Starting phenix.real_space_refine
on Fri Sep 11 21:49:11 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oyb_3860/09_2026/5oyb_3860.cif"
  }
  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-2.2.1-6174/lib/python3.11/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: 5.69, per 1000 atoms: 0.48
  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: 0.88
  Conformation dependent library (CDL) restraints added in 589.4 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: 0.25
  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: 1.67

  Time building geometry restraints manager: 1.19 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.950
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
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/Z
  covalent geometry    : bond        0.00703 /  0.45 (12064)
  covalent geometry    : angle       1.18499 /  0.74 (16320)
  SS BOND              : bond        0.03093 /  1.39 (    8)
  SS BOND              : angle       4.95446 /  2.56 (   16)
  hydrogen bonds       : bond        0.14327 /  9.20 (  620)
  hydrogen bonds       : angle       9.05459 /  6.23 ( 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  : 0.348 
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: 0.8876 (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: 0.8844 (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: 0.1237
  time to fit residues: 48.4978
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  : 0.482 
-------------------------------------------------------------------------------
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:    9.9990
   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...
** 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 = 0.3552 r_free = 0.3552 target = 0.101106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.078351 restraints weight = 31964.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080163 restraints weight = 17979.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081252 restraints weight = 12951.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.081789 restraints weight = 10798.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.081970 restraints weight = 9854.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12072  Z= 0.134
  Angle     :  0.656  11.413  16336  Z= 0.333
  Chirality :  0.042   0.193   1796
  Planarity :  0.005   0.041   2044
  Dihedral  :  5.616  54.509   1598
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.25 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.21), residues: 1416
  helix:  0.19 (0.17), residues: 844
  sheet:  0.36 (0.82), residues: 28
  loop : -3.29 (0.22), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 515 
 TYR   0.018   0.001   TYR A 514 
 PHE   0.040   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/Z
  covalent geometry    : bond        0.00263 /  0.13 (12064)
  covalent geometry    : angle       0.65546 /  0.33 (16320)
  SS BOND              : bond        0.00383 /  0.16 (    8)
  SS BOND              : angle       1.24333 /  0.71 (   16)
  hydrogen bonds       : bond        0.04404 /  2.91 (  620)
  hydrogen bonds       : angle       4.98474 /  3.44 ( 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
  209 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 180
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8679 (mt) cc_final: 0.8387 (pp)
REVERT: A  458 TYR cc_start: 0.7666 (m-10) cc_final: 0.7396 (m-80)
REVERT: A  500 MET cc_start: 0.8570 (mtt) cc_final: 0.8277 (mtm)
REVERT: A  511 VAL cc_start: 0.8756 (t) cc_final: 0.8501 (m)
REVERT: A  704 MET cc_start: 0.8648 (tpp) cc_final: 0.8307 (tpp)
REVERT: A  891 LYS cc_start: 0.8661 (tptt) cc_final: 0.8343 (pttm)
REVERT: B  125 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7522 (tpp80)
REVERT: B  174 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: B  176 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8135 (tpt)
REVERT: B  199 GLN cc_start: 0.6622 (mp10) cc_final: 0.6338 (mp10)
REVERT: B  458 TYR cc_start: 0.7587 (m-10) cc_final: 0.7317 (m-80)
REVERT: B  500 MET cc_start: 0.8547 (mtt) cc_final: 0.8267 (mtm)
REVERT: B  511 VAL cc_start: 0.8776 (t) cc_final: 0.8491 (m)
REVERT: B  704 MET cc_start: 0.8679 (tpp) cc_final: 0.8341 (tpp)
REVERT: B  891 LYS cc_start: 0.8718 (tptt) cc_final: 0.8356 (pttm)
  outliers start: 29
  outliers final: 10
  residues processed: 200
  average time/residue: 0.1107
  time to fit residues: 32.0625
Evaluate side-chains
  152 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 15 optimal weight:    0.4980
   chunk 93 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 183 HIS
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 229 GLN ** 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 = 0.3496 r_free = 0.3496 target = 0.098041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.074566 restraints weight = 32684.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.076337 restraints weight = 18406.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.077387 restraints weight = 13350.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.078057 restraints weight = 11194.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.078325 restraints weight = 10132.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12072  Z= 0.182
  Angle     :  0.681  10.569  16336  Z= 0.347
  Chirality :  0.044   0.202   1796
  Planarity :  0.005   0.051   2044
  Dihedral  :  5.175  47.578   1591
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.98 %
    Favored  : 83.44 %
  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: -0.65 (0.22), residues: 1416
  helix:  1.02 (0.18), residues: 834
  sheet: -1.71 (0.65), residues: 48
  loop : -2.79 (0.23), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 515 
 TYR   0.021   0.002   TYR B 222 
 PHE   0.040   0.002   PHE A 505 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.007   0.001   HIS B 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 (12064)
  covalent geometry    : angle       0.68061 /  0.35 (16320)
  SS BOND              : bond        0.00291 /  0.15 (    8)
  SS BOND              : angle       1.00538 /  0.52 (   16)
  hydrogen bonds       : bond        0.04690 /  3.13 (  620)
  hydrogen bonds       : angle       4.60292 /  3.15 ( 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
  179 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8669 (mt) cc_final: 0.8382 (pp)
REVERT: A  341 MET cc_start: 0.8965 (tpp) cc_final: 0.8750 (tpp)
REVERT: A  500 MET cc_start: 0.8647 (mtt) cc_final: 0.8372 (mtm)
REVERT: A  507 ILE cc_start: 0.8417 (mt) cc_final: 0.8200 (mt)
REVERT: A  534 ILE cc_start: 0.4061 (OUTLIER) cc_final: 0.3850 (pp)
REVERT: A  704 MET cc_start: 0.8912 (tpp) cc_final: 0.8453 (tpp)
REVERT: A  891 LYS cc_start: 0.8665 (tptt) cc_final: 0.8308 (pttm)
REVERT: A  900 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8099 (mt-10)
REVERT: A  907 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6759 (mp)
REVERT: B  174 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8551 (pp)
REVERT: B  199 GLN cc_start: 0.6976 (mp10) cc_final: 0.6075 (mp10)
REVERT: B  341 MET cc_start: 0.8945 (tpp) cc_final: 0.8739 (tpp)
REVERT: B  500 MET cc_start: 0.8625 (mtt) cc_final: 0.8345 (mtm)
REVERT: B  704 MET cc_start: 0.8947 (tpp) cc_final: 0.8483 (tpp)
REVERT: B  891 LYS cc_start: 0.8701 (tptt) cc_final: 0.8366 (pttm)
REVERT: B  907 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6911 (mp)
  outliers start: 33
  outliers final: 16
  residues processed: 176
  average time/residue: 0.1046
  time to fit residues: 27.0339
Evaluate side-chains
  149 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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  534 ILE
Chi-restraints excluded: chain A residue  553 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  907 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  276 VAL
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  907 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0770
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.7742

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.097973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.074771 restraints weight = 32425.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076571 restraints weight = 18243.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.077645 restraints weight = 13170.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.078152 restraints weight = 11009.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.078567 restraints weight = 10078.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12072  Z= 0.157
  Angle     :  0.639  10.312  16336  Z= 0.327
  Chirality :  0.043   0.202   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  5.014  46.773   1588
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.75 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.22), residues: 1416
  helix:  1.22 (0.18), residues: 860
  sheet: -1.34 (0.66), residues: 48
  loop : -2.72 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 515 
 TYR   0.016   0.001   TYR B 687 
 PHE   0.037   0.001   PHE B 505 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.006   0.001   HIS A 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 (12064)
  covalent geometry    : angle       0.63885 /  0.33 (16320)
  SS BOND              : bond        0.00280 /  0.16 (    8)
  SS BOND              : angle       0.84060 /  0.45 (   16)
  hydrogen bonds       : bond        0.04377 /  2.92 (  620)
  hydrogen bonds       : angle       4.35277 /  2.98 ( 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: 41
    poor density    : 143
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8684 (mt) cc_final: 0.8434 (pp)
REVERT: A  186 GLU cc_start: 0.8812 (pm20) cc_final: 0.8437 (pm20)
REVERT: A  391 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.6569 (tmm)
REVERT: A  500 MET cc_start: 0.8626 (mtt) cc_final: 0.8334 (mtm)
REVERT: A  507 ILE cc_start: 0.8414 (mt) cc_final: 0.8156 (mt)
REVERT: A  534 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3925 (pp)
REVERT: A  704 MET cc_start: 0.8983 (tpp) cc_final: 0.8517 (tpp)
REVERT: A  891 LYS cc_start: 0.8531 (tptt) cc_final: 0.8246 (pttm)
REVERT: B  174 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8598 (pp)
REVERT: B  391 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6662 (tmm)
REVERT: B  500 MET cc_start: 0.8643 (mtt) cc_final: 0.8337 (mtm)
REVERT: B  704 MET cc_start: 0.8994 (tpp) cc_final: 0.8518 (tpp)
REVERT: B  891 LYS cc_start: 0.8587 (tptt) cc_final: 0.8270 (pttm)
  outliers start: 41
  outliers final: 22
  residues processed: 173
  average time/residue: 0.0984
  time to fit residues: 25.5951
Evaluate side-chains
  158 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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  272 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  534 ILE
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 B residue  126 PHE
Chi-restraints excluded: chain B residue  174 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  391 MET
Chi-restraints excluded: chain B residue  494 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    0.0470
   chunk 17 optimal weight:    3.9990
   chunk 136 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 127 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 132 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
A 431 GLN
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 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 = 0.3554 r_free = 0.3554 target = 0.101048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.077954 restraints weight = 32018.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079762 restraints weight = 18219.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.080893 restraints weight = 13169.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.081509 restraints weight = 11029.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081684 restraints weight = 10055.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12072  Z= 0.111
  Angle     :  0.607   9.776  16336  Z= 0.302
  Chirality :  0.041   0.204   1796
  Planarity :  0.004   0.044   2044
  Dihedral  :  4.642  46.041   1588
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.17 %
    Favored  : 81.41 %
  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:  0.13 (0.23), residues: 1416
  helix:  1.60 (0.18), residues: 860
  sheet: -0.55 (0.73), residues: 48
  loop : -2.66 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.014   0.001   TYR B 514 
 PHE   0.031   0.001   PHE B 499 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.002   0.001   HIS A 807 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.11 (12064)
  covalent geometry    : angle       0.60693 /  0.30 (16320)
  SS BOND              : bond        0.00242 /  0.12 (    8)
  SS BOND              : angle       0.78241 /  0.43 (   16)
  hydrogen bonds       : bond        0.03584 /  2.37 (  620)
  hydrogen bonds       : angle       3.96043 /  2.73 ( 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
  191 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4541 (tmm) cc_final: 0.4227 (tpt)
REVERT: A  174 LEU cc_start: 0.8701 (mt) cc_final: 0.8456 (pp)
REVERT: A  186 GLU cc_start: 0.8700 (pm20) cc_final: 0.8492 (pm20)
REVERT: A  500 MET cc_start: 0.8634 (mtt) cc_final: 0.8318 (mtm)
REVERT: A  507 ILE cc_start: 0.8322 (mt) cc_final: 0.8055 (mt)
REVERT: A  524 MET cc_start: 0.5586 (ptp) cc_final: 0.5355 (ptt)
REVERT: A  534 ILE cc_start: 0.4159 (OUTLIER) cc_final: 0.3931 (pp)
REVERT: A  907 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7033 (mp)
REVERT: B  500 MET cc_start: 0.8593 (mtt) cc_final: 0.8302 (mtm)
REVERT: B  534 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3915 (pp)
REVERT: B  907 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7048 (mp)
  outliers start: 31
  outliers final: 16
  residues processed: 180
  average time/residue: 0.0970
  time to fit residues: 25.9263
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  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  534 ILE
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  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  534 ILE
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:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 133 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 195 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 = 0.3490 r_free = 0.3490 target = 0.097519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.074168 restraints weight = 32317.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.075819 restraints weight = 18491.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.076848 restraints weight = 13529.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.077460 restraints weight = 11406.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.077690 restraints weight = 10365.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12072  Z= 0.181
  Angle     :  0.704  10.706  16336  Z= 0.353
  Chirality :  0.044   0.210   1796
  Planarity :  0.004   0.036   2044
  Dihedral  :  4.981  46.786   1588
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.27 %
    Favored  : 80.16 %
  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:  0.12 (0.23), residues: 1416
  helix:  1.54 (0.18), residues: 862
  sheet: -0.33 (0.75), residues: 48
  loop : -2.61 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 515 
 TYR   0.017   0.001   TYR A 338 
 PHE   0.030   0.002   PHE A 505 
 TRP   0.018   0.001   TRP B 427 
 HIS   0.008   0.001   HIS A 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.18 (12064)
  covalent geometry    : angle       0.69845 /  0.35 (16320)
  SS BOND              : bond        0.00294 /  0.18 (    8)
  SS BOND              : angle       2.84385 /  1.56 (   16)
  hydrogen bonds       : bond        0.04541 /  3.03 (  620)
  hydrogen bonds       : angle       4.25226 /  2.92 ( 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
  173 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8704 (mt) cc_final: 0.8497 (pp)
REVERT: A  176 MET cc_start: 0.8331 (tpt) cc_final: 0.8064 (tpt)
REVERT: A  500 MET cc_start: 0.8627 (mtt) cc_final: 0.8318 (mtm)
REVERT: A  534 ILE cc_start: 0.4173 (OUTLIER) cc_final: 0.3944 (pp)
REVERT: A  906 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7900 (tm-30)
REVERT: A  907 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.6774 (mt)
REVERT: B  117 MET cc_start: 0.4707 (tmm) cc_final: 0.4157 (tpt)
REVERT: B  125 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7282 (tpp80)
REVERT: B  176 MET cc_start: 0.8281 (tpt) cc_final: 0.7760 (tpt)
REVERT: B  500 MET cc_start: 0.8622 (mtt) cc_final: 0.8303 (mtm)
REVERT: B  534 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3894 (pp)
REVERT: B  906 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7904 (tm-30)
REVERT: B  907 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7388 (mt)
  outliers start: 33
  outliers final: 19
  residues processed: 166
  average time/residue: 0.0988
  time to fit residues: 24.8316
Evaluate side-chains
  152 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  553 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  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  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  534 ILE
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
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 120 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 57 optimal weight:    0.6980
   chunk 105 optimal weight:   20.0000
   chunk 130 optimal weight:    0.5980
   chunk 110 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.1982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.099112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.075913 restraints weight = 32191.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.077635 restraints weight = 18329.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078669 restraints weight = 13403.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.079184 restraints weight = 11273.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.079601 restraints weight = 10334.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.4340

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= 0.130
  Angle     :  0.658  11.090  16336  Z= 0.323
  Chirality :  0.042   0.188   1796
  Planarity :  0.004   0.041   2044
  Dihedral  :  4.800  45.780   1588
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.66 %
    Favored  : 80.08 %
  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:  0.38 (0.23), residues: 1416
  helix:  1.75 (0.18), residues: 862
  sheet:  0.04 (0.78), residues: 48
  loop : -2.53 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 125 
 TYR   0.014   0.001   TYR A 119 
 PHE   0.029   0.001   PHE A 505 
 TRP   0.021   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (12064)
  covalent geometry    : angle       0.65577 /  0.32 (16320)
  SS BOND              : bond        0.00553 /  0.24 (    8)
  SS BOND              : angle       1.90935 /  1.05 (   16)
  hydrogen bonds       : bond        0.03997 /  2.65 (  620)
  hydrogen bonds       : angle       4.07285 /  2.81 ( 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
  165 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7817 (mmt) cc_final: 0.7386 (mmm)
REVERT: A  391 MET cc_start: 0.8508 (tpt) cc_final: 0.8155 (mmm)
REVERT: A  500 MET cc_start: 0.8601 (mtt) cc_final: 0.8298 (mtm)
REVERT: A  511 VAL cc_start: 0.8799 (t) cc_final: 0.8554 (m)
REVERT: A  534 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3943 (pp)
REVERT: A  906 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (tm-30)
REVERT: B  117 MET cc_start: 0.4629 (tmm) cc_final: 0.4169 (tpt)
REVERT: B  176 MET cc_start: 0.8235 (tpt) cc_final: 0.7931 (tpt)
REVERT: B  500 MET cc_start: 0.8620 (mtt) cc_final: 0.8264 (mtm)
REVERT: B  534 ILE cc_start: 0.4176 (OUTLIER) cc_final: 0.3969 (pp)
REVERT: B  906 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7942 (tm-30)
REVERT: B  907 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7118 (mt)
  outliers start: 29
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1006
  time to fit residues: 24.1328
Evaluate side-chains
  154 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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  354 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  534 ILE
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  906 GLU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  553 LEU
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  906 GLU
Chi-restraints excluded: chain B residue  907 LEU
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:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 124 optimal weight:    0.2980
   chunk 126 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3485 r_free = 0.3485 target = 0.097159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.073961 restraints weight = 32089.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.075662 restraints weight = 17968.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.076719 restraints weight = 13016.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.077315 restraints weight = 10905.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.077597 restraints weight = 9934.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12072  Z= 0.174
  Angle     :  0.693  10.978  16336  Z= 0.345
  Chirality :  0.044   0.209   1796
  Planarity :  0.004   0.036   2044
  Dihedral  :  4.941  46.442   1588
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.97 %
    Favored  : 79.45 %
  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:  0.33 (0.23), residues: 1416
  helix:  1.70 (0.17), residues: 864
  sheet:  0.28 (0.79), residues: 48
  loop : -2.58 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.015   0.001   TYR B 338 
 PHE   0.028   0.001   PHE A 505 
 TRP   0.017   0.001   TRP B 427 
 HIS   0.007   0.001   HIS B 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 (12064)
  covalent geometry    : angle       0.69181 /  0.34 (16320)
  SS BOND              : bond        0.00339 /  0.19 (    8)
  SS BOND              : angle       1.67763 /  0.91 (   16)
  hydrogen bonds       : bond        0.04486 /  2.98 (  620)
  hydrogen bonds       : angle       4.20854 /  2.90 ( 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
  167 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7916 (mmt) cc_final: 0.7585 (mmm)
REVERT: A  391 MET cc_start: 0.8590 (tpt) cc_final: 0.8346 (tmm)
REVERT: A  500 MET cc_start: 0.8674 (mtt) cc_final: 0.8349 (mtm)
REVERT: A  511 VAL cc_start: 0.8805 (t) cc_final: 0.8581 (m)
REVERT: B  500 MET cc_start: 0.8638 (mtt) cc_final: 0.8300 (mtm)
REVERT: B  534 ILE cc_start: 0.4353 (OUTLIER) cc_final: 0.4143 (pp)
REVERT: B  906 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8049 (tm-30)
REVERT: B  907 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7104 (mt)
  outliers start: 33
  outliers final: 21
  residues processed: 160
  average time/residue: 0.0963
  time to fit residues: 23.2917
Evaluate side-chains
  147 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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  354 LEU
Chi-restraints excluded: chain A residue  494 LEU
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 B residue  126 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  534 ILE
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
Chi-restraints excluded: chain B residue  906 GLU
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 136 optimal weight:    0.7980
   chunk 93 optimal weight:    0.8980
   chunk 140 optimal weight:    0.0040
   chunk 98 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0970
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.101072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.078062 restraints weight = 31773.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.079890 restraints weight = 18096.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.080996 restraints weight = 13043.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.081500 restraints weight = 10911.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081933 restraints weight = 10018.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12072  Z= 0.114
  Angle     :  0.650   9.533  16336  Z= 0.317
  Chirality :  0.042   0.210   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  4.613  45.592   1588
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.36 %
    Favored  : 79.45 %
  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:  0.64 (0.23), residues: 1416
  helix:  1.98 (0.18), residues: 862
  sheet:  0.59 (0.79), residues: 48
  loop : -2.54 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 788 
 TYR   0.012   0.001   TYR B 514 
 PHE   0.038   0.001   PHE B 505 
 TRP   0.023   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 807 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 (12064)
  covalent geometry    : angle       0.64929 /  0.32 (16320)
  SS BOND              : bond        0.00302 /  0.14 (    8)
  SS BOND              : angle       1.23513 /  0.67 (   16)
  hydrogen bonds       : bond        0.03503 /  2.30 (  620)
  hydrogen bonds       : angle       3.93994 /  2.71 ( 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
  171 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7639 (mmt) cc_final: 0.7359 (mmm)
REVERT: A  391 MET cc_start: 0.8404 (tpt) cc_final: 0.8064 (tmm)
REVERT: A  500 MET cc_start: 0.8577 (mtt) cc_final: 0.8271 (mtm)
REVERT: B  117 MET cc_start: 0.7023 (tpt) cc_final: 0.6459 (tmm)
REVERT: B  176 MET cc_start: 0.8200 (tpt) cc_final: 0.8000 (tpt)
REVERT: B  500 MET cc_start: 0.8622 (mtt) cc_final: 0.8258 (mtm)
REVERT: B  534 ILE cc_start: 0.4309 (OUTLIER) cc_final: 0.4101 (pp)
REVERT: B  906 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7970 (tm-30)
REVERT: B  907 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7250 (mm)
  outliers start: 28
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0956
  time to fit residues: 23.1351
Evaluate side-chains
  154 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
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  494 LEU
Chi-restraints excluded: chain A residue  503 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 B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  534 ILE
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
Chi-restraints excluded: chain B residue  907 LEU
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:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    0.4980
   chunk 128 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.076275 restraints weight = 32200.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.078034 restraints weight = 18352.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.079119 restraints weight = 13272.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.079718 restraints weight = 11137.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.080076 restraints weight = 10154.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12072  Z= 0.138
  Angle     :  0.688   9.852  16336  Z= 0.338
  Chirality :  0.043   0.209   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  4.643  45.728   1588
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.22 %
    Favored  : 79.14 %
  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:  0.64 (0.23), residues: 1416
  helix:  1.96 (0.18), residues: 862
  sheet:  0.78 (0.78), residues: 48
  loop : -2.52 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.012   0.001   TYR B 222 
 PHE   0.039   0.001   PHE B 505 
 TRP   0.019   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 (12064)
  covalent geometry    : angle       0.68663 /  0.34 (16320)
  SS BOND              : bond        0.00283 /  0.14 (    8)
  SS BOND              : angle       1.37077 /  0.75 (   16)
  hydrogen bonds       : bond        0.03977 /  2.63 (  620)
  hydrogen bonds       : angle       4.05828 /  2.79 ( 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
  157 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7697 (mmt) cc_final: 0.7325 (mmm)
REVERT: A  391 MET cc_start: 0.8423 (tpt) cc_final: 0.8104 (tpp)
REVERT: A  500 MET cc_start: 0.8644 (mtt) cc_final: 0.8338 (mtm)
REVERT: B  117 MET cc_start: 0.7342 (tpt) cc_final: 0.6766 (tmm)
REVERT: B  500 MET cc_start: 0.8630 (mtt) cc_final: 0.8330 (mtm)
REVERT: B  906 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (tm-30)
REVERT: B  907 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7244 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 152
  average time/residue: 0.0903
  time to fit residues: 21.1411
Evaluate side-chains
  145 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  503 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 B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  494 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
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 117 optimal weight:    4.9990
   chunk 139 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 102 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0980
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.0184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.099948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.076771 restraints weight = 32159.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.078606 restraints weight = 17899.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.079754 restraints weight = 12758.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.080284 restraints weight = 10602.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080712 restraints weight = 9678.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4817

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= 0.127
  Angle     :  0.681   9.613  16336  Z= 0.333
  Chirality :  0.043   0.210   1796
  Planarity :  0.004   0.038   2044
  Dihedral  :  4.585  45.199   1588
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.14 %
    Favored  : 79.14 %
  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:  0.68 (0.23), residues: 1416
  helix:  1.95 (0.18), residues: 866
  sheet:  0.37 (0.78), residues: 52
  loop : -2.43 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 125 
 TYR   0.013   0.001   TYR B 514 
 PHE   0.041   0.001   PHE B 505 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 (12064)
  covalent geometry    : angle       0.68015 /  0.33 (16320)
  SS BOND              : bond        0.00288 /  0.14 (    8)
  SS BOND              : angle       1.35482 /  0.74 (   16)
  hydrogen bonds       : bond        0.03831 /  2.53 (  620)
  hydrogen bonds       : angle       4.00605 /  2.76 ( 1842)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1924.41 seconds
wall clock time: 33 minutes 59.18 seconds (2039.18 seconds total)