed outlier: 4.030A  pdb=" N   GLU B 705 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   MET B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 723 through 744
      removed outlier: 3.846A  pdb=" N   ILE B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 782
      removed outlier: 4.277A  pdb=" N   ASN B 762 " --> pdb=" O   GLY B 758 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE B 774 " --> pdb=" O   LEU B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
      removed outlier: 3.643A  pdb=" N   TYR B 795 " --> pdb=" O   TYR B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 854 through 885
      removed outlier: 4.110A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASP B 883 " --> pdb=" O   SER B 879 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 909
      removed outlier: 3.645A  pdb=" N   SER B 894 " --> pdb=" O   PRO B 890 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127
      removed outlier: 6.762A  pdb=" N   PHE A 126 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189
    Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616
      removed outlier: 4.045A  pdb=" N   PHE A 620 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127
      removed outlier: 6.761A  pdb=" N   PHE B 126 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189
    Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 616
      removed outlier: 4.045A  pdb=" N   PHE B 620 " --> pdb=" O   ILE B 616 " (cutoff:3.500A)

    620 hydrogen bonds defined for protein.
    1842 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2745
        1.33 -     1.45: 2648
        1.45 -     1.58: 6549
        1.58 -     1.70: 0
        1.70 -     1.82: 122
  Bond restraints: 12064
  Sorted by residual:
  bond pdb=" CA  TYR B 222 "
       pdb=" CB  TYR B 222 "
    ideal  model  delta    sigma   weight residual
    1.526  1.549 -0.023 9.30e-03 1.16e+04 5.86e+00
  bond pdb=" CA  HIS B 453 "
       pdb=" C   HIS B 453 "
    ideal  model  delta    sigma   weight residual
    1.525  1.553 -0.028 1.19e-02 7.06e+03 5.62e+00
  bond pdb=" N   LEU A 381 "
       pdb=" CA  LEU A 381 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.15e-02 7.56e+03 5.59e+00
  bond pdb=" C   THR A 700 "
       pdb=" N   PRO A 701 "
    ideal  model  delta    sigma   weight residual
    1.337  1.363 -0.026 1.11e-02 8.12e+03 5.53e+00
  bond pdb=" CA  TYR A 222 "
       pdb=" CB  TYR A 222 "
    ideal  model  delta    sigma   weight residual
    1.526  1.548 -0.022 9.30e-03 1.16e+04 5.49e+00
  ... (remaining 12059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 14701
        1.82 -     3.63: 1398
        3.63 -     5.45: 161
        5.45 -     7.27: 46
        7.27 -     9.09: 14
  Bond angle restraints: 16320
  Sorted by residual:
  angle pdb=" N   LYS B 192 "
        pdb=" CA  LYS B 192 "
        pdb=" C   LYS B 192 "
      ideal   model   delta    sigma   weight residual
     110.97  116.57   -5.60 1.09e+00 8.42e-01 2.64e+01
  angle pdb=" N   LYS A 192 "
        pdb=" CA  LYS A 192 "
        pdb=" C   LYS A 192 "
      ideal   model   delta    sigma   weight residual
     110.97  116.53   -5.56 1.09e+00 8.42e-01 2.60e+01
  angle pdb=" C   HIS A 453 "
        pdb=" N   PRO A 454 "
        pdb=" CA  PRO A 454 "
      ideal   model   delta    sigma   weight residual
     120.04  114.85    5.19 1.08e+00 8.57e-01 2.31e+01
  angle pdb=" C   HIS B 453 "
        pdb=" N   PRO B 454 "
        pdb=" CA  PRO B 454 "
      ideal   model   delta    sigma   weight residual
     120.04  114.85    5.19 1.08e+00 8.57e-01 2.31e+01
  angle pdb=" N   THR B 594 "
        pdb=" CA  THR B 594 "
        pdb=" C   THR B 594 "
      ideal   model   delta    sigma   weight residual
     113.57  119.80   -6.23 1.38e+00 5.25e-01 2.04e+01
  ... (remaining 16315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 6490
       16.01 -    32.01: 568
       32.01 -    48.01: 136
       48.01 -    64.02: 14
       64.02 -    80.02: 10
  Dihedral angle restraints: 7218
    sinusoidal: 2966
      harmonic: 4252
  Sorted by residual:
  dihedral pdb=" CB  CYS A 625 "
           pdb=" SG  CYS A 625 "
           pdb=" SG  CYS A 630 "
           pdb=" CB  CYS A 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.75  -68.75     1      1.00e+01 1.00e-02 6.12e+01
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.74  -68.74     1      1.00e+01 1.00e-02 6.12e+01
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.40  -47.60     1      1.00e+01 1.00e-02 3.13e+01
  ... (remaining 7215 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1346
       0.108 -    0.217: 369
       0.217 -    0.325: 63
       0.325 -    0.434: 14
       0.434 -    0.542: 4
  Chirality restraints: 1796
  Sorted by residual:
  chirality pdb=" CA  PHE B 505 "
            pdb=" N   PHE B 505 "
            pdb=" C   PHE B 505 "
            pdb=" CB  PHE B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.35e+00
  chirality pdb=" CA  PHE A 505 "
            pdb=" N   PHE A 505 "
            pdb=" C   PHE A 505 "
            pdb=" CB  PHE A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.30e+00
  chirality pdb=" CA  THR B 594 "
            pdb=" N   THR B 594 "
            pdb=" C   THR B 594 "
            pdb=" CB  THR B 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.50 2.00e-01 2.50e+01 6.20e+00
  ... (remaining 1793 not shown)

  Planarity restraints: 2044
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 406 "   -0.045 5.00e-02 4.00e+02   6.80e-02 7.40e+00
        pdb=" N   PRO A 407 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 406 "    0.045 5.00e-02 4.00e+02   6.79e-02 7.38e+00
        pdb=" N   PRO B 407 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 222 "   -0.043 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO A 223 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2041 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.40: 40
        2.40 -     3.02: 5734
        3.02 -     3.65: 17494
        3.65 -     4.27: 23937
        4.27 -     4.90: 39059
  Nonbonded interactions: 86264
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 734 "
            pdb="CA    CA B1001 "
     model   vdw
     1.771 2.510
  nonbonded pdb=" OE2 GLU A 734 "
            pdb="CA    CA A1001 "
     model   vdw
     1.771 2.510
  nonbonded pdb=" OE2 GLU A 702 "
            pdb="CA    CA A1001 "
     model   vdw
     1.843 2.510
  nonbonded pdb=" OE2 GLU B 702 "
            pdb="CA    CA B1001 "
     model   vdw
     1.844 2.510
  nonbonded pdb=" OE2 GLU A 705 "
            pdb="CA    CA A1002 "
     model   vdw
     2.116 2.510
  ... (remaining 86259 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: 0.02
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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.380
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.007   0.065  12072  Z= 0.449
  Angle     :  1.195  13.777  16336  Z= 0.741
  Chirality :  0.104   0.542   1796
  Planarity :  0.007   0.068   2044
  Dihedral  : 12.851  80.023   4442
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  :  6.80 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.58 %
  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 are not related in a simple way.
  whole: -3.98 (0.17), residues: 1416
  helix: -2.00 (0.14), residues: 824
  sheet: -2.35 (0.72), residues: 48
  loop : -3.61 (0.21), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 125 
 TYR   0.018   0.003   TYR A 119 
 PHE   0.025   0.003   PHE B 585 
 TRP   0.027   0.003   TRP A 427 
 HIS   0.008   0.002   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 (12064)
  covalent geometry    : angle       1.18499 (16320)
  SS BOND              : bond        0.03093 (    8)
  SS BOND              : angle       4.95446 (   16)
  hydrogen bonds       : bond        0.14327 (  620)
  hydrogen bonds       : angle       9.05459 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 247
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 TYR cc_start: 0.9105 (p90) cc_final: 0.8884 (p90)
REVERT: A  368 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8875 (mt-10)
REVERT: A  391 MET cc_start: 0.8996 (tpt) cc_final: 0.8440 (mmm)
REVERT: A  436 TYR cc_start: 0.8330 (t80) cc_final: 0.8081 (t80)
REVERT: A  500 MET cc_start: 0.8523 (mtt) cc_final: 0.8209 (mtm)
REVERT: A  577 GLU cc_start: 0.9055 (tp30) cc_final: 0.8846 (tt0)
REVERT: A  632 MET cc_start: 0.9051 (mmp) cc_final: 0.8840 (tpp)
REVERT: A  745 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8404 (tp30)
REVERT: A  891 LYS cc_start: 0.8800 (tptt) cc_final: 0.8390 (ptpp)
REVERT: A  900 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8259 (mt-10)
REVERT: B  117 MET cc_start: 0.4586 (tmm) cc_final: 0.3647 (tpp)
REVERT: B  222 TYR cc_start: 0.9114 (p90) cc_final: 0.8887 (p90)
REVERT: B  368 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8841 (mt-10)
REVERT: B  391 MET cc_start: 0.9019 (tpt) cc_final: 0.8473 (mmm)
REVERT: B  436 TYR cc_start: 0.8355 (t80) cc_final: 0.8073 (t80)
REVERT: B  500 MET cc_start: 0.8537 (mtt) cc_final: 0.8214 (mtm)
REVERT: B  577 GLU cc_start: 0.9057 (tp30) cc_final: 0.8850 (tt0)
REVERT: B  632 MET cc_start: 0.8992 (mmp) cc_final: 0.8790 (tpp)
REVERT: B  891 LYS cc_start: 0.8810 (tptt) cc_final: 0.8391 (ptpp)
REVERT: B  900 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8256 (mt-10)
  outliers start: 40
  outliers final: 6
  residues processed: 283
  average time/residue: 0.1247
  time to fit residues: 48.9165
Evaluate side-chains
  146 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 140
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  640 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0670
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
B 183 HIS
B 206 GLN
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.078438 restraints weight = 32005.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080180 restraints weight = 17946.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081257 restraints weight = 12952.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.081796 restraints weight = 10837.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082029 restraints weight = 9880.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12072  Z= 0.131
  Angle     :  0.657  11.861  16336  Z= 0.331
  Chirality :  0.042   0.186   1796
  Planarity :  0.005   0.040   2044
  Dihedral  :  5.599  54.726   1598
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.72 %
    Favored  : 86.25 %
  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 are not related in a simple way.
  whole: -1.58 (0.21), residues: 1416
  helix:  0.21 (0.17), residues: 844
  sheet:  0.33 (0.81), residues: 28
  loop : -3.26 (0.22), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 515 
 TYR   0.017   0.001   TYR A 514 
 PHE   0.041   0.001   PHE B 505 
 TRP   0.018   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 849 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (12064)
  covalent geometry    : angle       0.65573 (16320)
  SS BOND              : bond        0.00384 (    8)
  SS BOND              : angle       1.25501 (   16)
  hydrogen bonds       : bond        0.04331 (  620)
  hydrogen bonds       : angle       4.94095 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8702 (mt) cc_final: 0.8408 (pp)
REVERT: A  458 TYR cc_start: 0.7626 (m-10) cc_final: 0.7345 (m-80)
REVERT: A  500 MET cc_start: 0.8585 (mtt) cc_final: 0.8304 (mtm)
REVERT: A  511 VAL cc_start: 0.8766 (t) cc_final: 0.8510 (m)
REVERT: A  704 MET cc_start: 0.8642 (tpp) cc_final: 0.8312 (tpp)
REVERT: A  891 LYS cc_start: 0.8626 (tptt) cc_final: 0.8268 (pttm)
REVERT: B  125 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7449 (tpp80)
REVERT: B  174 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8549 (pp)
REVERT: B  176 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8156 (tpt)
REVERT: B  199 GLN cc_start: 0.6698 (mp10) cc_final: 0.6357 (mp10)
REVERT: B  458 TYR cc_start: 0.7608 (m-10) cc_final: 0.7333 (m-80)
REVERT: B  500 MET cc_start: 0.8558 (mtt) cc_final: 0.8280 (mtm)
REVERT: B  511 VAL cc_start: 0.8784 (t) cc_final: 0.8493 (m)
REVERT: B  704 MET cc_start: 0.8666 (tpp) cc_final: 0.8351 (tpp)
REVERT: B  891 LYS cc_start: 0.8721 (tptt) cc_final: 0.8350 (pttm)
  outliers start: 26
  outliers final: 11
  residues processed: 198
  average time/residue: 0.1120
  time to fit residues: 31.8279
Evaluate side-chains
  154 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 130 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0040
   chunk 60 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.101847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.078486 restraints weight = 32200.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.080324 restraints weight = 18268.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081425 restraints weight = 13147.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.082051 restraints weight = 11041.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.082345 restraints weight = 10029.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12072  Z= 0.119
  Angle     :  0.625  10.062  16336  Z= 0.313
  Chirality :  0.042   0.190   1796
  Planarity :  0.004   0.050   2044
  Dihedral  :  4.915  47.350   1591
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.22 %
    Favored  : 83.59 %
  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 are not related in a simple way.
  whole: -0.54 (0.22), residues: 1416
  helix:  1.11 (0.18), residues: 834
  sheet:  1.08 (0.82), residues: 28
  loop : -2.89 (0.23), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 515 
 TYR   0.022   0.001   TYR A 222 
 PHE   0.038   0.001   PHE A 505 
 TRP   0.018   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12064)
  covalent geometry    : angle       0.62442 (16320)
  SS BOND              : bond        0.00256 (    8)
  SS BOND              : angle       0.90557 (   16)
  hydrogen bonds       : bond        0.03844 (  620)
  hydrogen bonds       : angle       4.36407 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8681 (mt) cc_final: 0.8390 (pp)
REVERT: A  341 MET cc_start: 0.8938 (tpp) cc_final: 0.8678 (tpp)
REVERT: A  500 MET cc_start: 0.8611 (mtt) cc_final: 0.8316 (mtm)
REVERT: A  511 VAL cc_start: 0.8782 (t) cc_final: 0.8532 (m)
REVERT: A  624 GLU cc_start: 0.7987 (tp30) cc_final: 0.7779 (tp30)
REVERT: A  891 LYS cc_start: 0.8551 (tptt) cc_final: 0.8214 (pttm)
REVERT: A  907 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6941 (mp)
REVERT: B  174 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8575 (pp)
REVERT: B  186 GLU cc_start: 0.8643 (pm20) cc_final: 0.8440 (pm20)
REVERT: B  500 MET cc_start: 0.8622 (mtt) cc_final: 0.8322 (mtm)
REVERT: B  511 VAL cc_start: 0.8786 (t) cc_final: 0.8530 (m)
REVERT: B  773 ILE cc_start: 0.9270 (pt) cc_final: 0.9010 (mp)
REVERT: B  891 LYS cc_start: 0.8609 (tptt) cc_final: 0.8291 (pttm)
REVERT: B  907 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6976 (mp)
  outliers start: 28
  outliers final: 12
  residues processed: 171
  average time/residue: 0.1093
  time to fit residues: 27.4645
Evaluate side-chains
  147 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.097431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.074200 restraints weight = 32443.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.075967 restraints weight = 18410.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.076999 restraints weight = 13341.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.077626 restraints weight = 11206.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.077934 restraints weight = 10188.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12072  Z= 0.189
  Angle     :  0.665  10.289  16336  Z= 0.342
  Chirality :  0.043   0.207   1796
  Planarity :  0.004   0.041   2044
  Dihedral  :  5.070  47.645   1588
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.14 %
    Favored  : 82.89 %
  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 are not related in a simple way.
  whole: -0.35 (0.22), residues: 1416
  helix:  1.16 (0.18), residues: 858
  sheet: -1.31 (0.68), residues: 48
  loop : -2.67 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 213 
 TYR   0.019   0.002   TYR B 338 
 PHE   0.038   0.002   PHE B 505 
 TRP   0.019   0.001   TRP A 427 
 HIS   0.008   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (12064)
  covalent geometry    : angle       0.66502 (16320)
  SS BOND              : bond        0.00302 (    8)
  SS BOND              : angle       0.88172 (   16)
  hydrogen bonds       : bond        0.04676 (  620)
  hydrogen bonds       : angle       4.38776 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8681 (mt) cc_final: 0.8434 (pp)
REVERT: A  391 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7947 (tmm)
REVERT: A  500 MET cc_start: 0.8650 (mtt) cc_final: 0.8341 (mtm)
REVERT: A  511 VAL cc_start: 0.8748 (t) cc_final: 0.8546 (m)
REVERT: A  587 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9051 (mm)
REVERT: A  891 LYS cc_start: 0.8620 (tptt) cc_final: 0.8285 (pttm)
REVERT: A  904 MET cc_start: 0.8761 (tmm) cc_final: 0.8539 (tmm)
REVERT: B  174 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8625 (pp)
REVERT: B  391 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6636 (tmm)
REVERT: B  500 MET cc_start: 0.8672 (mtt) cc_final: 0.7925 (mtm)
REVERT: B  511 VAL cc_start: 0.8806 (t) cc_final: 0.8600 (m)
REVERT: B  891 LYS cc_start: 0.8604 (tptt) cc_final: 0.8258 (pttm)
  outliers start: 38
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1066
  time to fit residues: 27.4196
Evaluate side-chains
  150 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 136 optimal weight:    0.1980
   chunk 35 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 127 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 132 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
B 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.100070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.076953 restraints weight = 31876.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078761 restraints weight = 17754.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.079863 restraints weight = 12768.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080395 restraints weight = 10677.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.080816 restraints weight = 9761.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12072  Z= 0.114
  Angle     :  0.612   9.784  16336  Z= 0.307
  Chirality :  0.041   0.192   1796
  Planarity :  0.004   0.043   2044
  Dihedral  :  4.733  46.355   1588
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.25 %
    Favored  : 81.17 %
  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 are not related in a simple way.
  whole:  0.05 (0.23), residues: 1416
  helix:  1.52 (0.18), residues: 858
  sheet: -0.74 (0.73), residues: 48
  loop : -2.64 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 687 
 PHE   0.031   0.001   PHE B 505 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (12064)
  covalent geometry    : angle       0.61205 (16320)
  SS BOND              : bond        0.00250 (    8)
  SS BOND              : angle       0.78588 (   16)
  hydrogen bonds       : bond        0.03864 (  620)
  hydrogen bonds       : angle       4.01867 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8755 (mt) cc_final: 0.8518 (pp)
REVERT: A  391 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.6684 (tmm)
REVERT: A  500 MET cc_start: 0.8620 (mtt) cc_final: 0.8283 (mtm)
REVERT: A  511 VAL cc_start: 0.8828 (t) cc_final: 0.8622 (m)
REVERT: A  891 LYS cc_start: 0.8437 (tptt) cc_final: 0.8236 (pttm)
REVERT: A  907 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7043 (mp)
REVERT: B  125 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8220 (tpp80)
REVERT: B  500 MET cc_start: 0.8631 (mtt) cc_final: 0.8294 (mtm)
REVERT: B  511 VAL cc_start: 0.8792 (t) cc_final: 0.8592 (m)
REVERT: B  907 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6839 (mp)
  outliers start: 33
  outliers final: 16
  residues processed: 170
  average time/residue: 0.1092
  time to fit residues: 27.1431
Evaluate side-chains
  143 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 126 optimal weight:    0.0050
   chunk 65 optimal weight:    0.9990
   chunk 133 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 124 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.4800

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 ASN
A 431 GLN
B 406 ASN
B 431 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.098794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.075448 restraints weight = 32101.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.077227 restraints weight = 18071.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.078289 restraints weight = 13020.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078914 restraints weight = 10935.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.079200 restraints weight = 9950.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12072  Z= 0.144
  Angle     :  0.669  10.721  16336  Z= 0.334
  Chirality :  0.043   0.200   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.911  46.437   1588
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.03 %
    Favored  : 80.55 %
  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 are not related in a simple way.
  whole:  0.19 (0.23), residues: 1416
  helix:  1.56 (0.18), residues: 860
  sheet: -0.25 (0.75), residues: 48
  loop : -2.50 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.015   0.001   TYR A 687 
 PHE   0.029   0.001   PHE A 505 
 TRP   0.018   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (12064)
  covalent geometry    : angle       0.66588 (16320)
  SS BOND              : bond        0.00391 (    8)
  SS BOND              : angle       2.29310 (   16)
  hydrogen bonds       : bond        0.04157 (  620)
  hydrogen bonds       : angle       4.10245 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8730 (mt) cc_final: 0.8492 (pp)
REVERT: A  176 MET cc_start: 0.8330 (tpt) cc_final: 0.8018 (tpt)
REVERT: A  500 MET cc_start: 0.8649 (mtt) cc_final: 0.8303 (mtm)
REVERT: A  511 VAL cc_start: 0.8847 (t) cc_final: 0.8583 (m)
REVERT: A  906 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7952 (tm-30)
REVERT: A  907 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7185 (mt)
REVERT: B  117 MET cc_start: 0.4704 (tmm) cc_final: 0.4140 (tpt)
REVERT: B  125 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8260 (tpp80)
REVERT: B  176 MET cc_start: 0.8294 (tpt) cc_final: 0.7769 (tpt)
REVERT: B  500 MET cc_start: 0.8656 (mtt) cc_final: 0.8308 (mtm)
REVERT: B  906 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7634 (tm-30)
  outliers start: 31
  outliers final: 18
  residues processed: 161
  average time/residue: 0.0980
  time to fit residues: 23.6473
Evaluate side-chains
  141 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  906 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0060
   chunk 57 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 130 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
B 406 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.100224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.077011 restraints weight = 32193.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078817 restraints weight = 17895.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.079948 restraints weight = 12886.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.080573 restraints weight = 10748.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.080857 restraints weight = 9740.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12072  Z= 0.121
  Angle     :  0.649  10.932  16336  Z= 0.319
  Chirality :  0.042   0.188   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  4.757  45.789   1588
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.19 %
    Favored  : 80.70 %
  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 are not related in a simple way.
  whole:  0.35 (0.23), residues: 1416
  helix:  1.74 (0.18), residues: 862
  sheet:  0.08 (0.76), residues: 48
  loop : -2.60 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 125 
 TYR   0.013   0.001   TYR A 687 
 PHE   0.030   0.001   PHE A 505 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12064)
  covalent geometry    : angle       0.64704 (16320)
  SS BOND              : bond        0.00346 (    8)
  SS BOND              : angle       1.64938 (   16)
  hydrogen bonds       : bond        0.03786 (  620)
  hydrogen bonds       : angle       4.01420 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4579 (tmm) cc_final: 0.4103 (tpt)
REVERT: A  369 MET cc_start: 0.8032 (mmm) cc_final: 0.7784 (mmt)
REVERT: A  500 MET cc_start: 0.8598 (mtt) cc_final: 0.7811 (mtm)
REVERT: A  511 VAL cc_start: 0.8854 (t) cc_final: 0.8591 (m)
REVERT: A  906 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7940 (tm-30)
REVERT: A  907 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7300 (mt)
REVERT: B  117 MET cc_start: 0.4584 (tmm) cc_final: 0.4103 (tpt)
REVERT: B  176 MET cc_start: 0.8272 (tpt) cc_final: 0.7968 (tpt)
REVERT: B  369 MET cc_start: 0.7858 (mmt) cc_final: 0.7570 (mmm)
REVERT: B  391 MET cc_start: 0.8612 (tpt) cc_final: 0.8332 (mmm)
REVERT: B  500 MET cc_start: 0.8595 (mtt) cc_final: 0.7742 (mtm)
  outliers start: 27
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1002
  time to fit residues: 23.4037
Evaluate side-chains
  148 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  625 CYS
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9980
   chunk 126 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 HIS ** 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 = 0.3551 r_free = 0.3551 target = 0.100947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.077709 restraints weight = 32131.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.079488 restraints weight = 17821.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.080626 restraints weight = 12849.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081162 restraints weight = 10712.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.081599 restraints weight = 9789.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12072  Z= 0.116
  Angle     :  0.656  11.242  16336  Z= 0.318
  Chirality :  0.042   0.199   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.634  45.873   1588
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.73 %
    Favored  : 80.23 %
  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 are not related in a simple way.
  whole:  0.57 (0.23), residues: 1416
  helix:  1.91 (0.18), residues: 862
  sheet:  0.46 (0.79), residues: 48
  loop : -2.53 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 125 
 TYR   0.012   0.001   TYR A 687 
 PHE   0.029   0.001   PHE A 505 
 TRP   0.019   0.001   TRP A 427 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12064)
  covalent geometry    : angle       0.65474 (16320)
  SS BOND              : bond        0.00307 (    8)
  SS BOND              : angle       1.40323 (   16)
  hydrogen bonds       : bond        0.03672 (  620)
  hydrogen bonds       : angle       3.95620 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4535 (tmm) cc_final: 0.4083 (tpt)
REVERT: A  500 MET cc_start: 0.8578 (mtt) cc_final: 0.7787 (mtm)
REVERT: A  906 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7862 (tm-30)
REVERT: A  907 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.6776 (mm)
REVERT: B  117 MET cc_start: 0.4456 (tmm) cc_final: 0.4186 (tpt)
REVERT: B  369 MET cc_start: 0.7839 (mmt) cc_final: 0.7411 (mmm)
REVERT: B  391 MET cc_start: 0.8654 (tpt) cc_final: 0.8305 (mmm)
REVERT: B  500 MET cc_start: 0.8598 (mtt) cc_final: 0.7841 (mtm)
  outliers start: 26
  outliers final: 20
  residues processed: 150
  average time/residue: 0.1124
  time to fit residues: 25.2235
Evaluate side-chains
  150 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 136 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0670
   overall best weight:    1.1324

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

Flipped N/Q/H residues before XYZ refinement:
A 406 ASN
B 229 GLN
** B 453 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 = 0.3538 r_free = 0.3538 target = 0.100024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.076809 restraints weight = 31926.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078568 restraints weight = 17950.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.079678 restraints weight = 12970.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080312 restraints weight = 10861.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.080611 restraints weight = 9848.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12072  Z= 0.128
  Angle     :  0.667   9.803  16336  Z= 0.323
  Chirality :  0.043   0.213   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  4.631  45.463   1588
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.89 %
    Favored  : 80.55 %
  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 are not related in a simple way.
  whole:  0.66 (0.23), residues: 1416
  helix:  1.97 (0.18), residues: 862
  sheet:  0.53 (0.78), residues: 48
  loop : -2.48 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 125 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.028   0.001   PHE A 505 
 TRP   0.018   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12064)
  covalent geometry    : angle       0.66553 (16320)
  SS BOND              : bond        0.00284 (    8)
  SS BOND              : angle       1.46702 (   16)
  hydrogen bonds       : bond        0.03837 (  620)
  hydrogen bonds       : angle       3.99959 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4552 (tmm) cc_final: 0.4115 (tpt)
REVERT: A  369 MET cc_start: 0.7735 (mmt) cc_final: 0.7471 (mmm)
REVERT: A  500 MET cc_start: 0.8589 (mtt) cc_final: 0.8266 (mtm)
REVERT: A  906 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7935 (tm-30)
REVERT: A  907 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.6805 (mm)
REVERT: B  117 MET cc_start: 0.4554 (tmm) cc_final: 0.4077 (tpt)
REVERT: B  369 MET cc_start: 0.7810 (mmt) cc_final: 0.7410 (mmm)
REVERT: B  391 MET cc_start: 0.8650 (tpt) cc_final: 0.8309 (mmm)
REVERT: B  500 MET cc_start: 0.8606 (mtt) cc_final: 0.7848 (mtm)
  outliers start: 20
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0987
  time to fit residues: 21.7274
Evaluate side-chains
  144 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0010
   chunk 19 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 HIS ** 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 = 0.3576 r_free = 0.3576 target = 0.102240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.078941 restraints weight = 32221.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.080769 restraints weight = 18076.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081930 restraints weight = 13006.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.082568 restraints weight = 10811.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.082957 restraints weight = 9798.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.4805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12072  Z= 0.113
  Angle     :  0.660  11.824  16336  Z= 0.317
  Chirality :  0.042   0.202   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.488  45.269   1588
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.97 %
    Favored  : 80.39 %
  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 are not related in a simple way.
  whole:  0.77 (0.23), residues: 1416
  helix:  2.04 (0.18), residues: 862
  sheet:  0.74 (0.80), residues: 48
  loop : -2.42 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 237 
 TYR   0.011   0.001   TYR B 222 
 PHE   0.029   0.001   PHE A 505 
 TRP   0.019   0.001   TRP A 427 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (12064)
  covalent geometry    : angle       0.65853 (16320)
  SS BOND              : bond        0.00293 (    8)
  SS BOND              : angle       1.32254 (   16)
  hydrogen bonds       : bond        0.03459 (  620)
  hydrogen bonds       : angle       3.93153 ( 1842)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7866 (tpp80)
REVERT: A  500 MET cc_start: 0.8567 (mtt) cc_final: 0.8222 (mtm)
REVERT: A  518 THR cc_start: 0.5742 (m) cc_final: 0.5530 (m)
REVERT: A  906 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7910 (tm-30)
REVERT: A  907 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7018 (mm)
REVERT: B  125 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7836 (tpp80)
REVERT: B  369 MET cc_start: 0.7773 (mmt) cc_final: 0.7388 (mmm)
REVERT: B  391 MET cc_start: 0.8640 (tpt) cc_final: 0.8341 (mmm)
REVERT: B  500 MET cc_start: 0.8602 (mtt) cc_final: 0.8260 (mtm)
  outliers start: 21
  outliers final: 16
  residues processed: 152
  average time/residue: 0.0986
  time to fit residues: 22.7859
Evaluate side-chains
  145 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  625 CYS
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 117 optimal weight:    4.9990
   chunk 139 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0980
   chunk 102 optimal weight:    5.9990
   chunk 74 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0670
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.102957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.079720 restraints weight = 31750.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.081587 restraints weight = 17921.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.082719 restraints weight = 12955.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.083352 restraints weight = 10825.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.083593 restraints weight = 9830.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12072  Z= 0.117
  Angle     :  0.683  11.202  16336  Z= 0.328
  Chirality :  0.042   0.198   1796
  Planarity :  0.004   0.038   2044
  Dihedral  :  4.255  44.399   1586
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.67 %
    Favored  : 79.84 %
  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 are not related in a simple way.
  whole:  0.86 (0.23), residues: 1416
  helix:  2.12 (0.18), residues: 860
  sheet:  0.82 (0.80), residues: 48
  loop : -2.38 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 237 
 TYR   0.011   0.001   TYR B 222 
 PHE   0.027   0.001   PHE A 505 
 TRP   0.018   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (12064)
  covalent geometry    : angle       0.68259 (16320)
  SS BOND              : bond        0.00280 (    8)
  SS BOND              : angle       1.22872 (   16)
  hydrogen bonds       : bond        0.03461 (  620)
  hydrogen bonds       : angle       3.91018 ( 1842)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.55 seconds
wall clock time: 34 minutes 55.14 seconds (2095.14 seconds total)