Starting phenix.real_space_refine
on Thu Sep 18 21:30:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dxm_47291/09_2025/9dxm_47291_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dxm_47291/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dxm_47291/09_2025/9dxm_47291_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dxm_47291/09_2025/9dxm_47291_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dxm_47291/09_2025/9dxm_47291.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dxm_47291/09_2025/9dxm_47291.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.84, per 1000 atoms: 0.19
  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: 1.99
  Conformation dependent library (CDL) restraints added in 583.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.51
  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: 4.73

  Time building geometry restraints manager: 2.71 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:             2.800
  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:             0.120
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.200
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.001   ARG A 555 
 TYR   0.016   0.002   TYR A 508 
 PHE   0.018   0.002   PHE A 570 
 TRP   0.012   0.001   TRP A 807 
 HIS   0.004   0.001   HIS A 496 

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

*********************** 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  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   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: 0.7832 (t0)
REVERT: B  109 ASP cc_start: 0.8680 (m-30) cc_final: 0.8176 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.2993
  time to fit residues: 22.4534
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.068641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.048637 restraints weight = 90388.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 3.11
r_work: 0.2790 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10279  Z= 0.153
  Angle     :  0.533   6.134  13930  Z= 0.285
  Chirality :  0.038   0.129   1582
  Planarity :  0.004   0.048   1733
  Dihedral  :  8.345 175.735   1333
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.33 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.25), residues: 1210
  helix:  1.48 (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
 ARG   0.003   0.000   ARG A  26 
 TYR   0.014   0.001   TYR A1105 
 PHE   0.013   0.001   PHE A 412 
 TRP   0.010   0.001   TRP A 807 
 HIS   0.005   0.001   HIS A1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10279)
  covalent geometry    : angle       0.53349 (13930)
  hydrogen bonds       : bond        0.04667 (  628)
  hydrogen bonds       : angle       4.79120 ( 1845)

*********************** 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
  48 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  847 MET cc_start: 0.7540 (ptt) cc_final: 0.7253 (ptm)
REVERT: B  105 ASN cc_start: 0.8715 (t0) cc_final: 0.7857 (t0)
REVERT: B  109 ASP cc_start: 0.8659 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 48
  average time/residue: 0.2330
  time to fit residues: 16.8529
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.067534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.047592 restraints weight = 91420.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.09
r_work: 0.2760 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10279  Z= 0.239
  Angle     :  0.540   5.988  13930  Z= 0.290
  Chirality :  0.039   0.131   1582
  Planarity :  0.004   0.049   1733
  Dihedral  :  8.179 174.123   1333
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.25), residues: 1210
  helix:  1.53 (0.18), residues: 875
  sheet: -0.24 (0.71), residues: 50
  loop :  0.05 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.014   0.002   TYR A 863 
 PHE   0.014   0.001   PHE A 660 
 TRP   0.011   0.001   TRP A 807 
 HIS   0.006   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (10279)
  covalent geometry    : angle       0.54036 (13930)
  hydrogen bonds       : bond        0.04387 (  628)
  hydrogen bonds       : angle       4.67744 ( 1845)

*********************** 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
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8698 (t0) cc_final: 0.7857 (t0)
REVERT: B  109 ASP cc_start: 0.8674 (m-30) cc_final: 0.8139 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2384
  time to fit residues: 15.7823
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  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.068451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048541 restraints weight = 90733.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.10
r_work: 0.2790 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10279  Z= 0.134
  Angle     :  0.491   6.234  13930  Z= 0.258
  Chirality :  0.036   0.128   1582
  Planarity :  0.003   0.046   1733
  Dihedral  :  8.059 178.760   1333
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.86 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.25), residues: 1210
  helix:  1.78 (0.18), residues: 876
  sheet: -0.40 (0.72), residues: 50
  loop :  0.04 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.013   0.001   TYR A 863 
 PHE   0.012   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10279)
  covalent geometry    : angle       0.49121 (13930)
  hydrogen bonds       : bond        0.03861 (  628)
  hydrogen bonds       : angle       4.34405 ( 1845)

*********************** 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  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8655 (t0) cc_final: 0.7871 (t0)
REVERT: B  109 ASP cc_start: 0.8634 (m-30) cc_final: 0.8110 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.2322
  time to fit residues: 16.2918
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  : 0.589 
-------------------------------------------------------------------------------
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 32 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 52 optimal weight:    0.2980
   chunk 70 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.068966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.049120 restraints weight = 90907.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 3.12
r_work: 0.2804 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1491

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= 0.122
  Angle     :  0.478   6.296  13930  Z= 0.249
  Chirality :  0.036   0.130   1582
  Planarity :  0.003   0.045   1733
  Dihedral  :  7.873 178.823   1333
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.22 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.25), residues: 1210
  helix:  1.98 (0.18), residues: 876
  sheet: -0.48 (0.74), residues: 50
  loop :  0.01 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.013   0.001   TYR A 863 
 PHE   0.017   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A 807 
 HIS   0.004   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10279)
  covalent geometry    : angle       0.47836 (13930)
  hydrogen bonds       : bond        0.03547 (  628)
  hydrogen bonds       : angle       4.15183 ( 1845)

*********************** 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
  47 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ASN cc_start: 0.8634 (t0) cc_final: 0.7844 (t0)
REVERT: B  109 ASP cc_start: 0.8614 (m-30) cc_final: 0.8094 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2410
  time to fit residues: 16.5271
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  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.068290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.048409 restraints weight = 90794.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 3.10
r_work: 0.2784 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1603

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= 0.179
  Angle     :  0.499   6.588  13930  Z= 0.262
  Chirality :  0.037   0.129   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.819 178.584   1333
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.25), residues: 1210
  helix:  1.97 (0.18), residues: 876
  sheet: -0.64 (0.73), residues: 50
  loop : -0.04 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 719 
 TYR   0.013   0.001   TYR A 863 
 PHE   0.014   0.001   PHE A 412 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.004   0.001   HIS A 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (10279)
  covalent geometry    : angle       0.49862 (13930)
  hydrogen bonds       : bond        0.03647 (  628)
  hydrogen bonds       : angle       4.18099 ( 1845)

*********************** 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
  43 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2175
  time to fit residues: 14.3318
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  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    0.0870
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0870
   chunk 84 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.9940

-------------------------------------------------------------------------------
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 = 0.068937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048975 restraints weight = 90619.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 3.13
r_work: 0.2804 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10279  Z= 0.117
  Angle     :  0.472   7.015  13930  Z= 0.245
  Chirality :  0.036   0.130   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.672 175.656   1333
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.01 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.25), residues: 1210
  helix:  2.12 (0.18), residues: 875
  sheet: -0.77 (0.73), residues: 50
  loop : -0.03 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.023   0.001   TYR A1105 
 PHE   0.014   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A  75 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10279)
  covalent geometry    : angle       0.47213 (13930)
  hydrogen bonds       : bond        0.03397 (  628)
  hydrogen bonds       : angle       4.02190 ( 1845)

*********************** 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
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.2372
  time to fit residues: 16.0628
Evaluate side-chains
  45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.069445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.050711 restraints weight = 89357.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 2.94
r_work: 0.2806 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10279  Z= 0.138
  Angle     :  0.486  11.093  13930  Z= 0.250
  Chirality :  0.036   0.131   1582
  Planarity :  0.003   0.042   1733
  Dihedral  :  7.628 175.554   1333
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.92 %
    Favored  : 93.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.25), residues: 1210
  helix:  2.13 (0.18), residues: 876
  sheet: -0.86 (0.72), residues: 50
  loop :  0.02 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.012   0.001   TYR A1105 
 PHE   0.014   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A 807 
 HIS   0.003   0.001   HIS A 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10279)
  covalent geometry    : angle       0.48637 (13930)
  hydrogen bonds       : bond        0.03395 (  628)
  hydrogen bonds       : angle       4.02372 ( 1845)

*********************** 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  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2354
  time to fit residues: 15.6796
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  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.068495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.048641 restraints weight = 90861.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.11
r_work: 0.2790 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10279  Z= 0.154
  Angle     :  0.490   8.063  13930  Z= 0.255
  Chirality :  0.036   0.130   1582
  Planarity :  0.003   0.044   1733
  Dihedral  :  7.582 174.477   1333
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.25), residues: 1210
  helix:  2.16 (0.18), residues: 875
  sheet: -0.95 (0.73), residues: 50
  loop : -0.01 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.016   0.001   TYR A1105 
 PHE   0.014   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A  75 
 HIS   0.003   0.001   HIS A 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10279)
  covalent geometry    : angle       0.49028 (13930)
  hydrogen bonds       : bond        0.03434 (  628)
  hydrogen bonds       : angle       4.03511 ( 1845)

*********************** 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
  44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1077 TYR cc_start: 0.8585 (t80) cc_final: 0.8221 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2252
  time to fit residues: 15.0393
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  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0970
   chunk 107 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.068090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.048038 restraints weight = 90113.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 3.18
r_work: 0.2756 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1946

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= 0.109
  Angle     :  0.472   8.522  13930  Z= 0.242
  Chirality :  0.036   0.132   1582
  Planarity :  0.003   0.043   1733
  Dihedral  :  7.463 172.229   1333
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.25), residues: 1210
  helix:  2.27 (0.18), residues: 876
  sheet: -1.01 (0.72), residues: 50
  loop :  0.08 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.016   0.001   TYR A1105 
 PHE   0.014   0.001   PHE A 412 
 TRP   0.008   0.001   TRP A  75 
 HIS   0.004   0.001   HIS A1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10279)
  covalent geometry    : angle       0.47159 (13930)
  hydrogen bonds       : bond        0.03240 (  628)
  hydrogen bonds       : angle       3.91461 ( 1845)

********************** 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
  46 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1077 TYR cc_start: 0.8574 (t80) cc_final: 0.8225 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2275
  time to fit residues: 15.9116
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  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 118 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.067917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.048426 restraints weight = 89408.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 3.10
r_work: 0.2757 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10279  Z= 0.111
  Angle     :  0.473   8.146  13930  Z= 0.243
  Chirality :  0.036   0.132   1582
  Planarity :  0.003   0.043   1733
  Dihedral  :  7.403 171.441   1333
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.25), residues: 1210
  helix:  2.31 (0.18), residues: 877
  sheet: -1.00 (0.72), residues: 50
  loop :  0.00 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  26 
 TYR   0.016   0.001   TYR A1105 
 PHE   0.029   0.001   PHE A1078 
 TRP   0.008   0.001   TRP A  75 
 HIS   0.002   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10279)
  covalent geometry    : angle       0.47258 (13930)
  hydrogen bonds       : bond        0.03202 (  628)
  hydrogen bonds       : angle       3.89759 ( 1845)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4217.73 seconds
wall clock time: 72 minutes 35.47 seconds (4355.47 seconds total)