Starting phenix.real_space_refine
on Wed May 14 20:37:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pwl_17994/05_2025/8pwl_17994.cif"
  }
  resolution = 4.73
  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=   0.008 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      91      5.16       5
     C    7769      2.51       5
     N    2132      2.21       5
     O    2274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 830, 6603
          Classifications: {'peptide': 830}
          Link IDs: {'PTRANS': 38, 'TRANS': 791}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 711, 5663
          Classifications: {'peptide': 711}
          Link IDs: {'PTRANS': 29, 'TRANS': 681}
          Chain breaks: 2
  Time building chain proxies: 7.43, per 1000 atoms: 0.61
  Number of scatterers: 12266
  At special positions: 0
  Unit cell: (79.23, 136.776, 168.468, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      91     16.00
     O    2274      8.00
     N    2132      7.00
     C    7769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.98
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2918

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 8 sheets defined
      66.9% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 4.311A  pdb=" N   GLU A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 32
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 3.853A  pdb=" N   ALA A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 52
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 3.704A  pdb=" N   ILE A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 3.674A  pdb=" N   GLY A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 133 through 142
      removed outlier: 3.886A  pdb=" N   ASN A 141 " --> pdb=" O   TRP A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 153
      removed outlier: 3.592A  pdb=" N   ASP A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 152 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
      removed outlier: 3.562A  pdb=" N   VAL A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 186
    Processing helix  chain 'A' and resid 199 through 208
      removed outlier: 3.919A  pdb=" N   PHE A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 241 through 252
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 4.251A  pdb=" N   GLN A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 282
      removed outlier: 3.776A  pdb=" N   GLN A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A 276 " --> pdb=" O   MET A 272 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 307
      removed outlier: 3.664A  pdb=" N   GLU A 297 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 334
      removed outlier: 3.572A  pdb=" N   LYS A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLY A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 383
      removed outlier: 3.627A  pdb=" N   LYS A 358 " --> pdb=" O   SER A 354 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
      removed outlier: 3.558A  pdb=" N   LEU A 362 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 465
      removed outlier: 3.563A  pdb=" N   MET A 461 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   CYS A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   CYS A 463 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 3.607A  pdb=" N   PHE A 479 " --> pdb=" O   ARG A 475 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   HIS A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.733A  pdb=" N   PHE A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 491 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 501
      removed outlier: 4.469A  pdb=" N   ASP A 500 " --> pdb=" O   LYS A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 508 through 515
      removed outlier: 3.623A  pdb=" N   ARG A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 3.826A  pdb=" N   GLU A 529 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 560
      No H-bonds generated for 'chain 'A' and resid 558 through 560'
    Processing helix  chain 'A' and resid 561 through 573
    Processing helix  chain 'A' and resid 574 through 581
    Processing helix  chain 'A' and resid 593 through 609
      removed outlier: 3.788A  pdb=" N   VAL A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.578A  pdb=" N   VAL A 633 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 654
    Processing helix  chain 'A' and resid 663 through 672
      removed outlier: 3.653A  pdb=" N   TYR A 667 " --> pdb=" O   THR A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 684
      removed outlier: 3.613A  pdb=" N   VAL A 680 " --> pdb=" O   ASN A 676 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 683 " --> pdb=" O   ASP A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 695
    Processing helix  chain 'A' and resid 736 through 751
    Processing helix  chain 'A' and resid 753 through 766
    Processing helix  chain 'A' and resid 769 through 774
    Processing helix  chain 'A' and resid 777 through 787
    Processing helix  chain 'A' and resid 792 through 799
    Processing helix  chain 'A' and resid 810 through 823
      removed outlier: 3.850A  pdb=" N   GLN A 814 " --> pdb=" O   ASP A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 836
    Processing helix  chain 'A' and resid 887 through 901
    Processing helix  chain 'B' and resid 3 through 17
    Processing helix  chain 'B' and resid 26 through 39
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 52
    Processing helix  chain 'B' and resid 67 through 76
    Processing helix  chain 'B' and resid 78 through 87
      removed outlier: 3.559A  pdb=" N   VAL B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 109
      removed outlier: 3.621A  pdb=" N   LEU B 104 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 120
    Processing helix  chain 'B' and resid 133 through 142
      removed outlier: 4.000A  pdb=" N   TRP B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 152
    Processing helix  chain 'B' and resid 166 through 175
    Processing helix  chain 'B' and resid 176 through 186
      removed outlier: 3.593A  pdb=" N   VAL B 180 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 208
      removed outlier: 3.613A  pdb=" N   PHE B 203 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 219
    Processing helix  chain 'B' and resid 231 through 240
      removed outlier: 3.771A  pdb=" N   LEU B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 252
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 269 through 280
      removed outlier: 3.871A  pdb=" N   VAL B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 309
      removed outlier: 3.662A  pdb=" N   GLU B 297 " --> pdb=" O   THR B 293 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B 298 " --> pdb=" O   SER B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 334
      removed outlier: 3.627A  pdb=" N   PHE B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 383
      Proline residue:  B 359  - end of helix
      removed outlier: 4.130A  pdb=" N   TRP B 364 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 465
      removed outlier: 3.842A  pdb=" N   MET B 461 " --> pdb=" O   GLN B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 483
      removed outlier: 3.701A  pdb=" N   ILE B 477 " --> pdb=" O   SER B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 494
      removed outlier: 4.055A  pdb=" N   LEU B 487 " --> pdb=" O   HIS B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 501
      removed outlier: 3.983A  pdb=" N   ASP B 500 " --> pdb=" O   LYS B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 507
      removed outlier: 3.674A  pdb=" N   LEU B 506 " --> pdb=" O   HIS B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 520
      removed outlier: 3.664A  pdb=" N   SER B 513 " --> pdb=" O   PRO B 509 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG B 514 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   HIS B 517 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ILE B 518 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 536
      removed outlier: 3.523A  pdb=" N   HIS B 536 " --> pdb=" O   TYR B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 573
    Processing helix  chain 'B' and resid 574 through 581
      removed outlier: 3.602A  pdb=" N   LEU B 578 " --> pdb=" O   ASN B 574 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLN B 580 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 593 through 610
      removed outlier: 3.506A  pdb=" N   VAL B 597 " --> pdb=" O   GLY B 593 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASN B 610 " --> pdb=" O   ASN B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 614
    Processing helix  chain 'B' and resid 636 through 654
    Processing helix  chain 'B' and resid 663 through 672
    Processing helix  chain 'B' and resid 676 through 682
      removed outlier: 3.732A  pdb=" N   VAL B 680 " --> pdb=" O   ASN B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 696
      removed outlier: 3.505A  pdb=" N   ALA B 688 " --> pdb=" O   ASP B 684 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASP B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 737 through 751
    Processing helix  chain 'B' and resid 753 through 766
      removed outlier: 3.540A  pdb=" N   MET B 766 " --> pdb=" O   GLN B 762 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 774
    Processing helix  chain 'B' and resid 777 through 787
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
      removed outlier: 5.799A  pdb=" N   LEU A 555 " --> pdb=" O   ARG A 585 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618
    Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 714
    Processing sheet with id=AA4, first strand: chain 'A' and resid 850 through 851
    Processing sheet with id=AA5, first strand: chain 'A' and resid 859 through 863
      removed outlier: 3.550A  pdb=" N   THR A 872 " --> pdb=" O   LYS A 881 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 554 through 557
      removed outlier: 6.063A  pdb=" N   LEU B 555 " --> pdb=" O   ARG B 585 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 616 through 618
    Processing sheet with id=AA8, first strand: chain 'B' and resid 710 through 714

    641 hydrogen bonds defined for protein.
    1887 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: 4.41

  Time building geometry restraints manager: 3.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4104
        1.34 -     1.46: 2639
        1.46 -     1.58: 5644
        1.58 -     1.69: 0
        1.69 -     1.81: 140
  Bond restraints: 12527
  Sorted by residual:
  bond pdb=" CA  THR A 351 "
       pdb=" C   THR A 351 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.73e-01
  bond pdb=" CB  MET A   5 "
       pdb=" CG  MET A   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.04e-01
  bond pdb=" C   MET A  35 "
       pdb=" N   PRO A  36 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.94e-01
  bond pdb=" C   THR A 351 "
       pdb=" N   PRO A 352 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.19e-02 7.06e+03 5.82e-01
  bond pdb=" CB  ASP A 500 "
       pdb=" CG  ASP A 500 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.80e-01
  ... (remaining 12522 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 16656
        1.51 -     3.02: 240
        3.02 -     4.53: 44
        4.53 -     6.03: 27
        6.03 -     7.54: 8
  Bond angle restraints: 16975
  Sorted by residual:
  angle pdb=" CA  MET A   1 "
        pdb=" CB  MET A   1 "
        pdb=" CG  MET A   1 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.89e+00
  angle pdb=" C   MET A   1 "
        pdb=" CA  MET A   1 "
        pdb=" CB  MET A   1 "
      ideal   model   delta    sigma   weight residual
     110.10  115.03   -4.93 1.90e+00 2.77e-01 6.73e+00
  angle pdb=" CB  MET A   1 "
        pdb=" CG  MET A   1 "
        pdb=" SD  MET A   1 "
      ideal   model   delta    sigma   weight residual
     112.70  120.24   -7.54 3.00e+00 1.11e-01 6.32e+00
  angle pdb=" CB  MET A   5 "
        pdb=" CG  MET A   5 "
        pdb=" SD  MET A   5 "
      ideal   model   delta    sigma   weight residual
     112.70  120.11   -7.41 3.00e+00 1.11e-01 6.09e+00
  angle pdb=" N   THR A 351 "
        pdb=" CA  THR A 351 "
        pdb=" C   THR A 351 "
      ideal   model   delta    sigma   weight residual
     109.81  115.15   -5.34 2.21e+00 2.05e-01 5.83e+00
  ... (remaining 16970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 6772
       16.25 -    32.50: 606
       32.50 -    48.75: 155
       48.75 -    65.01: 25
       65.01 -    81.26: 10
  Dihedral angle restraints: 7568
    sinusoidal: 3069
      harmonic: 4499
  Sorted by residual:
  dihedral pdb=" CA  TRP B 370 "
           pdb=" C   TRP B 370 "
           pdb=" N   LEU B 371 "
           pdb=" CA  LEU B 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LYS A 358 "
           pdb=" C   LYS A 358 "
           pdb=" N   PRO A 359 "
           pdb=" CA  PRO A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  MET A 749 "
           pdb=" C   MET A 749 "
           pdb=" N   THR A 750 "
           pdb=" CA  THR A 750 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.24  -17.76     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 7565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1266
       0.032 -    0.063: 487
       0.063 -    0.095: 102
       0.095 -    0.127: 48
       0.127 -    0.158: 2
  Chirality restraints: 1905
  Sorted by residual:
  chirality pdb=" CG  LEU A 371 "
            pdb=" CB  LEU A 371 "
            pdb=" CD1 LEU A 371 "
            pdb=" CD2 LEU A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  THR A 351 "
            pdb=" N   THR A 351 "
            pdb=" C   THR A 351 "
            pdb=" CB  THR A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  ILE B 768 "
            pdb=" N   ILE B 768 "
            pdb=" C   ILE B 768 "
            pdb=" CB  ILE B 768 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1902 not shown)

  Planarity restraints: 2206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 358 "   -0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 359 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 100 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.02e+00
        pdb=" N   PRO B 101 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 101 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 101 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 199 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO A 200 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 200 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 200 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2203 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2656
        2.78 -     3.31: 12751
        3.31 -     3.84: 20609
        3.84 -     4.37: 24398
        4.37 -     4.90: 38856
  Nonbonded interactions: 99270
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 500 "
            pdb=" N   HIS A 501 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" NH2 ARG B 527 "
            pdb=" O   LEU B 775 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   ALA B  18 "
            pdb=" NE  ARG B  19 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OG1 THR A 144 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   GLU A 821 "
            pdb=" NH2 ARG A 828 "
     model   vdw
     2.362 3.120
  ... (remaining 99265 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 335 or resid 353 through 787))
  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:             2.490
  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:          0.550
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     30.460
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
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      :  0.002   0.025  12527  Z= 0.085
  Angle     :  0.510   7.543  16975  Z= 0.243
  Chirality :  0.037   0.158   1905
  Planarity :  0.003   0.051   2206
  Dihedral  : 13.554  81.257   4650
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -0.12 (0.21), residues: 1529
  helix: -0.02 (0.17), residues: 951
  sheet:  1.37 (0.60), residues: 81
  loop : -0.14 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 364 
 HIS   0.006   0.001   HIS B 765 
 PHE   0.014   0.001   PHE B 476 
 TYR   0.016   0.001   TYR B 632 
 ARG   0.002   0.000   ARG A 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25582 (  641)
  hydrogen bonds       : angle       7.12460 ( 1887)
  covalent geometry    : bond        0.00177 (12527)
  covalent geometry    : angle       0.50985 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.8134 (ttt) cc_final: 0.7601 (ttt)
REVERT: B  447 MET cc_start: 0.6652 (ppp) cc_final: 0.6400 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1979
  time to fit residues: 53.2867
Evaluate side-chains
  137 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 116 optimal weight:    0.0030
   chunk 64 optimal weight:    0.0000
   chunk 39 optimal weight:    5.9990
   chunk 78 optimal weight:   30.0000
   chunk 62 optimal weight:    8.9990
   chunk 120 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 73 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 139 optimal weight:    6.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 HIS
B 659 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.073997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.047235 restraints weight = 67263.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.048663 restraints weight = 51903.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.049798 restraints weight = 42835.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12527  Z= 0.160
  Angle     :  0.577   7.708  16975  Z= 0.306
  Chirality :  0.040   0.144   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.707  19.753   1659
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  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:  0.52 (0.21), residues: 1529
  helix:  0.50 (0.16), residues: 967
  sheet:  1.39 (0.60), residues: 81
  loop :  0.11 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 137 
 HIS   0.009   0.001   HIS B 765 
 PHE   0.022   0.002   PHE B 641 
 TYR   0.012   0.001   TYR A 120 
 ARG   0.003   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05301 (  641)
  hydrogen bonds       : angle       4.86890 ( 1887)
  covalent geometry    : bond        0.00315 (12527)
  covalent geometry    : angle       0.57734 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6113 (tmm) cc_final: 0.5163 (tmm)
REVERT: A  169 HIS cc_start: 0.9172 (m90) cc_final: 0.8972 (m170)
REVERT: A  272 MET cc_start: 0.8994 (ttt) cc_final: 0.8629 (ttt)
REVERT: A  516 MET cc_start: 0.9483 (tpp) cc_final: 0.9156 (tpp)
REVERT: A  766 MET cc_start: 0.9368 (mtm) cc_final: 0.9125 (mtt)
REVERT: B   35 MET cc_start: 0.9345 (mmp) cc_final: 0.8949 (mmm)
REVERT: B   39 MET cc_start: 0.9124 (mpp) cc_final: 0.8374 (mpp)
REVERT: B  370 TRP cc_start: 0.9316 (m-90) cc_final: 0.9048 (m100)
REVERT: B  476 PHE cc_start: 0.9127 (p90) cc_final: 0.8810 (p90)
REVERT: B  512 MET cc_start: 0.9304 (ptp) cc_final: 0.8962 (ptp)
REVERT: B  693 TRP cc_start: 0.9792 (t60) cc_final: 0.9461 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2044
  time to fit residues: 51.4624
Evaluate side-chains
  130 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 111 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 152 optimal weight:    0.0000
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.8980
   chunk 150 optimal weight:    9.9990
   chunk 139 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
B  70 HIS
B 483 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.075090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.048284 restraints weight = 67944.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.049866 restraints weight = 51830.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.051001 restraints weight = 42222.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12527  Z= 0.111
  Angle     :  0.544   8.813  16975  Z= 0.277
  Chirality :  0.039   0.142   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.758  19.600   1659
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.77 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.43 (0.21), residues: 1529
  helix:  0.47 (0.16), residues: 978
  sheet:  1.15 (0.59), residues: 81
  loop :  0.01 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 693 
 HIS   0.017   0.001   HIS B 765 
 PHE   0.022   0.001   PHE B 760 
 TYR   0.014   0.001   TYR B 460 
 ARG   0.002   0.000   ARG B 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  641)
  hydrogen bonds       : angle       4.54027 ( 1887)
  covalent geometry    : bond        0.00225 (12527)
  covalent geometry    : angle       0.54440 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5793 (tmm) cc_final: 0.4926 (tmm)
REVERT: A  467 MET cc_start: 0.7849 (ptp) cc_final: 0.7585 (ptt)
REVERT: A  516 MET cc_start: 0.9480 (tpp) cc_final: 0.9144 (tpp)
REVERT: A  766 MET cc_start: 0.9340 (mtm) cc_final: 0.8944 (mpp)
REVERT: B  297 GLU cc_start: 0.9176 (mp0) cc_final: 0.8884 (mp0)
REVERT: B  370 TRP cc_start: 0.9360 (m-90) cc_final: 0.9074 (m100)
REVERT: B  476 PHE cc_start: 0.9135 (p90) cc_final: 0.8794 (p90)
REVERT: B  512 MET cc_start: 0.9225 (ptp) cc_final: 0.9008 (ptp)
REVERT: B  516 MET cc_start: 0.8490 (tpt) cc_final: 0.8275 (tpt)
REVERT: B  693 TRP cc_start: 0.9777 (t60) cc_final: 0.9573 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2054
  time to fit residues: 53.6226
Evaluate side-chains
  136 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.072402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.045774 restraints weight = 68621.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.047187 restraints weight = 53438.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.048250 restraints weight = 44167.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12527  Z= 0.147
  Angle     :  0.568   7.470  16975  Z= 0.292
  Chirality :  0.039   0.148   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.872  19.262   1659
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  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:  0.51 (0.22), residues: 1529
  helix:  0.52 (0.16), residues: 974
  sheet:  0.95 (0.59), residues: 81
  loop :  0.14 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 137 
 HIS   0.013   0.001   HIS B 765 
 PHE   0.025   0.002   PHE A 490 
 TYR   0.015   0.002   TYR A 120 
 ARG   0.005   0.000   ARG A 475 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  641)
  hydrogen bonds       : angle       4.46029 ( 1887)
  covalent geometry    : bond        0.00296 (12527)
  covalent geometry    : angle       0.56810 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5752 (tmm) cc_final: 0.4718 (tmm)
REVERT: A  169 HIS cc_start: 0.9159 (m90) cc_final: 0.8951 (m170)
REVERT: A  272 MET cc_start: 0.8961 (ttt) cc_final: 0.8633 (ttt)
REVERT: A  467 MET cc_start: 0.7746 (ptp) cc_final: 0.7394 (ptt)
REVERT: A  516 MET cc_start: 0.9465 (tpp) cc_final: 0.9166 (tpp)
REVERT: A  766 MET cc_start: 0.9332 (mtm) cc_final: 0.8977 (mpp)
REVERT: B  147 LEU cc_start: 0.9483 (mt) cc_final: 0.9231 (mt)
REVERT: B  297 GLU cc_start: 0.9207 (mp0) cc_final: 0.8842 (mp0)
REVERT: B  370 TRP cc_start: 0.9358 (m-90) cc_final: 0.9086 (m100)
REVERT: B  476 PHE cc_start: 0.9136 (p90) cc_final: 0.8797 (p90)
REVERT: B  512 MET cc_start: 0.9195 (ptp) cc_final: 0.8604 (ptp)
REVERT: B  693 TRP cc_start: 0.9777 (t60) cc_final: 0.9570 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1985
  time to fit residues: 50.0969
Evaluate side-chains
  132 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 127 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 144 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.075176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.048490 restraints weight = 66968.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.050038 restraints weight = 51440.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.051208 restraints weight = 42192.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12527  Z= 0.101
  Angle     :  0.551   8.833  16975  Z= 0.273
  Chirality :  0.040   0.152   1905
  Planarity :  0.004   0.048   2206
  Dihedral  :  3.846  19.981   1659
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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:  0.52 (0.22), residues: 1529
  helix:  0.54 (0.16), residues: 978
  sheet:  0.87 (0.59), residues: 81
  loop :  0.12 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 
 PHE   0.021   0.001   PHE B 641 
 TYR   0.014   0.001   TYR A 288 
 ARG   0.004   0.000   ARG A  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  641)
  hydrogen bonds       : angle       4.33164 ( 1887)
  covalent geometry    : bond        0.00208 (12527)
  covalent geometry    : angle       0.55125 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5660 (tmm) cc_final: 0.4535 (tmm)
REVERT: A  467 MET cc_start: 0.7850 (ptp) cc_final: 0.7555 (ptt)
REVERT: A  512 MET cc_start: 0.9610 (tpp) cc_final: 0.9314 (tpp)
REVERT: A  515 PHE cc_start: 0.9526 (m-80) cc_final: 0.9285 (m-80)
REVERT: A  516 MET cc_start: 0.9471 (tpp) cc_final: 0.9172 (tpp)
REVERT: A  766 MET cc_start: 0.9316 (mtm) cc_final: 0.8936 (mpp)
REVERT: B  297 GLU cc_start: 0.9177 (mp0) cc_final: 0.8781 (mp0)
REVERT: B  370 TRP cc_start: 0.9352 (m-90) cc_final: 0.9072 (m100)
REVERT: B  447 MET cc_start: 0.8346 (ppp) cc_final: 0.8105 (ppp)
REVERT: B  476 PHE cc_start: 0.9111 (p90) cc_final: 0.8746 (p90)
REVERT: B  512 MET cc_start: 0.9111 (ptp) cc_final: 0.8798 (ptm)
REVERT: B  632 TYR cc_start: 0.9072 (t80) cc_final: 0.8859 (t80)
REVERT: B  693 TRP cc_start: 0.9762 (t60) cc_final: 0.9538 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1973
  time to fit residues: 52.5747
Evaluate side-chains
  135 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 142 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 126 optimal weight:    0.0570
   chunk 13 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.4702

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.074296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.047404 restraints weight = 68914.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.048908 restraints weight = 52929.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.050004 restraints weight = 43387.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12527  Z= 0.111
  Angle     :  0.547   8.030  16975  Z= 0.274
  Chirality :  0.039   0.145   1905
  Planarity :  0.004   0.051   2206
  Dihedral  :  3.835  19.221   1659
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  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:  0.58 (0.22), residues: 1529
  helix:  0.61 (0.17), residues: 967
  sheet:  0.82 (0.59), residues: 81
  loop :  0.12 (0.30), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 370 
 HIS   0.016   0.001   HIS B 765 
 PHE   0.031   0.001   PHE B 760 
 TYR   0.013   0.001   TYR B 460 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03404 (  641)
  hydrogen bonds       : angle       4.34084 ( 1887)
  covalent geometry    : bond        0.00232 (12527)
  covalent geometry    : angle       0.54729 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5817 (tmm) cc_final: 0.4394 (tmm)
REVERT: A   66 ARG cc_start: 0.8999 (pmt170) cc_final: 0.8681 (ptm160)
REVERT: A  272 MET cc_start: 0.8985 (ttt) cc_final: 0.8639 (ttt)
REVERT: A  467 MET cc_start: 0.7818 (ptp) cc_final: 0.7425 (ptt)
REVERT: A  512 MET cc_start: 0.9562 (tpp) cc_final: 0.9282 (tpp)
REVERT: A  516 MET cc_start: 0.9464 (tpp) cc_final: 0.9147 (tpp)
REVERT: A  670 ILE cc_start: 0.9832 (tp) cc_final: 0.9572 (pt)
REVERT: A  766 MET cc_start: 0.9316 (mtm) cc_final: 0.8947 (mpp)
REVERT: B   35 MET cc_start: 0.9296 (mmp) cc_final: 0.9083 (mmm)
REVERT: B  297 GLU cc_start: 0.9097 (mp0) cc_final: 0.8816 (mp0)
REVERT: B  370 TRP cc_start: 0.9352 (m-90) cc_final: 0.9084 (m100)
REVERT: B  476 PHE cc_start: 0.9132 (p90) cc_final: 0.8769 (p90)
REVERT: B  512 MET cc_start: 0.9140 (ptp) cc_final: 0.8826 (ptm)
REVERT: B  632 TYR cc_start: 0.9075 (t80) cc_final: 0.8855 (t80)
REVERT: B  693 TRP cc_start: 0.9762 (t60) cc_final: 0.9535 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1985
  time to fit residues: 50.8877
Evaluate side-chains
  128 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 127 optimal weight:    0.7980
   chunk 88 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
A 110 GLN
A 539 GLN
B  70 HIS
B 174 ASN
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.074128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.047082 restraints weight = 68441.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.048582 restraints weight = 52937.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.049691 restraints weight = 43520.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12527  Z= 0.116
  Angle     :  0.577  10.297  16975  Z= 0.283
  Chirality :  0.040   0.172   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.860  19.480   1659
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  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: 1529
  helix:  0.55 (0.17), residues: 975
  sheet:  0.74 (0.60), residues: 79
  loop :  0.18 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 
 PHE   0.027   0.001   PHE B 760 
 TYR   0.013   0.001   TYR A 288 
 ARG   0.003   0.000   ARG A 655 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  641)
  hydrogen bonds       : angle       4.33541 ( 1887)
  covalent geometry    : bond        0.00251 (12527)
  covalent geometry    : angle       0.57748 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6509 (tmm) cc_final: 0.5986 (tmm)
REVERT: A   66 ARG cc_start: 0.8981 (pmt170) cc_final: 0.8586 (ptm160)
REVERT: A  467 MET cc_start: 0.7830 (ptp) cc_final: 0.7454 (ptt)
REVERT: A  512 MET cc_start: 0.9587 (tpp) cc_final: 0.9296 (tpp)
REVERT: A  515 PHE cc_start: 0.9563 (m-80) cc_final: 0.9288 (m-80)
REVERT: A  516 MET cc_start: 0.9479 (tpp) cc_final: 0.9169 (tpp)
REVERT: A  670 ILE cc_start: 0.9830 (tp) cc_final: 0.9535 (pt)
REVERT: A  766 MET cc_start: 0.9310 (mtm) cc_final: 0.8946 (mpp)
REVERT: B  297 GLU cc_start: 0.9059 (mp0) cc_final: 0.8808 (mp0)
REVERT: B  370 TRP cc_start: 0.9371 (m-90) cc_final: 0.9094 (m100)
REVERT: B  476 PHE cc_start: 0.9135 (p90) cc_final: 0.8769 (p90)
REVERT: B  512 MET cc_start: 0.9080 (ptp) cc_final: 0.8755 (ptm)
REVERT: B  632 TYR cc_start: 0.9090 (t80) cc_final: 0.8869 (t80)
REVERT: B  693 TRP cc_start: 0.9758 (t60) cc_final: 0.9528 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2009
  time to fit residues: 52.1009
Evaluate side-chains
  135 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 144 optimal weight:    0.1980
   chunk 108 optimal weight:    0.0070
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    0.6402

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.075451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.048520 restraints weight = 68050.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.050067 restraints weight = 52036.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.051214 restraints weight = 42562.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12527  Z= 0.099
  Angle     :  0.561   7.303  16975  Z= 0.275
  Chirality :  0.039   0.144   1905
  Planarity :  0.004   0.051   2206
  Dihedral  :  3.834  19.675   1659
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  0.62 (0.22), residues: 1529
  helix:  0.61 (0.17), residues: 972
  sheet:  0.76 (0.61), residues: 79
  loop :  0.21 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 
 PHE   0.021   0.001   PHE B 760 
 TYR   0.016   0.001   TYR A 120 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  641)
  hydrogen bonds       : angle       4.23061 ( 1887)
  covalent geometry    : bond        0.00209 (12527)
  covalent geometry    : angle       0.56068 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6690 (tmm) cc_final: 0.6085 (tmm)
REVERT: A  364 TRP cc_start: 0.7394 (m100) cc_final: 0.6031 (m100)
REVERT: A  467 MET cc_start: 0.7748 (ptp) cc_final: 0.7295 (ptt)
REVERT: A  512 MET cc_start: 0.9574 (tpp) cc_final: 0.9272 (tpp)
REVERT: A  515 PHE cc_start: 0.9527 (m-80) cc_final: 0.9275 (m-80)
REVERT: A  516 MET cc_start: 0.9461 (tpp) cc_final: 0.9142 (tpp)
REVERT: A  670 ILE cc_start: 0.9828 (tp) cc_final: 0.9537 (pt)
REVERT: A  766 MET cc_start: 0.9316 (mtm) cc_final: 0.8944 (mpp)
REVERT: B  370 TRP cc_start: 0.9363 (m-90) cc_final: 0.9093 (m100)
REVERT: B  447 MET cc_start: 0.8273 (ppp) cc_final: 0.8028 (ppp)
REVERT: B  476 PHE cc_start: 0.9146 (p90) cc_final: 0.8788 (p90)
REVERT: B  512 MET cc_start: 0.9101 (ptp) cc_final: 0.8769 (ptm)
REVERT: B  632 TYR cc_start: 0.9065 (t80) cc_final: 0.8844 (t80)
REVERT: B  693 TRP cc_start: 0.9752 (t60) cc_final: 0.9515 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2112
  time to fit residues: 56.2651
Evaluate side-chains
  140 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 133 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 144 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0470
   chunk 14 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0020
   chunk 85 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7088

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.075707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.048760 restraints weight = 67672.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.050300 restraints weight = 52128.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.051454 restraints weight = 42817.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12527  Z= 0.097
  Angle     :  0.566   8.263  16975  Z= 0.276
  Chirality :  0.040   0.143   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.796  20.124   1659
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  0.61 (0.22), residues: 1529
  helix:  0.62 (0.17), residues: 976
  sheet:  0.75 (0.61), residues: 79
  loop :  0.17 (0.31), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 
 PHE   0.022   0.001   PHE B 760 
 TYR   0.017   0.001   TYR A 120 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03218 (  641)
  hydrogen bonds       : angle       4.18158 ( 1887)
  covalent geometry    : bond        0.00207 (12527)
  covalent geometry    : angle       0.56632 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6379 (tmm) cc_final: 0.5985 (tmm)
REVERT: A  272 MET cc_start: 0.8910 (ttt) cc_final: 0.8547 (ttt)
REVERT: A  364 TRP cc_start: 0.7347 (m100) cc_final: 0.5998 (m100)
REVERT: A  467 MET cc_start: 0.7753 (ptp) cc_final: 0.7286 (ptt)
REVERT: A  512 MET cc_start: 0.9578 (tpp) cc_final: 0.9279 (tpp)
REVERT: A  515 PHE cc_start: 0.9533 (m-80) cc_final: 0.9284 (m-80)
REVERT: A  516 MET cc_start: 0.9471 (tpp) cc_final: 0.9152 (tpp)
REVERT: A  670 ILE cc_start: 0.9834 (tp) cc_final: 0.9539 (pt)
REVERT: A  766 MET cc_start: 0.9316 (mtm) cc_final: 0.8935 (mpp)
REVERT: B  203 PHE cc_start: 0.9398 (m-10) cc_final: 0.9191 (m-10)
REVERT: B  370 TRP cc_start: 0.9359 (m-90) cc_final: 0.9084 (m100)
REVERT: B  476 PHE cc_start: 0.9160 (p90) cc_final: 0.8805 (p90)
REVERT: B  512 MET cc_start: 0.9080 (ptp) cc_final: 0.8747 (ptm)
REVERT: B  632 TYR cc_start: 0.9060 (t80) cc_final: 0.8851 (t80)
REVERT: B  693 TRP cc_start: 0.9754 (t60) cc_final: 0.9515 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1983
  time to fit residues: 51.9597
Evaluate side-chains
  133 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 141 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
B 517 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.075468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.048534 restraints weight = 67478.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.050130 restraints weight = 51811.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.051310 restraints weight = 42279.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12527  Z= 0.113
  Angle     :  0.571   8.183  16975  Z= 0.284
  Chirality :  0.040   0.145   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.820  20.724   1659
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  0.60 (0.22), residues: 1529
  helix:  0.65 (0.17), residues: 983
  sheet:  0.66 (0.61), residues: 79
  loop :  0.07 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 364 
 HIS   0.015   0.001   HIS B 765 
 PHE   0.026   0.001   PHE B 760 
 TYR   0.019   0.001   TYR A 120 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (  641)
  hydrogen bonds       : angle       4.24187 ( 1887)
  covalent geometry    : bond        0.00240 (12527)
  covalent geometry    : angle       0.57067 (16975)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6533 (tmm) cc_final: 0.5932 (tmm)
REVERT: A  272 MET cc_start: 0.8921 (ttt) cc_final: 0.8565 (ttt)
REVERT: A  364 TRP cc_start: 0.7429 (m100) cc_final: 0.6067 (m100)
REVERT: A  467 MET cc_start: 0.7790 (ptp) cc_final: 0.7305 (ptt)
REVERT: A  512 MET cc_start: 0.9570 (tpp) cc_final: 0.9278 (tpp)
REVERT: A  515 PHE cc_start: 0.9557 (m-80) cc_final: 0.9298 (m-80)
REVERT: A  516 MET cc_start: 0.9499 (tpp) cc_final: 0.9187 (tpp)
REVERT: A  670 ILE cc_start: 0.9844 (tp) cc_final: 0.9549 (pt)
REVERT: A  766 MET cc_start: 0.9318 (mtm) cc_final: 0.8875 (mtp)
REVERT: B  370 TRP cc_start: 0.9358 (m-90) cc_final: 0.9079 (m100)
REVERT: B  476 PHE cc_start: 0.9164 (p90) cc_final: 0.8811 (p90)
REVERT: B  512 MET cc_start: 0.9124 (ptp) cc_final: 0.8793 (ptm)
REVERT: B  632 TYR cc_start: 0.9084 (t80) cc_final: 0.8871 (t80)
REVERT: B  693 TRP cc_start: 0.9752 (t60) cc_final: 0.9513 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2004
  time to fit residues: 52.3909
Evaluate side-chains
  134 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 128 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 153 optimal weight:    0.0030
   chunk 80 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 102 optimal weight:    9.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.077184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.050099 restraints weight = 65682.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.051693 restraints weight = 50095.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.052906 restraints weight = 40813.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12527  Z= 0.098
  Angle     :  0.574   7.799  16975  Z= 0.277
  Chirality :  0.040   0.142   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.788  21.243   1659
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  0.62 (0.22), residues: 1529
  helix:  0.65 (0.17), residues: 980
  sheet:  0.68 (0.61), residues: 79
  loop :  0.13 (0.31), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 
 PHE   0.021   0.001   PHE B 760 
 TYR   0.018   0.001   TYR A 120 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  641)
  hydrogen bonds       : angle       4.15053 ( 1887)
  covalent geometry    : bond        0.00206 (12527)
  covalent geometry    : angle       0.57366 (16975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4095.07 seconds
wall clock time: 72 minutes 49.59 seconds (4369.59 seconds total)