Starting phenix.real_space_refine
on Tue May 20 19:03:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dxm_47291/05_2025/9dxm_47291_trim.cif"
  }
  resolution = 3.2
  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=   0.002 sd=   0.015
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: 7
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    6512      2.51       5
     N    1646      2.21       5
     O    1842      1.98       5
     H   10147      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 20203
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 17368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1053, 17368
          Classifications: {'peptide': 1053}
          Link IDs: {'PTRANS': 40, 'TRANS': 1012}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 2802
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 6, 'TRANS': 164}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.62, per 1000 atoms: 0.43
  Number of scatterers: 20203
  At special positions: 0
  Unit cell: (85.078, 99.946, 130.508, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      52     16.00
     P       3     15.00
     Mg      1     11.99
     O    1842      8.00
     N    1646      7.00
     C    6512      6.00
     H   10147      1.00
    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: 4.88
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2362

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 1 sheets defined
      78.8% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
      removed outlier: 3.899A  pdb=" N   ILE A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 39
    Processing helix  chain 'A' and resid 41 through 53
    Processing helix  chain 'A' and resid 56 through 74
    Processing helix  chain 'A' and resid 79 through 96
    Processing helix  chain 'A' and resid 102 through 121
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.749A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 141 through 153
      removed outlier: 3.580A  pdb=" N   ASN A 151 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ASN A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 173
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.558A  pdb=" N   LYS A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 3.546A  pdb=" N   ILE A 202 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.173A  pdb=" N   THR A 211 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 212 " --> pdb=" O   ASP A 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 212'
    Processing helix  chain 'A' and resid 220 through 235
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 236 through 248
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.805A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 3.562A  pdb=" N   SER A 267 " --> pdb=" O   ASP A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 297 through 311
      removed outlier: 3.642A  pdb=" N   TYR A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASN A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 334 through 347
      removed outlier: 3.647A  pdb=" N   CYS A 347 " --> pdb=" O   ASP A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 355
      Proline residue:  A 353  - end of helix
    Processing helix  chain 'A' and resid 360 through 374
    Processing helix  chain 'A' and resid 377 through 393
      removed outlier: 3.801A  pdb=" N   THR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ASP A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 3.605A  pdb=" N   GLN A 411 " --> pdb=" O   PRO A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 428 through 436
      removed outlier: 4.398A  pdb=" N   ILE A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 464
    Processing helix  chain 'A' and resid 464 through 480
    Processing helix  chain 'A' and resid 482 through 490
    Processing helix  chain 'A' and resid 498 through 525
      removed outlier: 3.689A  pdb=" N   LYS A 522 " --> pdb=" O   CYS A 518 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
    Processing helix  chain 'A' and resid 556 through 571
      removed outlier: 3.644A  pdb=" N   LYS A 562 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 569 " --> pdb=" O   GLN A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 591
      removed outlier: 3.704A  pdb=" N   PHE A 580 " --> pdb=" O   ASP A 576 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   THR A 581 " --> pdb=" O   ASN A 577 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LYS A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 627
    Processing helix  chain 'A' and resid 627 through 633
      removed outlier: 3.539A  pdb=" N   LEU A 631 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 646
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 668
      removed outlier: 4.098A  pdb=" N   SER A 656 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 686
      removed outlier: 3.765A  pdb=" N   ARG A 676 " --> pdb=" O   MET A 672 " (cutoff:3.500A)
      Proline residue:  A 683  - end of helix
    Processing helix  chain 'A' and resid 687 through 689
      No H-bonds generated for 'chain 'A' and resid 687 through 689'
    Processing helix  chain 'A' and resid 690 through 697
    Processing helix  chain 'A' and resid 699 through 708
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'A' and resid 726 through 730
    Processing helix  chain 'A' and resid 733 through 751
      removed outlier: 3.607A  pdb=" N   SER A 749 " --> pdb=" O   LYS A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 764
    Processing helix  chain 'A' and resid 769 through 785
      Proline residue:  A 782  - end of helix
    Processing helix  chain 'A' and resid 787 through 802
      removed outlier: 4.176A  pdb=" N   HIS A 802 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 810
      removed outlier: 3.575A  pdb=" N   GLY A 809 " --> pdb=" O   ASN A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 813
      No H-bonds generated for 'chain 'A' and resid 811 through 813'
    Processing helix  chain 'A' and resid 814 through 822
    Processing helix  chain 'A' and resid 849 through 877
      removed outlier: 3.583A  pdb=" N   SER A 877 " --> pdb=" O   SER A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 887 through 897
      removed outlier: 3.567A  pdb=" N   ILE A 896 " --> pdb=" O   LEU A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 922
    Processing helix  chain 'A' and resid 922 through 929
    Processing helix  chain 'A' and resid 934 through 960
      Proline residue:  A 940  - end of helix
      Proline residue:  A 944  - end of helix
      removed outlier: 3.864A  pdb=" N   SER A 960 " --> pdb=" O   GLN A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 1003
    Processing helix  chain 'A' and resid 1017 through 1030
      removed outlier: 3.615A  pdb=" N   LYS A1025 " --> pdb=" O   MET A1021 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A1026 " --> pdb=" O   GLU A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1047
      Proline residue:  A1036  - end of helix
    Processing helix  chain 'A' and resid 1049 through 1068
      removed outlier: 5.504A  pdb=" N   THR A1065 " --> pdb=" O   LYS A1061 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   SER A1066 " --> pdb=" O   CYS A1062 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A1068 " --> pdb=" O   LEU A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1086
    Processing helix  chain 'A' and resid 1102 through 1115
    Processing helix  chain 'B' and resid 24 through 34
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 96 through 102
      removed outlier: 3.877A  pdb=" N   TYR B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 112
    Processing helix  chain 'B' and resid 139 through 145
    Processing helix  chain 'B' and resid 155 through 159
      removed outlier: 4.411A  pdb=" N   ASN B 158 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 172
    Processing sheet with id=AA1, first strand: chain 'B' and resid 147 through 150
      removed outlier: 3.807A  pdb=" N   GLN B 147 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ALA B  88 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   CYS B 122 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE B  90 " --> pdb=" O   CYS B 122 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ASN B 124 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   PHE B  92 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   CYS B  87 " --> pdb=" O   THR B  12 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LYS B  14 " --> pdb=" O   CYS B  87 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ILE B  89 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   MET B  91 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B  18 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 8.813A  pdb=" N   ASP B  93 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   PHE B  13 " --> pdb=" O   ASP B  64 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   TRP B  66 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   LEU B  15 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU B  17 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   TYR B  55 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)

    628 hydrogen bonds defined for protein.
    1845 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: 6.82

  Time building geometry restraints manager: 5.91 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10122
        1.03 -     1.23: 32
        1.23 -     1.42: 4258
        1.42 -     1.62: 5935
        1.62 -     1.81: 79
  Bond restraints: 20426
  Sorted by residual:
  bond pdb=" CA  SER A 876 "
       pdb=" CB  SER A 876 "
    ideal  model  delta    sigma   weight residual
    1.529  1.470  0.059 1.64e-02 3.72e+03 1.30e+01
  bond pdb=" N   LYS B 144 "
       pdb=" CA  LYS B 144 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.32e-02 5.74e+03 8.03e+00
  bond pdb=" C   LYS B 144 "
       pdb=" O   LYS B 144 "
    ideal  model  delta    sigma   weight residual
    1.235  1.271 -0.036 1.33e-02 5.65e+03 7.27e+00
  bond pdb=" N   SER A 668 "
       pdb=" CA  SER A 668 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.22e-02 6.72e+03 7.00e+00
  bond pdb=" N   GLY A   5 "
       pdb=" CA  GLY A   5 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.27e+00
  ... (remaining 20421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 35958
        1.40 -     2.80: 959
        2.80 -     4.20: 65
        4.20 -     5.60: 27
        5.60 -     7.00: 2
  Bond angle restraints: 37011
  Sorted by residual:
  angle pdb=" CA  THR B  44 "
        pdb=" CB  THR B  44 "
        pdb=" OG1 THR B  44 "
      ideal   model   delta    sigma   weight residual
     109.60  104.65    4.95 1.50e+00 4.44e-01 1.09e+01
  angle pdb=" CA  THR B  44 "
        pdb=" C   THR B  44 "
        pdb=" O   THR B  44 "
      ideal   model   delta    sigma   weight residual
     120.81  117.32    3.49 1.15e+00 7.56e-01 9.23e+00
  angle pdb=" CA  LYS B 143 "
        pdb=" C   LYS B 143 "
        pdb=" O   LYS B 143 "
      ideal   model   delta    sigma   weight residual
     120.24  116.98    3.26 1.11e+00 8.12e-01 8.62e+00
  angle pdb=" CA  ASN A 230 "
        pdb=" C   ASN A 230 "
        pdb=" O   ASN A 230 "
      ideal   model   delta    sigma   weight residual
     119.97  116.74    3.23 1.15e+00 7.56e-01 7.88e+00
  angle pdb=" N   ARG B 142 "
        pdb=" CA  ARG B 142 "
        pdb=" C   ARG B 142 "
      ideal   model   delta    sigma   weight residual
     111.28  108.24    3.04 1.09e+00 8.42e-01 7.77e+00
  ... (remaining 37006 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.79: 9317
       33.79 -    67.58: 203
       67.58 -   101.37: 23
      101.37 -   135.16: 0
      135.16 -   168.95: 2
  Dihedral angle restraints: 9545
    sinusoidal: 5191
      harmonic: 4354
  Sorted by residual:
  dihedral pdb=" O3B GTP B 201 "
           pdb=" O3A GTP B 201 "
           pdb=" PB  GTP B 201 "
           pdb=" PA  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  122.13  168.95     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C8  GTP B 201 "
           pdb=" C1' GTP B 201 "
           pdb=" N9  GTP B 201 "
           pdb=" O4' GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -32.73  137.33     1      2.00e+01 2.50e-03 4.16e+01
  dihedral pdb=" O5' GTP B 201 "
           pdb=" O3A GTP B 201 "
           pdb=" PA  GTP B 201 "
           pdb=" PB  GTP B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88 -177.83   91.96     1      2.00e+01 2.50e-03 2.48e+01
  ... (remaining 9542 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1070
       0.035 -    0.069: 380
       0.069 -    0.104: 93
       0.104 -    0.138: 37
       0.138 -    0.173: 2
  Chirality restraints: 1582
  Sorted by residual:
  chirality pdb=" CA  ILE A 898 "
            pdb=" N   ILE A 898 "
            pdb=" C   ILE A 898 "
            pdb=" CB  ILE A 898 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  PRO A 647 "
            pdb=" N   PRO A 647 "
            pdb=" C   PRO A 647 "
            pdb=" CB  PRO A 647 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ILE B  89 "
            pdb=" N   ILE B  89 "
            pdb=" C   ILE B  89 "
            pdb=" CB  ILE B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 1579 not shown)

  Planarity restraints: 2904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 230 "    0.129 2.00e-02 2.50e+03   1.39e-01 2.90e+02
        pdb=" CG  ASN A 230 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 230 "   -0.126 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 230 "    0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN A 230 "   -0.203 2.00e-02 2.50e+03
        pdb="HD22 ASN A 230 "    0.205 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 142 "   -0.193 9.50e-02 1.11e+02   1.02e-01 1.44e+02
        pdb=" NE  ARG B 142 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 142 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 142 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 142 "    0.021 2.00e-02 2.50e+03
        pdb="HH11 ARG B 142 "    0.157 2.00e-02 2.50e+03
        pdb="HH12 ARG B 142 "   -0.154 2.00e-02 2.50e+03
        pdb="HH21 ARG B 142 "    0.059 2.00e-02 2.50e+03
        pdb="HH22 ARG B 142 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 898 "   -0.017 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" N   PHE A 899 "    0.055 2.00e-02 2.50e+03
        pdb=" CA  PHE A 899 "   -0.015 2.00e-02 2.50e+03
        pdb=" H   PHE A 899 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 2901 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 593
        2.14 -     2.75: 38934
        2.75 -     3.37: 60041
        3.37 -     3.98: 74832
        3.98 -     4.60: 120116
  Nonbonded interactions: 294516
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 596 "
            pdb=" H   GLU A 596 "
     model   vdw
     1.524 2.450
  nonbonded pdb=" OE1 GLU A 218 "
            pdb=" H   GLU A 218 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" HG1 THR B  56 "
            pdb=" O   GLU B 177 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" O   VAL A 818 "
            pdb=" HG  SER A 821 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" O   LEU A 697 "
            pdb="HE21 GLN A 797 "
     model   vdw
     1.616 2.450
  ... (remaining 294511 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
========== 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:             5.740
  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:          0.720
  Check model and map are aligned:         0.060
  Set scattering table:                    0.160
  Process input model:                     39.370
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
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   0.059  10279  Z= 0.271
  Angle     :  0.596   7.003  13930  Z= 0.336
  Chirality :  0.039   0.173   1582
  Planarity :  0.004   0.052   1733
  Dihedral  : 11.968 168.951   3828
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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:  1.29 (0.24), residues: 1210
  helix:  1.15 (0.18), residues: 857
  sheet:  0.19 (0.69), residues: 50
  loop :  0.43 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 807 
 HIS   0.004   0.001   HIS A 496 
 PHE   0.018   0.002   PHE A 570 
 TYR   0.016   0.002   TYR A 508 
 ARG   0.003   0.001   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13247 (  628)
  hydrogen bonds       : angle       5.91809 ( 1845)
  covalent geometry    : bond        0.00569 (10279)
  covalent geometry    : angle       0.59586 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  847 MET cc_start: 0.7455 (ptt) cc_final: 0.7152 (ptm)
REVERT: B  105 ASN cc_start: 0.8789 (t0) cc_final: 0.7831 (t0)
REVERT: B  109 ASP cc_start: 0.8680 (m-30) cc_final: 0.8175 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.6178
  time to fit residues: 47.0429
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    9.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.068499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048515 restraints weight = 89936.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.11
r_work: 0.2786 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10279  Z= 0.163
  Angle     :  0.537   6.245  13930  Z= 0.288
  Chirality :  0.038   0.128   1582
  Planarity :  0.004   0.048   1733
  Dihedral  :  8.343 175.635   1333
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.42 %
    Favored  : 95.40 %
  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:  1.58 (0.25), residues: 1210
  helix:  1.46 (0.18), residues: 874
  sheet: -0.03 (0.70), residues: 50
  loop :  0.18 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 807 
 HIS   0.004   0.001   HIS B  32 
 PHE   0.013   0.001   PHE A 412 
 TYR   0.014   0.001   TYR A1105 
 ARG   0.003   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04662 (  628)
  hydrogen bonds       : angle       4.80285 ( 1845)
  covalent geometry    : bond        0.00356 (10279)
  covalent geometry    : angle       0.53710 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 1.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  847 MET cc_start: 0.7540 (ptt) cc_final: 0.7250 (ptm)
REVERT: B  105 ASN cc_start: 0.8713 (t0) cc_final: 0.7852 (t0)
REVERT: B  109 ASP cc_start: 0.8661 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 46
  average time/residue: 0.4856
  time to fit residues: 34.4044
Evaluate side-chains
  43 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   overall best weight:    1.6388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.068310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.048371 restraints weight = 90489.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.11
r_work: 0.2784 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10279  Z= 0.168
  Angle     :  0.504   6.024  13930  Z= 0.267
  Chirality :  0.037   0.129   1582
  Planarity :  0.003   0.048   1733
  Dihedral  :  8.092 176.105   1333
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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:  1.84 (0.25), residues: 1210
  helix:  1.71 (0.18), residues: 875
  sheet: -0.24 (0.71), residues: 50
  loop :  0.12 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 807 
 HIS   0.009   0.001   HIS B  32 
 PHE   0.012   0.001   PHE A 412 
 TYR   0.014   0.001   TYR A 863 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (  628)
  hydrogen bonds       : angle       4.50160 ( 1845)
  covalent geometry    : bond        0.00374 (10279)
  covalent geometry    : angle       0.50374 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8695 (t0) cc_final: 0.7860 (t0)
REVERT: B  109 ASP cc_start: 0.8665 (m-30) cc_final: 0.8163 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.4997
  time to fit residues: 31.8478
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.3744

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.068644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.048745 restraints weight = 91485.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.12
r_work: 0.2795 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10279  Z= 0.142
  Angle     :  0.494   8.678  13930  Z= 0.258
  Chirality :  0.036   0.128   1582
  Planarity :  0.003   0.045   1733
  Dihedral  :  7.978 179.670   1333
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.77 %
    Favored  : 95.05 %
  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:  1.99 (0.25), residues: 1210
  helix:  1.86 (0.18), residues: 877
  sheet: -0.33 (0.73), residues: 50
  loop :  0.05 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 807 
 HIS   0.004   0.001   HIS B  32 
 PHE   0.014   0.001   PHE A 412 
 TYR   0.013   0.001   TYR A 863 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  628)
  hydrogen bonds       : angle       4.26413 ( 1845)
  covalent geometry    : bond        0.00317 (10279)
  covalent geometry    : angle       0.49404 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8663 (t0) cc_final: 0.7873 (t0)
REVERT: B  109 ASP cc_start: 0.8635 (m-30) cc_final: 0.8107 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.4697
  time to fit residues: 33.4308
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.068115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.048256 restraints weight = 91351.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.10
r_work: 0.2785 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10279  Z= 0.177
  Angle     :  0.502   8.848  13930  Z= 0.264
  Chirality :  0.037   0.129   1582
  Planarity :  0.003   0.046   1733
  Dihedral  :  7.913 179.610   1333
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.66 %
    Favored  : 94.16 %
  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:  2.02 (0.25), residues: 1210
  helix:  1.90 (0.18), residues: 877
  sheet: -0.50 (0.73), residues: 50
  loop :  0.01 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 807 
 HIS   0.005   0.001   HIS A1019 
 PHE   0.015   0.001   PHE A 412 
 TYR   0.013   0.001   TYR A 863 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  628)
  hydrogen bonds       : angle       4.25155 ( 1845)
  covalent geometry    : bond        0.00397 (10279)
  covalent geometry    : angle       0.50202 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 1.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8647 (t0) cc_final: 0.7844 (t0)
REVERT: B  109 ASP cc_start: 0.8619 (m-30) cc_final: 0.8105 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 45
  average time/residue: 0.4819
  time to fit residues: 32.6219
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0470
   chunk 118 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 103 optimal weight:    9.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.8680

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.068920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.048970 restraints weight = 91139.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 3.14
r_work: 0.2807 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10279  Z= 0.108
  Angle     :  0.476   9.661  13930  Z= 0.245
  Chirality :  0.036   0.130   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.721 176.023   1333
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.10 %
    Favored  : 93.81 %
  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:  2.24 (0.25), residues: 1210
  helix:  2.09 (0.18), residues: 876
  sheet: -0.61 (0.73), residues: 50
  loop :  0.03 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  75 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.014   0.001   PHE A 412 
 TYR   0.021   0.001   TYR A1105 
 ARG   0.003   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  628)
  hydrogen bonds       : angle       4.03124 ( 1845)
  covalent geometry    : bond        0.00240 (10279)
  covalent geometry    : angle       0.47646 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 1.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.5018
  time to fit residues: 35.0462
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 1.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.068081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.048105 restraints weight = 90982.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.11
r_work: 0.2780 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10279  Z= 0.190
  Angle     :  0.505  10.731  13930  Z= 0.264
  Chirality :  0.037   0.130   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.736 177.514   1333
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.19 %
    Favored  : 93.72 %
  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:  2.15 (0.25), residues: 1210
  helix:  2.03 (0.18), residues: 877
  sheet: -0.72 (0.72), residues: 50
  loop : -0.02 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 807 
 HIS   0.004   0.001   HIS A 652 
 PHE   0.015   0.001   PHE A 570 
 TYR   0.013   0.001   TYR A 104 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  628)
  hydrogen bonds       : angle       4.13475 ( 1845)
  covalent geometry    : bond        0.00428 (10279)
  covalent geometry    : angle       0.50544 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 1.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4847
  time to fit residues: 31.7234
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0060
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0770
   chunk 95 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7556

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.067536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.048167 restraints weight = 89585.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.09
r_work: 0.2757 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10279  Z= 0.102
  Angle     :  0.473  11.168  13930  Z= 0.242
  Chirality :  0.036   0.131   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.579 173.892   1333
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.28 %
    Favored  : 93.63 %
  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:  2.36 (0.25), residues: 1210
  helix:  2.20 (0.18), residues: 876
  sheet: -0.78 (0.73), residues: 50
  loop :  0.06 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  75 
 HIS   0.002   0.001   HIS B  32 
 PHE   0.014   0.001   PHE A 412 
 TYR   0.013   0.001   TYR A1105 
 ARG   0.003   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  628)
  hydrogen bonds       : angle       3.95423 ( 1845)
  covalent geometry    : bond        0.00227 (10279)
  covalent geometry    : angle       0.47306 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 1.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1077 TYR cc_start: 0.8547 (t80) cc_final: 0.8175 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4803
  time to fit residues: 32.3265
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 121 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.067144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.047868 restraints weight = 89313.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.05
r_work: 0.2756 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10279  Z= 0.126
  Angle     :  0.484   9.458  13930  Z= 0.249
  Chirality :  0.036   0.132   1582
  Planarity :  0.003   0.043   1733
  Dihedral  :  7.539 174.042   1333
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  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:  2.35 (0.25), residues: 1210
  helix:  2.21 (0.18), residues: 877
  sheet: -0.83 (0.73), residues: 50
  loop :  0.00 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  75 
 HIS   0.003   0.001   HIS B 107 
 PHE   0.014   0.001   PHE A 412 
 TYR   0.013   0.001   TYR A1105 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03325 (  628)
  hydrogen bonds       : angle       3.95928 ( 1845)
  covalent geometry    : bond        0.00284 (10279)
  covalent geometry    : angle       0.48378 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1077 TYR cc_start: 0.8552 (t80) cc_final: 0.8180 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.4889
  time to fit residues: 30.9426
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    0.3980
   chunk 40 optimal weight:    0.3980
   chunk 92 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.068356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.048246 restraints weight = 90230.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.23
r_work: 0.2762 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10279  Z= 0.097
  Angle     :  0.471  11.662  13930  Z= 0.239
  Chirality :  0.035   0.131   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.399 171.311   1333
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  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:  2.49 (0.25), residues: 1210
  helix:  2.32 (0.18), residues: 877
  sheet: -0.86 (0.73), residues: 50
  loop :  0.04 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  75 
 HIS   0.002   0.000   HIS A 652 
 PHE   0.013   0.001   PHE A 412 
 TYR   0.011   0.001   TYR A 863 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03138 (  628)
  hydrogen bonds       : angle       3.85965 ( 1845)
  covalent geometry    : bond        0.00217 (10279)
  covalent geometry    : angle       0.47066 (13930)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1077 TYR cc_start: 0.8546 (t80) cc_final: 0.8179 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.4752
  time to fit residues: 31.8305
Evaluate side-chains
  42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 77 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1018 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.067843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.048563 restraints weight = 89185.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 3.06
r_work: 0.2772 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10279  Z= 0.102
  Angle     :  0.471  10.436  13930  Z= 0.240
  Chirality :  0.036   0.133   1582
  Planarity :  0.003   0.043   1733
  Dihedral  :  7.347 170.873   1333
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  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:  2.56 (0.25), residues: 1210
  helix:  2.38 (0.18), residues: 877
  sheet: -0.90 (0.73), residues: 50
  loop :  0.03 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  75 
 HIS   0.002   0.000   HIS B 107 
 PHE   0.013   0.001   PHE A 412 
 TYR   0.010   0.001   TYR A 863 
 ARG   0.002   0.000   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03114 (  628)
  hydrogen bonds       : angle       3.84573 ( 1845)
  covalent geometry    : bond        0.00228 (10279)
  covalent geometry    : angle       0.47135 (13930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7625.86 seconds
wall clock time: 131 minutes 57.15 seconds (7917.15 seconds total)