Starting phenix.real_space_refine
on Fri Dec  8 10:42:32 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9e_9013/12_2023/6e9e_9013.pdb"
  }
  resolution = 3.4
  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=  -0.005 sd=   0.030
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: 6
    Type Number    sf(0)   Gaussians
     P      51      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    4985      2.51       5
     N    1401      2.21       5
     O    1695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  572": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  849": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8163
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1088
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1088
          Classifications: {'RNA': 51}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 19}
          Link IDs: {'rna2p': 12, 'rna3p': 38}
    Chain: "A"
      Number of atoms: 7074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 863, 7074
          Classifications: {'peptide': 863}
          Link IDs: {'PTRANS': 13, 'TRANS': 849}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.02, per 1000 atoms: 0.61
  Number of scatterers: 8163
  At special positions: 0
  Unit cell: (102.7, 85.32, 101.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P      51     15.00
     Mg      1     11.99
     O    1695      8.00
     N    1401      7.00
     C    4985      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  - 3.50
        Amino acid           : False - 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: 3.57
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      63.3% alpha, 2.3% beta
      2 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 2.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 3.782A  pdb=" N   LEU A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 204
      removed outlier: 3.652A  pdb=" N   GLN A 179 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 183 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASP A 186 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU A 188 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   THR A 196 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 231 through 234
      removed outlier: 3.565A  pdb=" N   GLU A 234 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 234'
    Processing helix  chain 'A' and resid 237 through 252
    Processing helix  chain 'A' and resid 253 through 258
      removed outlier: 4.024A  pdb=" N   LEU A 256 " --> pdb=" O   ASN A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 280 through 299
      removed outlier: 3.542A  pdb=" N   LEU A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 286 " --> pdb=" O   LYS A 282 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   HIS A 296 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 4.016A  pdb=" N   PHE A 308 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 336
      removed outlier: 3.968A  pdb=" N   VAL A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 324 " --> pdb=" O   PHE A 320 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      Proline residue:  A 331  - end of helix
      removed outlier: 3.503A  pdb=" N   GLU A 334 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 352
      removed outlier: 3.707A  pdb=" N   ILE A 347 " --> pdb=" O   ASN A 343 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A 352 " --> pdb=" O   GLN A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
    Processing helix  chain 'A' and resid 373 through 377
      removed outlier: 3.849A  pdb=" N   ASN A 377 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.796A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 422
      removed outlier: 3.785A  pdb=" N   MET A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASN A 421 " --> pdb=" O   THR A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 436
      removed outlier: 3.898A  pdb=" N   SER A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 458
      removed outlier: 3.503A  pdb=" N   LYS A 443 " --> pdb=" O   LYS A 439 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 445 " --> pdb=" O   ASP A 441 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASP A 452 " --> pdb=" O   CYS A 448 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   TYR A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 471 through 479
      removed outlier: 3.613A  pdb=" N   LYS A 475 " --> pdb=" O   GLY A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.827A  pdb=" N   LYS A 491 " --> pdb=" O   LYS A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 512
      removed outlier: 3.544A  pdb=" N   TYR A 508 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 543
      removed outlier: 3.742A  pdb=" N   ILE A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR A 525 " --> pdb=" O   ASP A 521 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE A 536 " --> pdb=" O   ASN A 532 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 537 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A 539 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 557
      removed outlier: 3.751A  pdb=" N   PHE A 556 " --> pdb=" O   TYR A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 3.925A  pdb=" N   ALA A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE A 572 " --> pdb=" O   GLU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 593
      removed outlier: 3.846A  pdb=" N   TYR A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 591 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 613
      removed outlier: 3.616A  pdb=" N   GLU A 606 " --> pdb=" O   GLU A 602 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS A 607 " --> pdb=" O   GLU A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 642 through 650
      removed outlier: 3.954A  pdb=" N   ARG A 648 " --> pdb=" O   LYS A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 659
      removed outlier: 3.523A  pdb=" N   ILE A 655 " --> pdb=" O   ASN A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 670
    Processing helix  chain 'A' and resid 673 through 685
      removed outlier: 3.623A  pdb=" N   ARG A 679 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 683 " --> pdb=" O   ARG A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 707
    Processing helix  chain 'A' and resid 709 through 714
      removed outlier: 3.715A  pdb=" N   SER A 714 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 779
      removed outlier: 3.624A  pdb=" N   GLU A 732 " --> pdb=" O   THR A 728 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS A 736 " --> pdb=" O   GLU A 732 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE A 740 " --> pdb=" O   LYS A 736 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 741 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   MET A 748 " --> pdb=" O   TYR A 744 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 752 " --> pdb=" O   MET A 748 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 761 " --> pdb=" O   ASN A 757 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TYR A 762 " --> pdb=" O   VAL A 758 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 763 " --> pdb=" O   ASN A 759 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE A 764 " --> pdb=" O   ALA A 760 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 765 " --> pdb=" O   ARG A 761 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 775 " --> pdb=" O   ARG A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 799
      removed outlier: 3.584A  pdb=" N   MET A 795 " --> pdb=" O   THR A 791 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA A 796 " --> pdb=" O   ASN A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 818
      removed outlier: 4.077A  pdb=" N   ALA A 816 " --> pdb=" O   ASP A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 838
    Processing helix  chain 'A' and resid 841 through 853
      removed outlier: 3.718A  pdb=" N   VAL A 845 " --> pdb=" O   GLU A 841 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN A 850 " --> pdb=" O   ASN A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 860
      removed outlier: 3.542A  pdb=" N   ASN A 860 " --> pdb=" O   ASN A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 888
      removed outlier: 3.977A  pdb=" N   GLN A 883 " --> pdb=" O   HIS A 879 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A 886 " --> pdb=" O   ILE A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 909
      removed outlier: 3.625A  pdb=" N   HIS A 909 " --> pdb=" O   LYS A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 921
      removed outlier: 3.858A  pdb=" N   LYS A 918 " --> pdb=" O   LYS A 914 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ALA A 919 " --> pdb=" O   ASP A 915 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 936
      removed outlier: 3.627A  pdb=" N   TYR A 931 " --> pdb=" O   ASN A 927 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82
    Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94
      removed outlier: 3.504A  pdb=" N   GLU A 100 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110
    Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266

    301 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      4 hydrogen bonds
      6 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2434
        1.34 -     1.46: 1608
        1.46 -     1.57: 4221
        1.57 -     1.69: 101
        1.69 -     1.81: 47
  Bond restraints: 8411
  Sorted by residual:
  bond pdb=" C   THR A 922 "
       pdb=" N   PRO A 923 "
    ideal  model  delta    sigma   weight residual
    1.335  1.386 -0.051 1.19e-02 7.06e+03 1.84e+01
  bond pdb=" N   VAL A 193 "
       pdb=" CA  VAL A 193 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.22e-02 6.72e+03 7.18e+00
  bond pdb=" CA  SER A 437 "
       pdb=" CB  SER A 437 "
    ideal  model  delta    sigma   weight residual
    1.534  1.491  0.043 1.72e-02 3.38e+03 6.29e+00
  bond pdb=" N   LYS A 439 "
       pdb=" CA  LYS A 439 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.29e-02 6.01e+03 5.94e+00
  bond pdb=" N   ILE A 190 "
       pdb=" CA  ILE A 190 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 1.19e-02 7.06e+03 5.60e+00
  ... (remaining 8406 not shown)

  Histogram of bond angle deviations from ideal:
       99.10 -   106.07: 345
      106.07 -   113.04: 4472
      113.04 -   120.01: 3080
      120.01 -   126.97: 3507
      126.97 -   133.94: 160
  Bond angle restraints: 11564
  Sorted by residual:
  angle pdb=" C   VAL A 193 "
        pdb=" N   TYR A 194 "
        pdb=" CA  TYR A 194 "
      ideal   model   delta    sigma   weight residual
     120.72  128.79   -8.07 1.67e+00 3.59e-01 2.33e+01
  angle pdb=" N   LEU A 350 "
        pdb=" CA  LEU A 350 "
        pdb=" C   LEU A 350 "
      ideal   model   delta    sigma   weight residual
     112.45  107.48    4.97 1.39e+00 5.18e-01 1.28e+01
  angle pdb=" C   CYS A 661 "
        pdb=" N   LYS A 662 "
        pdb=" CA  LYS A 662 "
      ideal   model   delta    sigma   weight residual
     120.58  124.80   -4.22 1.32e+00 5.74e-01 1.02e+01
  angle pdb=" CA  ILE A 190 "
        pdb=" C   ILE A 190 "
        pdb=" O   ILE A 190 "
      ideal   model   delta    sigma   weight residual
     120.95  117.75    3.20 1.04e+00 9.25e-01 9.44e+00
  angle pdb=" N   LYS A 189 "
        pdb=" CA  LYS A 189 "
        pdb=" C   LYS A 189 "
      ideal   model   delta    sigma   weight residual
     111.03  107.71    3.32 1.11e+00 8.12e-01 8.93e+00
  ... (remaining 11559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.81: 4868
       20.81 -    41.61: 156
       41.61 -    62.42: 49
       62.42 -    83.22: 36
       83.22 -   104.03: 2
  Dihedral angle restraints: 5111
    sinusoidal: 2546
      harmonic: 2565
  Sorted by residual:
  dihedral pdb=" CA  ASN A 651 "
           pdb=" C   ASN A 651 "
           pdb=" N   PRO A 652 "
           pdb=" CA  PRO A 652 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.72  -28.28     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" O4'   A B  13 "
           pdb=" C1'   A B  13 "
           pdb=" N9    A B  13 "
           pdb=" C4    A B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  122.69  -54.69     1      1.70e+01 3.46e-03 1.40e+01
  dihedral pdb=" CA  GLN A  92 "
           pdb=" C   GLN A  92 "
           pdb=" N   LYS A  93 "
           pdb=" CA  LYS A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.86   18.14     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 966
       0.043 -    0.086: 285
       0.086 -    0.130: 57
       0.130 -    0.173: 6
       0.173 -    0.216: 3
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  LYS A 189 "
            pdb=" N   LYS A 189 "
            pdb=" C   LYS A 189 "
            pdb=" CB  LYS A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  LEU A 191 "
            pdb=" N   LEU A 191 "
            pdb=" C   LEU A 191 "
            pdb=" CB  LEU A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" CB  ILE A 190 "
            pdb=" CA  ILE A 190 "
            pdb=" CG1 ILE A 190 "
            pdb=" CG2 ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.43e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 348 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.14e+00
        pdb=" C   GLN A 348 "    0.052 2.00e-02 2.50e+03
        pdb=" O   GLN A 348 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ILE A 349 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 135 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A 136 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 136 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 136 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 916 "    0.015 2.00e-02 2.50e+03   1.36e-02 3.25e+00
        pdb=" CG  PHE A 916 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 916 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 916 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 916 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 916 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 916 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 99
        2.61 -     3.18: 7326
        3.18 -     3.75: 11538
        3.75 -     4.33: 17581
        4.33 -     4.90: 28017
  Nonbonded interactions: 64561
  Sorted by model distance:
  nonbonded pdb=" OP1   U B  41 "
            pdb=" OG  SER A 575 "
     model   vdw
     2.037 2.440
  nonbonded pdb=" OE2 GLU A 361 "
            pdb=" NZ  LYS A 488 "
     model   vdw
     2.198 2.520
  nonbonded pdb=" O   VAL A 724 "
            pdb=" NH2 ARG A 735 "
     model   vdw
     2.214 2.520
  nonbonded pdb=" OP1   A B  37 "
            pdb=" NZ  LYS A 753 "
     model   vdw
     2.226 2.520
  nonbonded pdb=" O4    U B  43 "
            pdb=" NZ  LYS A 475 "
     model   vdw
     2.227 2.520
  ... (remaining 64556 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             0.860
  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:             0.000
  Extract box with map and model:          3.780
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     27.100
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
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      :  0.006   0.062   8411  Z= 0.376
  Angle     :  0.733   8.068  11564  Z= 0.426
  Chirality :  0.042   0.216   1317
  Planarity :  0.003   0.046   1290
  Dihedral  : 13.266 104.026   3451
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.32 %
    Favored  : 97.43 %
  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: -4.95 (0.22), residues: 851
  helix: -3.69 (0.15), residues: 511
  sheet: -3.80 (0.86), residues: 23
  loop : -2.12 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.003   TRP A 455 
   HIS   0.005   0.002   HIS A  99 
   PHE   0.031   0.002   PHE A 916 
   TYR   0.022   0.002   TYR A 912 
   ARG   0.008   0.001   ARG A 666 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 0.814 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 150
  average time/residue: 0.3325
  time to fit residues: 61.1791
Evaluate side-chains
  52 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.844 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0815
  time to fit residues: 1.3239
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 611 ASN
A 792 ASN
A 864 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8411  Z= 0.189
  Angle     :  0.567   7.003  11564  Z= 0.300
  Chirality :  0.040   0.152   1317
  Planarity :  0.003   0.032   1290
  Dihedral  : 14.893 103.206   1670
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.82 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.83 (0.26), residues: 851
  helix: -1.80 (0.19), residues: 529
  sheet: -3.60 (0.84), residues: 14
  loop : -1.61 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP A 829 
   HIS   0.003   0.001   HIS A 879 
   PHE   0.016   0.001   PHE A 916 
   TYR   0.014   0.001   TYR A 880 
   ARG   0.006   0.001   ARG A 138 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.881 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 68
  average time/residue: 0.2377
  time to fit residues: 22.0742
Evaluate side-chains
  39 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.900 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0769
  time to fit residues: 1.3276
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.2980
   chunk 68 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 82 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8411  Z= 0.130
  Angle     :  0.475   7.235  11564  Z= 0.249
  Chirality :  0.037   0.154   1317
  Planarity :  0.002   0.025   1290
  Dihedral  : 14.795 106.559   1670
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  8.24 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.27), residues: 851
  helix: -0.62 (0.22), residues: 524
  sheet: -2.19 (0.88), residues: 24
  loop : -1.32 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.002   TRP A 829 
   HIS   0.003   0.001   HIS A 879 
   PHE   0.009   0.001   PHE A 916 
   TYR   0.010   0.001   TYR A 880 
   ARG   0.005   0.000   ARG A 138 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.857 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 0.3050
  time to fit residues: 26.6155
Evaluate side-chains
  38 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.949 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0750
  time to fit residues: 1.2657
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0970
   chunk 87 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 720 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8411  Z= 0.129
  Angle     :  0.452   7.067  11564  Z= 0.236
  Chirality :  0.036   0.160   1317
  Planarity :  0.002   0.023   1290
  Dihedral  : 14.730 106.957   1670
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.62 %
    Favored  : 90.73 %
  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: -0.86 (0.28), residues: 851
  helix: -0.06 (0.22), residues: 526
  sheet: -2.00 (0.83), residues: 31
  loop : -1.16 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 829 
   HIS   0.003   0.001   HIS A 879 
   PHE   0.008   0.001   PHE A 916 
   TYR   0.010   0.001   TYR A 880 
   ARG   0.003   0.000   ARG A 547 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.861 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 48
  average time/residue: 0.2234
  time to fit residues: 15.3051
Evaluate side-chains
  38 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.935 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0725
  time to fit residues: 1.2381
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 1 optimal weight:   10.0000
   chunk 65 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   chunk 60 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.4158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8411  Z= 0.104
  Angle     :  0.418   7.134  11564  Z= 0.216
  Chirality :  0.035   0.151   1317
  Planarity :  0.002   0.020   1290
  Dihedral  : 14.682 107.406   1670
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  9.14 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.25 (0.29), residues: 851
  helix:  0.44 (0.23), residues: 527
  sheet: -1.80 (0.87), residues: 31
  loop : -0.95 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 829 
   HIS   0.003   0.001   HIS A 767 
   PHE   0.014   0.001   PHE A 578 
   TYR   0.007   0.001   TYR A 880 
   ARG   0.003   0.000   ARG A 930 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.951 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 51
  average time/residue: 0.2212
  time to fit residues: 16.1458
Evaluate side-chains
  41 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.820 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0733
  time to fit residues: 1.2355
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 636 ASN
A 860 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8411  Z= 0.154
  Angle     :  0.450   7.291  11564  Z= 0.234
  Chirality :  0.036   0.154   1317
  Planarity :  0.002   0.020   1290
  Dihedral  : 14.659 108.380   1670
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  9.78 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.29), residues: 851
  helix:  0.64 (0.23), residues: 527
  sheet: -1.75 (0.89), residues: 31
  loop : -0.91 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 829 
   HIS   0.003   0.001   HIS A 879 
   PHE   0.013   0.001   PHE A 916 
   TYR   0.010   0.001   TYR A 920 
   ARG   0.003   0.000   ARG A 930 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.940 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 44
  average time/residue: 0.2578
  time to fit residues: 16.1114
Evaluate side-chains
  38 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0822
  time to fit residues: 1.5363
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8411  Z= 0.142
  Angle     :  0.437   7.255  11564  Z= 0.225
  Chirality :  0.036   0.157   1317
  Planarity :  0.002   0.021   1290
  Dihedral  : 14.640 111.251   1670
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.04 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.29), residues: 851
  helix:  0.86 (0.23), residues: 526
  sheet: -1.63 (0.87), residues: 34
  loop : -0.86 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 829 
   HIS   0.004   0.001   HIS A 879 
   PHE   0.011   0.001   PHE A 916 
   TYR   0.009   0.001   TYR A 920 
   ARG   0.003   0.000   ARG A 584 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.898 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 38
  average time/residue: 0.2329
  time to fit residues: 12.8761
Evaluate side-chains
  32 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.899 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2034
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 68 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8411  Z= 0.144
  Angle     :  0.444   7.774  11564  Z= 0.230
  Chirality :  0.036   0.151   1317
  Planarity :  0.002   0.020   1290
  Dihedral  : 14.631 111.691   1670
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 10.68 %
    Favored  : 89.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.33 (0.29), residues: 851
  helix:  0.99 (0.23), residues: 525
  sheet: -1.38 (0.83), residues: 39
  loop : -0.88 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 829 
   HIS   0.004   0.001   HIS A 767 
   PHE   0.012   0.001   PHE A 924 
   TYR   0.008   0.001   TYR A 920 
   ARG   0.003   0.000   ARG A 584 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.954 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 38
  average time/residue: 0.2536
  time to fit residues: 13.7756
Evaluate side-chains
  37 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.944 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1104
  time to fit residues: 1.3932
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0970
   chunk 35 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8411  Z= 0.165
  Angle     :  0.464   7.874  11564  Z= 0.238
  Chirality :  0.036   0.155   1317
  Planarity :  0.002   0.028   1290
  Dihedral  : 14.633 113.039   1670
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 11.07 %
    Favored  : 88.80 %
  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:  0.48 (0.29), residues: 851
  helix:  1.11 (0.24), residues: 518
  sheet: -1.31 (0.84), residues: 39
  loop : -0.79 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 829 
   HIS   0.004   0.001   HIS A 879 
   PHE   0.014   0.001   PHE A 924 
   TYR   0.011   0.001   TYR A 920 
   ARG   0.003   0.000   ARG A 338 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.878 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 36
  average time/residue: 0.2519
  time to fit residues: 12.8096
Evaluate side-chains
  30 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.882 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2578
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0060
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0970
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8411  Z= 0.119
  Angle     :  0.439   8.784  11564  Z= 0.223
  Chirality :  0.035   0.151   1317
  Planarity :  0.002   0.022   1290
  Dihedral  : 14.594 113.691   1670
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 11.33 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.30), residues: 851
  helix:  1.24 (0.24), residues: 518
  sheet: -1.38 (0.90), residues: 34
  loop : -0.77 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 829 
   HIS   0.003   0.001   HIS A 767 
   PHE   0.012   0.001   PHE A 924 
   TYR   0.007   0.001   TYR A 920 
   ARG   0.003   0.000   ARG A 930 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.904 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2432
  time to fit residues: 14.9069
Evaluate side-chains
  34 residues out of total 777 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1803
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.084621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.067753 restraints weight = 17401.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 2.09
r_work: 0.2647 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8411  Z= 0.269
  Angle     :  0.537   9.200  11564  Z= 0.276
  Chirality :  0.040   0.168   1317
  Planarity :  0.003   0.023   1290
  Dihedral  : 14.708 114.568   1670
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 11.45 %
    Favored  : 88.42 %
  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:  0.34 (0.29), residues: 851
  helix:  0.96 (0.23), residues: 520
  sheet: -1.72 (0.78), residues: 48
  loop : -0.68 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 829 
   HIS   0.004   0.001   HIS A 124 
   PHE   0.024   0.002   PHE A 916 
   TYR   0.016   0.001   TYR A 920 
   ARG   0.008   0.001   ARG A 897 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1644.14 seconds
wall clock time: 30 minutes 57.31 seconds (1857.31 seconds total)