Starting phenix.real_space_refine
on Wed Jul 30 00:55:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oyb_3860/07_2025/5oyb_3860.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 12.94, per 1000 atoms: 1.10
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.12
  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: 3.22

  Time building geometry restraints manager: 2.99 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     34.280
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  12072  Z= 0.449
  Angle     :  1.195  13.777  16336  Z= 0.741
  Chirality :  0.104   0.542   1796
  Planarity :  0.007   0.068   2044
  Dihedral  : 12.851  80.023   4442
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  :  6.80 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.58 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.027   0.003   TRP A 427 
 HIS   0.008   0.002   HIS A 284 
 PHE   0.025   0.003   PHE B 585 
 TYR   0.018   0.003   TYR A 119 
 ARG   0.004   0.001   ARG A 125 

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

*********************** 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  : 1.431 
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: 0.2701
  time to fit residues: 104.4060
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  : 1.235 
-------------------------------------------------------------------------------
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 119 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 57 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 128 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.100719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.077923 restraints weight = 31941.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.079697 restraints weight = 18028.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.080778 restraints weight = 13020.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12072  Z= 0.132
  Angle     :  0.660  11.746  16336  Z= 0.335
  Chirality :  0.042   0.186   1796
  Planarity :  0.005   0.042   2044
  Dihedral  :  5.637  53.961   1598
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.64 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.21), residues: 1416
  helix:  0.19 (0.17), residues: 842
  sheet:  0.31 (0.82), residues: 28
  loop : -3.28 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 849 
 PHE   0.040   0.001   PHE B 505 
 TYR   0.018   0.001   TYR A 338 
 ARG   0.008   0.001   ARG A 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04514 (  620)
  hydrogen bonds       : angle       5.03439 ( 1842)
  SS BOND              : bond        0.00433 (    8)
  SS BOND              : angle       1.25144 (   16)
  covalent geometry    : bond        0.00272 (12064)
  covalent geometry    : angle       0.65886 (16320)

*********************** 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  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8700 (mt) cc_final: 0.8396 (pp)
REVERT: A  458 TYR cc_start: 0.7589 (m-10) cc_final: 0.7322 (m-80)
REVERT: A  500 MET cc_start: 0.8588 (mtt) cc_final: 0.8296 (mtm)
REVERT: A  511 VAL cc_start: 0.8766 (t) cc_final: 0.8534 (m)
REVERT: A  704 MET cc_start: 0.8691 (tpp) cc_final: 0.8293 (tpp)
REVERT: A  891 LYS cc_start: 0.8702 (tptt) cc_final: 0.8354 (pttm)
REVERT: B  125 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7553 (tpp80)
REVERT: B  174 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8537 (pp)
REVERT: B  176 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8106 (tpt)
REVERT: B  199 GLN cc_start: 0.6578 (mp10) cc_final: 0.6262 (mp10)
REVERT: B  458 TYR cc_start: 0.7631 (m-10) cc_final: 0.7356 (m-80)
REVERT: B  500 MET cc_start: 0.8565 (mtt) cc_final: 0.8291 (mtm)
REVERT: B  511 VAL cc_start: 0.8811 (t) cc_final: 0.8524 (m)
REVERT: B  704 MET cc_start: 0.8670 (tpp) cc_final: 0.8282 (tpp)
REVERT: B  891 LYS cc_start: 0.8731 (tptt) cc_final: 0.8354 (pttm)
  outliers start: 29
  outliers final: 10
  residues processed: 200
  average time/residue: 0.2391
  time to fit residues: 67.7908
Evaluate side-chains
  151 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
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 1 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0030
   chunk 69 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 106 optimal weight:    0.0170
   chunk 135 optimal weight:    0.0570
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.3946

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.102391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079075 restraints weight = 32200.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.080931 restraints weight = 18179.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.082071 restraints weight = 13172.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12072  Z= 0.118
  Angle     :  0.624  10.148  16336  Z= 0.312
  Chirality :  0.041   0.186   1796
  Planarity :  0.004   0.049   2044
  Dihedral  :  4.917  47.651   1591
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.06 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.22), residues: 1416
  helix:  1.12 (0.18), residues: 834
  sheet:  1.14 (0.82), residues: 28
  loop : -2.92 (0.23), residues: 554

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  620)
  hydrogen bonds       : angle       4.36605 ( 1842)
  SS BOND              : bond        0.00274 (    8)
  SS BOND              : angle       0.85369 (   16)
  covalent geometry    : bond        0.00244 (12064)
  covalent geometry    : angle       0.62357 (16320)

*********************** 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
  176 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8637 (mt) cc_final: 0.8355 (pp)
REVERT: A  341 MET cc_start: 0.8789 (tpp) cc_final: 0.8508 (mmm)
REVERT: A  500 MET cc_start: 0.8603 (mtt) cc_final: 0.8281 (mtm)
REVERT: A  511 VAL cc_start: 0.8750 (t) cc_final: 0.8503 (m)
REVERT: A  891 LYS cc_start: 0.8546 (tptt) cc_final: 0.8217 (pttm)
REVERT: A  900 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8081 (mt-10)
REVERT: A  907 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6926 (mp)
REVERT: B  174 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8542 (pp)
REVERT: B  186 GLU cc_start: 0.8591 (pm20) cc_final: 0.8384 (pm20)
REVERT: B  199 GLN cc_start: 0.6965 (mp10) cc_final: 0.6709 (mp10)
REVERT: B  341 MET cc_start: 0.8781 (tpp) cc_final: 0.8509 (mmm)
REVERT: B  500 MET cc_start: 0.8632 (mtt) cc_final: 0.8296 (mtm)
REVERT: B  511 VAL cc_start: 0.8794 (t) cc_final: 0.8544 (m)
REVERT: B  534 ILE cc_start: 0.4170 (OUTLIER) cc_final: 0.3966 (pp)
REVERT: B  624 GLU cc_start: 0.7971 (tp30) cc_final: 0.7761 (tp30)
REVERT: B  891 LYS cc_start: 0.8595 (tptt) cc_final: 0.8304 (pttm)
REVERT: B  907 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6974 (mp)
  outliers start: 26
  outliers final: 12
  residues processed: 171
  average time/residue: 0.2303
  time to fit residues: 57.3860
Evaluate side-chains
  148 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 121 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 137 optimal weight:    0.9990
   chunk 118 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 131 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** 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 = 0.3510 r_free = 0.3510 target = 0.098790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.075474 restraints weight = 32327.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.077278 restraints weight = 18249.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.078351 restraints weight = 13242.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12072  Z= 0.159
  Angle     :  0.638  10.311  16336  Z= 0.326
  Chirality :  0.042   0.198   1796
  Planarity :  0.004   0.041   2044
  Dihedral  :  4.932  47.436   1588
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.30 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.22), residues: 1416
  helix:  1.28 (0.18), residues: 858
  sheet: -1.14 (0.70), residues: 48
  loop : -2.70 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 
 PHE   0.039   0.002   PHE B 505 
 TYR   0.017   0.001   TYR A 338 
 ARG   0.007   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  620)
  hydrogen bonds       : angle       4.27443 ( 1842)
  SS BOND              : bond        0.00279 (    8)
  SS BOND              : angle       0.86706 (   16)
  covalent geometry    : bond        0.00362 (12064)
  covalent geometry    : angle       0.63728 (16320)

*********************** 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
  183 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.8779 (mt) cc_final: 0.8517 (pp)
REVERT: A  176 MET cc_start: 0.8363 (tpt) cc_final: 0.8150 (tpt)
REVERT: A  391 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7917 (tmm)
REVERT: A  500 MET cc_start: 0.8667 (mtt) cc_final: 0.8309 (mtm)
REVERT: A  507 ILE cc_start: 0.8386 (mt) cc_final: 0.8167 (mt)
REVERT: A  511 VAL cc_start: 0.8846 (t) cc_final: 0.8575 (m)
REVERT: A  587 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9026 (mm)
REVERT: A  891 LYS cc_start: 0.8614 (tptt) cc_final: 0.8257 (pttm)
REVERT: A  900 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8146 (mt-10)
REVERT: B  500 MET cc_start: 0.8702 (mtt) cc_final: 0.8331 (mtm)
REVERT: B  507 ILE cc_start: 0.8384 (mt) cc_final: 0.8183 (mt)
REVERT: B  511 VAL cc_start: 0.8895 (t) cc_final: 0.8640 (m)
REVERT: B  534 ILE cc_start: 0.3990 (OUTLIER) cc_final: 0.3768 (pp)
REVERT: B  891 LYS cc_start: 0.8642 (tptt) cc_final: 0.8263 (pttm)
  outliers start: 36
  outliers final: 19
  residues processed: 173
  average time/residue: 0.2414
  time to fit residues: 60.6585
Evaluate side-chains
  152 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 79 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 135 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 215 GLN
A 296 ASN
B 296 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.100457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.077246 restraints weight = 31943.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.079078 restraints weight = 17779.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.080176 restraints weight = 12777.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12072  Z= 0.115
  Angle     :  0.618   9.945  16336  Z= 0.307
  Chirality :  0.041   0.197   1796
  Planarity :  0.004   0.042   2044
  Dihedral  :  4.685  46.356   1588
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.78 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.23), residues: 1416
  helix:  1.55 (0.18), residues: 860
  sheet: -0.64 (0.74), residues: 48
  loop : -2.62 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 402 
 PHE   0.031   0.001   PHE B 505 
 TYR   0.016   0.001   TYR A 687 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  620)
  hydrogen bonds       : angle       3.99717 ( 1842)
  SS BOND              : bond        0.00275 (    8)
  SS BOND              : angle       0.75623 (   16)
  covalent geometry    : bond        0.00244 (12064)
  covalent geometry    : angle       0.61769 (16320)

*********************** 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
  179 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8255 (tpp80)
REVERT: A  174 LEU cc_start: 0.8743 (mt) cc_final: 0.8501 (pp)
REVERT: A  176 MET cc_start: 0.8402 (tpt) cc_final: 0.8201 (tpt)
REVERT: A  391 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6628 (tmm)
REVERT: A  500 MET cc_start: 0.8647 (mtt) cc_final: 0.8321 (mtm)
REVERT: A  507 ILE cc_start: 0.8333 (mt) cc_final: 0.8083 (mt)
REVERT: A  511 VAL cc_start: 0.8830 (t) cc_final: 0.8612 (m)
REVERT: A  891 LYS cc_start: 0.8392 (tptt) cc_final: 0.8156 (pttm)
REVERT: A  900 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8107 (mt-10)
REVERT: A  907 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7005 (mp)
REVERT: B  186 GLU cc_start: 0.8664 (pm20) cc_final: 0.8433 (pm20)
REVERT: B  500 MET cc_start: 0.8639 (mtt) cc_final: 0.8287 (mtm)
REVERT: B  507 ILE cc_start: 0.8339 (mt) cc_final: 0.8070 (mt)
REVERT: B  511 VAL cc_start: 0.8806 (t) cc_final: 0.8596 (m)
REVERT: B  534 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3872 (pp)
REVERT: B  891 LYS cc_start: 0.8448 (tptt) cc_final: 0.8217 (pttm)
REVERT: B  907 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7018 (mp)
  outliers start: 33
  outliers final: 19
  residues processed: 172
  average time/residue: 0.2318
  time to fit residues: 58.3942
Evaluate side-chains
  154 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  687 TYR
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  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  503 VAL
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  907 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 111 optimal weight:    0.3980
   chunk 6 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 124 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.6184

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.098527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.075122 restraints weight = 32418.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.076882 restraints weight = 18080.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.077964 restraints weight = 13025.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4073

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= 0.150
  Angle     :  0.655  10.861  16336  Z= 0.328
  Chirality :  0.042   0.197   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.767  45.923   1588
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.33 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.23), residues: 1416
  helix:  1.59 (0.18), residues: 860
  sheet: -0.28 (0.74), residues: 48
  loop : -2.45 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 
 PHE   0.031   0.001   PHE B 505 
 TYR   0.017   0.001   TYR A 687 
 ARG   0.003   0.000   ARG B 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04214 (  620)
  hydrogen bonds       : angle       4.05651 ( 1842)
  SS BOND              : bond        0.00553 (    8)
  SS BOND              : angle       0.73397 (   16)
  covalent geometry    : bond        0.00340 (12064)
  covalent geometry    : angle       0.65493 (16320)

*********************** 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
  176 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 1.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4731 (tmm) cc_final: 0.4154 (tpt)
REVERT: A  125 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8279 (tpp80)
REVERT: A  315 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6099 (mp10)
REVERT: A  391 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7534 (tmm)
REVERT: A  500 MET cc_start: 0.8679 (mtt) cc_final: 0.8328 (mtm)
REVERT: A  507 ILE cc_start: 0.8328 (mt) cc_final: 0.8124 (mt)
REVERT: A  511 VAL cc_start: 0.8932 (t) cc_final: 0.8660 (m)
REVERT: A  900 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8122 (mt-10)
REVERT: A  907 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6955 (mp)
REVERT: B  117 MET cc_start: 0.4701 (tmm) cc_final: 0.4148 (tpt)
REVERT: B  176 MET cc_start: 0.8296 (tpt) cc_final: 0.7780 (tpt)
REVERT: B  315 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.6141 (mp10)
REVERT: B  500 MET cc_start: 0.8672 (mtt) cc_final: 0.8324 (mtm)
REVERT: B  534 ILE cc_start: 0.4142 (OUTLIER) cc_final: 0.3928 (pp)
REVERT: B  906 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7645 (tm-30)
  outliers start: 37
  outliers final: 21
  residues processed: 168
  average time/residue: 0.2215
  time to fit residues: 55.3697
Evaluate side-chains
  147 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  391 MET
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  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
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  315 GLN
Chi-restraints excluded: chain B residue  534 ILE
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 113 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0870
   chunk 54 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.9562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.099839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.076723 restraints weight = 32329.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078572 restraints weight = 17780.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.079687 restraints weight = 12682.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12072  Z= 0.120
  Angle     :  0.637  10.286  16336  Z= 0.313
  Chirality :  0.042   0.195   1796
  Planarity :  0.004   0.039   2044
  Dihedral  :  4.604  45.611   1588
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.88 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.23), residues: 1416
  helix:  1.81 (0.18), residues: 858
  sheet:  0.09 (0.75), residues: 48
  loop : -2.49 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 427 
 HIS   0.002   0.001   HIS A 402 
 PHE   0.028   0.001   PHE A 505 
 TYR   0.012   0.001   TYR A 514 
 ARG   0.003   0.000   ARG B 515 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  620)
  hydrogen bonds       : angle       3.97494 ( 1842)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       0.80393 (   16)
  covalent geometry    : bond        0.00263 (12064)
  covalent geometry    : angle       0.63724 (16320)

*********************** 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
  166 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4610 (tmm) cc_final: 0.4139 (tpt)
REVERT: A  500 MET cc_start: 0.8617 (mtt) cc_final: 0.8302 (mtm)
REVERT: A  507 ILE cc_start: 0.8255 (mt) cc_final: 0.8035 (mt)
REVERT: A  511 VAL cc_start: 0.8911 (t) cc_final: 0.8640 (m)
REVERT: A  900 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8090 (mt-10)
REVERT: A  906 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7958 (tm-30)
REVERT: A  907 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7255 (mt)
REVERT: B  117 MET cc_start: 0.4537 (tmm) cc_final: 0.4068 (tpt)
REVERT: B  176 MET cc_start: 0.8330 (tpt) cc_final: 0.7999 (tpt)
REVERT: B  500 MET cc_start: 0.8659 (mtt) cc_final: 0.8312 (mtm)
REVERT: B  534 ILE cc_start: 0.4106 (OUTLIER) cc_final: 0.3901 (pp)
  outliers start: 31
  outliers final: 20
  residues processed: 159
  average time/residue: 0.2230
  time to fit residues: 52.4155
Evaluate side-chains
  150 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  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  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  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  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  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 131 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 129 optimal weight:    0.7980
   chunk 138 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.100445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.077352 restraints weight = 32377.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.079084 restraints weight = 18673.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080110 restraints weight = 13610.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4450

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= 0.118
  Angle     :  0.638  11.310  16336  Z= 0.311
  Chirality :  0.042   0.204   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.537  45.678   1588
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.27 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.23), residues: 1416
  helix:  1.87 (0.18), residues: 866
  sheet:  0.32 (0.77), residues: 48
  loop : -2.48 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 402 
 PHE   0.028   0.001   PHE A 505 
 TYR   0.012   0.001   TYR A 687 
 ARG   0.004   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  620)
  hydrogen bonds       : angle       3.93983 ( 1842)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.76523 (   16)
  covalent geometry    : bond        0.00258 (12064)
  covalent geometry    : angle       0.63749 (16320)

*********************** 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
  165 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4580 (tmm) cc_final: 0.4161 (tpt)
REVERT: A  500 MET cc_start: 0.8606 (mtt) cc_final: 0.8297 (mtm)
REVERT: A  507 ILE cc_start: 0.8212 (mt) cc_final: 0.7960 (mt)
REVERT: A  906 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7851 (tm-30)
REVERT: A  907 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6631 (mm)
REVERT: B  117 MET cc_start: 0.4441 (tmm) cc_final: 0.4016 (tpt)
REVERT: B  369 MET cc_start: 0.7732 (mmt) cc_final: 0.7408 (mmm)
REVERT: B  500 MET cc_start: 0.8624 (mtt) cc_final: 0.8297 (mtm)
REVERT: B  534 ILE cc_start: 0.4176 (OUTLIER) cc_final: 0.3958 (pp)
  outliers start: 30
  outliers final: 20
  residues processed: 154
  average time/residue: 0.2045
  time to fit residues: 47.4326
Evaluate side-chains
  149 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
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  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  534 ILE
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  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 141 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.2986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.099659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.076343 restraints weight = 32284.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.078119 restraints weight = 18247.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.079208 restraints weight = 13132.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12072  Z= 0.134
  Angle     :  0.657  10.625  16336  Z= 0.323
  Chirality :  0.043   0.215   1796
  Planarity :  0.004   0.040   2044
  Dihedral  :  4.584  45.163   1588
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.88 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.23), residues: 1416
  helix:  1.94 (0.18), residues: 860
  sheet:  0.42 (0.77), residues: 48
  loop : -2.41 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 
 PHE   0.028   0.001   PHE A 505 
 TYR   0.012   0.001   TYR A 338 
 ARG   0.004   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  620)
  hydrogen bonds       : angle       3.97324 ( 1842)
  SS BOND              : bond        0.00276 (    8)
  SS BOND              : angle       0.76812 (   16)
  covalent geometry    : bond        0.00301 (12064)
  covalent geometry    : angle       0.65697 (16320)

*********************** 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
  156 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.4568 (tmm) cc_final: 0.4297 (tpt)
REVERT: A  369 MET cc_start: 0.7829 (mmt) cc_final: 0.7399 (mmm)
REVERT: A  500 MET cc_start: 0.8620 (mtt) cc_final: 0.8302 (mtm)
REVERT: A  507 ILE cc_start: 0.8240 (mt) cc_final: 0.8001 (mt)
REVERT: A  906 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (tm-30)
REVERT: A  907 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7016 (mm)
REVERT: B  117 MET cc_start: 0.4570 (tmm) cc_final: 0.4141 (tpt)
REVERT: B  369 MET cc_start: 0.7694 (mmt) cc_final: 0.7399 (mmm)
REVERT: B  500 MET cc_start: 0.8656 (mtt) cc_final: 0.8304 (mtm)
  outliers start: 27
  outliers final: 21
  residues processed: 148
  average time/residue: 0.2092
  time to fit residues: 47.1127
Evaluate side-chains
  147 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  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  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  182 TYR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  687 TYR
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 119 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 138 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.100552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.077177 restraints weight = 31540.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.078963 restraints weight = 17925.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.080021 restraints weight = 13043.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4664

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= 0.122
  Angle     :  0.653  10.402  16336  Z= 0.321
  Chirality :  0.042   0.204   1796
  Planarity :  0.004   0.037   2044
  Dihedral  :  4.542  45.160   1588
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.66 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.23), residues: 1416
  helix:  1.98 (0.18), residues: 864
  sheet:  0.57 (0.78), residues: 48
  loop : -2.34 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 402 
 PHE   0.029   0.001   PHE A 505 
 TYR   0.013   0.001   TYR A 514 
 ARG   0.004   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  620)
  hydrogen bonds       : angle       3.93528 ( 1842)
  SS BOND              : bond        0.00264 (    8)
  SS BOND              : angle       0.77469 (   16)
  covalent geometry    : bond        0.00267 (12064)
  covalent geometry    : angle       0.65263 (16320)

********************** 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
  158 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  117 MET cc_start: 0.4510 (tmm) cc_final: 0.3950 (tpt)
REVERT: A  369 MET cc_start: 0.7635 (mmt) cc_final: 0.7328 (mmm)
REVERT: A  500 MET cc_start: 0.8611 (mtt) cc_final: 0.8304 (mtm)
REVERT: A  507 ILE cc_start: 0.8187 (mt) cc_final: 0.7933 (mt)
REVERT: A  906 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8004 (tm-30)
REVERT: A  907 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7163 (mm)
REVERT: B  117 MET cc_start: 0.4539 (tmm) cc_final: 0.3705 (tpt)
REVERT: B  369 MET cc_start: 0.7751 (mmt) cc_final: 0.7538 (mmm)
REVERT: B  391 MET cc_start: 0.8894 (tpt) cc_final: 0.8106 (tmm)
REVERT: B  500 MET cc_start: 0.8643 (mtt) cc_final: 0.8301 (mtm)
  outliers start: 25
  outliers final: 22
  residues processed: 148
  average time/residue: 0.2091
  time to fit residues: 47.5045
Evaluate side-chains
  148 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  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  693 LEU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  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  693 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  794 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.099768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.076289 restraints weight = 31973.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.078050 restraints weight = 18168.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.079120 restraints weight = 13228.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12072  Z= 0.141
  Angle     :  0.681  10.329  16336  Z= 0.336
  Chirality :  0.043   0.203   1796
  Planarity :  0.004   0.038   2044
  Dihedral  :  4.604  45.177   1588
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.42 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.23), residues: 1416
  helix:  1.93 (0.18), residues: 864
  sheet:  0.68 (0.79), residues: 48
  loop : -2.35 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 402 
 PHE   0.027   0.001   PHE A 505 
 TYR   0.012   0.001   TYR A 338 
 ARG   0.004   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  620)
  hydrogen bonds       : angle       4.03816 ( 1842)
  SS BOND              : bond        0.00273 (    8)
  SS BOND              : angle       0.85884 (   16)
  covalent geometry    : bond        0.00319 (12064)
  covalent geometry    : angle       0.68115 (16320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4687.88 seconds
wall clock time: 83 minutes 46.35 seconds (5026.35 seconds total)