Starting phenix.real_space_refine
on Sat Aug 23 05:04:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d43_46548/08_2025/9d43_46548.map"
  }
  resolution = 3.39
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    6290      2.51       5
     N    1599      2.21       5
     O    1809      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9754
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9754
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1189, 9742
          Classifications: {'peptide': 1189}
          Link IDs: {'PTRANS': 44, 'TRANS': 1144}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 1189, 9742
          Classifications: {'peptide': 1189}
          Link IDs: {'PTRANS': 44, 'TRANS': 1144}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 9937
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 614 " occ=0.48
      ... (22 atoms not shown)
      pdb=" OH BTYR A 614 " occ=0.52
  Time building chain proxies: 3.08, per 1000 atoms: 0.32
  Number of scatterers: 9754
  At special positions: 0
  Unit cell: (85.49, 113.3, 112.27, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1809      8.00
     N    1599      7.00
     C    6290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 622.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2312

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 0 sheets defined
      82.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
      removed outlier: 4.055A  pdb=" N   ILE A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 38
      removed outlier: 3.527A  pdb=" N   GLN A  27 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS A  31 " --> pdb=" O   GLN A  27 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   PHE A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU A  38 " --> pdb=" O   ASP A  34 " (cutoff:3.500A)
    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
      removed outlier: 3.580A  pdb=" N   LYS A 106 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 4.011A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 138
      removed outlier: 3.577A  pdb=" N   GLN A 134 " --> pdb=" O   PRO A 130 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 151
      removed outlier: 3.758A  pdb=" N   ASN A 151 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 173
    Processing helix  chain 'A' and resid 176 through 182
    Processing helix  chain 'A' and resid 182 through 195
      Proline residue:  A 188  - end of helix
      removed outlier: 3.673A  pdb=" N   VAL A 194 " --> pdb=" O   CYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 3.765A  pdb=" N   ILE A 202 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 214
      removed outlier: 3.503A  pdb=" N   LYS A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 235
      removed outlier: 3.653A  pdb=" N   ILE A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      Proline residue:  A 226  - end of helix
    Processing helix  chain 'A' and resid 236 through 251
      removed outlier: 3.868A  pdb=" N   THR A 249 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.834A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 3.507A  pdb=" N   SER A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 293
    Processing helix  chain 'A' and resid 297 through 311
      removed outlier: 3.539A  pdb=" N   GLN A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET A 303 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 304 " --> pdb=" O   HIS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 3.560A  pdb=" N   LEU A 348 " --> pdb=" O   MET A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 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 384
      removed outlier: 3.814A  pdb=" N   THR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 394
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 405 through 417
    Processing helix  chain 'A' and resid 427 through 436
      removed outlier: 3.882A  pdb=" N   PHE A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.753A  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 482
    Processing helix  chain 'A' and resid 485 through 490
      removed outlier: 3.869A  pdb=" N   LEU A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 525
      removed outlier: 3.701A  pdb=" N   ALA A 504 " --> pdb=" O   PRO A 500 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG A 520 " --> pdb=" O   ASN A 516 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LYS A 522 " --> pdb=" O   CYS A 518 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 552
      removed outlier: 4.330A  pdb=" N   GLU A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER A 537 " --> pdb=" O   GLU A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 575
      removed outlier: 4.069A  pdb=" N   ALA A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   LEU A 569 " --> pdb=" O   GLN A 565 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   MET A 573 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 592
    Processing helix  chain 'A' and resid 603 through 627
      removed outlier: 3.855A  pdb=" N   ALA A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG A 610 " --> pdb=" O   SER A 606 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A 627 " --> pdb=" O   MET A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 633
    Processing helix  chain 'A' and resid 634 through 645
    Processing helix  chain 'A' and resid 649 through 668
      removed outlier: 3.720A  pdb=" N   GLU A 653 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE A 664 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 686
      removed outlier: 3.531A  pdb=" N   ILE A 680 " --> pdb=" O   ARG A 676 " (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 720
      removed outlier: 3.515A  pdb=" N   GLU A 714 " --> pdb=" O   VAL A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 751
      removed outlier: 3.565A  pdb=" N   LYS A 737 " --> pdb=" O   ASP A 733 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN A 748 " --> pdb=" O   THR A 744 " (cutoff:3.500A)
      removed outlier: 3.545A  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 770 through 785
      Proline residue:  A 782  - end of helix
    Processing helix  chain 'A' and resid 787 through 802
      removed outlier: 3.871A  pdb=" N   HIS A 802 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 810
      removed outlier: 4.124A  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 823
      removed outlier: 3.769A  pdb=" N   ILE A 823 " --> pdb=" O   LYS A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 879
      removed outlier: 4.055A  pdb=" N   GLY A 879 " --> pdb=" O   ILE A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 886 through 897
      removed outlier: 4.394A  pdb=" N   ASP A 890 " --> pdb=" O   ASP A 886 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU A 893 " --> pdb=" O   PRO A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 921
    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: 3.786A  pdb=" N   SER A 960 " --> pdb=" O   GLN A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 1003
    Processing helix  chain 'A' and resid 1018 through 1029
      removed outlier: 3.752A  pdb=" N   GLU A1022 " --> pdb=" O   ASN A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1047
      Proline residue:  A1036  - end of helix
      removed outlier: 3.535A  pdb=" N   HIS A1043 " --> pdb=" O   LYS A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1064
    Processing helix  chain 'A' and resid 1065 through 1067
      No H-bonds generated for 'chain 'A' and resid 1065 through 1067'
    Processing helix  chain 'A' and resid 1071 through 1081
      removed outlier: 3.615A  pdb=" N   ASP A1075 " --> pdb=" O   ASN A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1090
    Processing helix  chain 'A' and resid 1099 through 1118
      removed outlier: 3.654A  pdb=" N   LYS A1116 " --> pdb=" O   LEU A1112 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A1117 " --> pdb=" O   THR A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1130
      removed outlier: 3.932A  pdb=" N   ARG A1122 " --> pdb=" O   TYR A1118 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA A1123 " --> pdb=" O   PRO A1119 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A1124 " --> pdb=" O   SER A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1143
      removed outlier: 3.669A  pdb=" N   SER A1143 " --> pdb=" O   ARG A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1166
      removed outlier: 3.690A  pdb=" N   GLN A1150 " --> pdb=" O   GLU A1146 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A1152 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A1153 " --> pdb=" O   THR A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1176 through 1198

    618 hydrogen bonds defined for protein.
    1828 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: 1.09

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3111
        1.35 -     1.47: 2299
        1.47 -     1.58: 4466
        1.58 -     1.70: 0
        1.70 -     1.82: 89
  Bond restraints: 9965
  Sorted by residual:
  bond pdb=" N   MET A 627 "
       pdb=" CA  MET A 627 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.41e-02 5.03e+03 5.16e+00
  bond pdb=" C   MET A 627 "
       pdb=" N   PRO A 628 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.016 9.80e-03 1.04e+04 2.81e+00
  bond pdb=" CA  MET A 627 "
       pdb=" C   MET A 627 "
    ideal  model  delta    sigma   weight residual
    1.524  1.535 -0.012 1.26e-02 6.30e+03 8.52e-01
  bond pdb=" CB  MET A 967 "
       pdb=" CG  MET A 967 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.81e-01
  bond pdb=" CG  ARG A 555 "
       pdb=" CD  ARG A 555 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.70e-01
  ... (remaining 9960 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 13385
        2.25 -     4.51: 85
        4.51 -     6.76: 23
        6.76 -     9.02: 2
        9.02 -    11.27: 1
  Bond angle restraints: 13496
  Sorted by residual:
  angle pdb=" CB  MET A 967 "
        pdb=" CG  MET A 967 "
        pdb=" SD  MET A 967 "
      ideal   model   delta    sigma   weight residual
     112.70  123.97  -11.27 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" CA  LYS A  20 "
        pdb=" CB  LYS A  20 "
        pdb=" CG  LYS A  20 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" N   TRP A 253 "
        pdb=" CA  TRP A 253 "
        pdb=" C   TRP A 253 "
      ideal   model   delta    sigma   weight residual
     109.81  116.56   -6.75 2.21e+00 2.05e-01 9.33e+00
  angle pdb=" CA  MET A 627 "
        pdb=" C   MET A 627 "
        pdb=" N   PRO A 628 "
      ideal   model   delta    sigma   weight residual
     118.44  122.99   -4.55 1.59e+00 3.96e-01 8.19e+00
  angle pdb=" C   LYS A1199 "
        pdb=" N   ASN A1200 "
        pdb=" CA  ASN A1200 "
      ideal   model   delta    sigma   weight residual
     121.54  126.99   -5.45 1.91e+00 2.74e-01 8.15e+00
  ... (remaining 13491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 5289
       17.75 -    35.51: 604
       35.51 -    53.26: 131
       53.26 -    71.02: 24
       71.02 -    88.77: 6
  Dihedral angle restraints: 6054
    sinusoidal: 2508
      harmonic: 3546
  Sorted by residual:
  dihedral pdb=" CA  ARG A  26 "
           pdb=" C   ARG A  26 "
           pdb=" N   GLN A  27 "
           pdb=" CA  GLN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" N   ASN A 904 "
           pdb=" CA  ASN A 904 "
           pdb=" CB  ASN A 904 "
           pdb=" CG  ASN A 904 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.74   59.74     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A  91 "
           pdb=" CG  MET A  91 "
           pdb=" SD  MET A  91 "
           pdb=" CE  MET A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.15  -57.85     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 6051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1311
       0.054 -    0.107: 207
       0.107 -    0.161: 5
       0.161 -    0.214: 0
       0.214 -    0.268: 2
  Chirality restraints: 1525
  Sorted by residual:
  chirality pdb=" CA  MET A 627 "
            pdb=" N   MET A 627 "
            pdb=" C   MET A 627 "
            pdb=" CB  MET A 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  ILE A 767 "
            pdb=" CA  ILE A 767 "
            pdb=" CG1 ILE A 767 "
            pdb=" CG2 ILE A 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  SER A 888 "
            pdb=" N   SER A 888 "
            pdb=" C   SER A 888 "
            pdb=" CB  SER A 888 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.68e-01
  ... (remaining 1522 not shown)

  Planarity restraints: 1701
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  26 "   -0.099 9.50e-02 1.11e+02   4.48e-02 1.58e+00
        pdb=" NE  ARG A  26 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  26 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  26 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  26 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 646 "   -0.019 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO A 647 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 647 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 647 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 900 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO A 901 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 901 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 901 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1698 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 929
        2.74 -     3.28: 10104
        3.28 -     3.82: 16720
        3.82 -     4.36: 17936
        4.36 -     4.90: 31167
  Nonbonded interactions: 76856
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  36 "
            pdb=" OG  SER A  42 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ALA A 416 "
            pdb=" OH  TYR A 420 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OH  TYR A  47 "
            pdb=" OE1 GLU A  92 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OH  TYR A 335 "
            pdb=" OD2 ASP A 435 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   TRP A 121 "
            pdb=" NH2 ARG A 182 "
     model   vdw
     2.267 3.120
  ... (remaining 76851 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.180
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9965  Z= 0.092
  Angle     :  0.483  11.272  13496  Z= 0.237
  Chirality :  0.037   0.268   1525
  Planarity :  0.003   0.045   1701
  Dihedral  : 15.655  88.770   3742
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 13.21 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.93 (0.25), residues: 1186
  helix:  2.12 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -0.95 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  26 
 TYR   0.017   0.001   TYR A 404 
 PHE   0.012   0.001   PHE A 206 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 9965)
  covalent geometry    : angle       0.48255 (13496)
  hydrogen bonds       : bond        0.19958 (  618)
  hydrogen bonds       : angle       6.00234 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  775 MET cc_start: 0.8766 (tmm) cc_final: 0.8477 (tmm)
REVERT: A 1001 CYS cc_start: 0.8028 (m) cc_final: 0.7238 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.0900
  time to fit residues: 6.3552
Evaluate side-chains
  40 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  627 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.049177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.033842 restraints weight = 79836.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 5.93
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9965  Z= 0.147
  Angle     :  0.550   8.244  13496  Z= 0.277
  Chirality :  0.038   0.182   1525
  Planarity :  0.004   0.037   1701
  Dihedral  :  3.867  30.590   1290
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.85 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.26), residues: 1186
  helix:  2.32 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -0.83 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  26 
 TYR   0.014   0.001   TYR A 404 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.010   0.001   TRP A 747 
 HIS   0.005   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9965)
  covalent geometry    : angle       0.54961 (13496)
  hydrogen bonds       : bond        0.04284 (  618)
  hydrogen bonds       : angle       4.47707 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  598 ASN cc_start: 0.9448 (OUTLIER) cc_final: 0.9083 (p0)
REVERT: A  627 MET cc_start: 0.8635 (ptm) cc_final: 0.7767 (ppp)
REVERT: A  847 MET cc_start: 0.8746 (mmm) cc_final: 0.8527 (tpt)
REVERT: A 1001 CYS cc_start: 0.8063 (m) cc_final: 0.7267 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 45
  average time/residue: 0.0675
  time to fit residues: 5.2021
Evaluate side-chains
  43 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  598 ASN
Chi-restraints excluded: chain A residue  977 MET
Chi-restraints excluded: chain A residue 1082 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0060
   chunk 28 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A1019 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.049932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.034953 restraints weight = 74548.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2613 rms_B_bonded: 5.63
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9965  Z= 0.101
  Angle     :  0.495   8.752  13496  Z= 0.247
  Chirality :  0.037   0.170   1525
  Planarity :  0.003   0.036   1701
  Dihedral  :  3.704  17.034   1287
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.94 %
    Favored  : 86.24 %
  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:  2.30 (0.25), residues: 1186
  helix:  2.40 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -0.95 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  26 
 TYR   0.018   0.001   TYR A 301 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.007   0.001   TRP A 807 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 9965)
  covalent geometry    : angle       0.49529 (13496)
  hydrogen bonds       : bond        0.03459 (  618)
  hydrogen bonds       : angle       4.17707 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  404 TYR cc_start: 0.8130 (p90) cc_final: 0.7904 (p90)
REVERT: A  627 MET cc_start: 0.8652 (ptm) cc_final: 0.7948 (ppp)
REVERT: A  837 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7831 (t0)
REVERT: A 1001 CYS cc_start: 0.8132 (m) cc_final: 0.7345 (m)
  outliers start: 9
  outliers final: 3
  residues processed: 44
  average time/residue: 0.0663
  time to fit residues: 4.8324
Evaluate side-chains
  42 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  953 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3079 r_free = 0.3079 target = 0.049098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.033685 restraints weight = 91774.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.2567 rms_B_bonded: 6.24
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9965  Z= 0.128
  Angle     :  0.507   7.876  13496  Z= 0.250
  Chirality :  0.037   0.155   1525
  Planarity :  0.003   0.038   1701
  Dihedral  :  3.663  17.856   1287
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.03 %
    Favored  : 86.15 %
  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: 1186
  helix:  2.48 (0.18), residues: 861
  sheet:  None (None), residues: 0
  loop : -0.88 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  26 
 TYR   0.017   0.001   TYR A 301 
 PHE   0.010   0.001   PHE A 570 
 TRP   0.009   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 961 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9965)
  covalent geometry    : angle       0.50697 (13496)
  hydrogen bonds       : bond        0.03455 (  618)
  hydrogen bonds       : angle       4.10077 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  142 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8640 (tpt)
REVERT: A  627 MET cc_start: 0.8818 (ptm) cc_final: 0.8172 (ppp)
REVERT: A 1001 CYS cc_start: 0.8113 (m) cc_final: 0.7289 (m)
REVERT: A 1021 MET cc_start: 0.8629 (mmm) cc_final: 0.8370 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 45
  average time/residue: 0.0608
  time to fit residues: 4.6602
Evaluate side-chains
  44 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0870
   chunk 39 optimal weight:    0.3980
   chunk 23 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.2562

-------------------------------------------------------------------------------
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 = 0.3080 r_free = 0.3080 target = 0.049220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.034154 restraints weight = 79107.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.2580 rms_B_bonded: 5.78
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9965  Z= 0.120
  Angle     :  0.498   6.788  13496  Z= 0.246
  Chirality :  0.037   0.144   1525
  Planarity :  0.003   0.037   1701
  Dihedral  :  3.668  17.588   1287
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.94 %
    Favored  : 85.79 %
  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:  2.49 (0.25), residues: 1186
  helix:  2.54 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -0.90 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  26 
 TYR   0.018   0.001   TYR A 404 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.008   0.001   TRP A 807 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9965)
  covalent geometry    : angle       0.49752 (13496)
  hydrogen bonds       : bond        0.03227 (  618)
  hydrogen bonds       : angle       4.03083 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  627 MET cc_start: 0.8872 (ptm) cc_final: 0.8438 (ppp)
REVERT: A  837 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (t0)
REVERT: A 1001 CYS cc_start: 0.8174 (m) cc_final: 0.7460 (m)
  outliers start: 14
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0645
  time to fit residues: 5.3401
Evaluate side-chains
  50 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3063 r_free = 0.3063 target = 0.048521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.033329 restraints weight = 78265.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.2552 rms_B_bonded: 5.77
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9965  Z= 0.152
  Angle     :  0.514   7.031  13496  Z= 0.254
  Chirality :  0.038   0.138   1525
  Planarity :  0.003   0.038   1701
  Dihedral  :  3.718  18.624   1287
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.85 %
    Favored  : 85.52 %
  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:  2.50 (0.25), residues: 1186
  helix:  2.51 (0.18), residues: 867
  sheet:  None (None), residues: 0
  loop : -0.83 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.015   0.001   TYR A 301 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.010   0.001   TRP A 113 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9965)
  covalent geometry    : angle       0.51412 (13496)
  hydrogen bonds       : bond        0.03509 (  618)
  hydrogen bonds       : angle       4.08627 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  142 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8659 (tpt)
REVERT: A  627 MET cc_start: 0.8869 (ptm) cc_final: 0.8012 (ppp)
  outliers start: 18
  outliers final: 11
  residues processed: 51
  average time/residue: 0.0626
  time to fit residues: 5.4541
Evaluate side-chains
  48 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 23 optimal weight:    0.7980
   chunk 83 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 88 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0170
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
A1004 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.049685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.034698 restraints weight = 73775.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2601 rms_B_bonded: 5.63
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9965  Z= 0.095
  Angle     :  0.485   8.215  13496  Z= 0.239
  Chirality :  0.036   0.125   1525
  Planarity :  0.003   0.038   1701
  Dihedral  :  3.652  17.252   1287
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.39 %
    Favored  : 85.34 %
  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:  2.48 (0.25), residues: 1186
  helix:  2.51 (0.18), residues: 868
  sheet:  None (None), residues: 0
  loop : -0.89 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.018   0.001   TYR A 404 
 PHE   0.010   0.001   PHE A 206 
 TRP   0.007   0.001   TRP A 807 
 HIS   0.002   0.000   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 9965)
  covalent geometry    : angle       0.48550 (13496)
  hydrogen bonds       : bond        0.02972 (  618)
  hydrogen bonds       : angle       3.95229 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  142 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8611 (tpt)
REVERT: A  627 MET cc_start: 0.8824 (ptm) cc_final: 0.7957 (ppp)
REVERT: A  837 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7817 (t0)
REVERT: A 1001 CYS cc_start: 0.8146 (m) cc_final: 0.7527 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 50
  average time/residue: 0.0616
  time to fit residues: 5.0918
Evaluate side-chains
  50 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.3980
   chunk 96 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    0.4980
   chunk 71 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3099 r_free = 0.3099 target = 0.049933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.034912 restraints weight = 75504.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2609 rms_B_bonded: 5.70
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9965  Z= 0.096
  Angle     :  0.479   7.994  13496  Z= 0.234
  Chirality :  0.036   0.118   1525
  Planarity :  0.003   0.038   1701
  Dihedral  :  3.597  17.430   1287
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.48 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.57 (0.25), residues: 1186
  helix:  2.57 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -0.88 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.016   0.001   TYR A 301 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.008   0.001   TRP A 807 
 HIS   0.003   0.000   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 9965)
  covalent geometry    : angle       0.47943 (13496)
  hydrogen bonds       : bond        0.02854 (  618)
  hydrogen bonds       : angle       3.88750 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  142 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8634 (tpt)
REVERT: A  404 TYR cc_start: 0.8099 (p90) cc_final: 0.7863 (p90)
REVERT: A  452 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7499 (mtp180)
REVERT: A  627 MET cc_start: 0.8810 (ptm) cc_final: 0.8255 (ppp)
  outliers start: 12
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0793
  time to fit residues: 6.1477
Evaluate side-chains
  49 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  452 ARG
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0370
   chunk 22 optimal weight:    0.1980
   chunk 114 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.9460

-------------------------------------------------------------------------------
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 = 0.3094 r_free = 0.3094 target = 0.049707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.035032 restraints weight = 60790.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 5.18
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9965  Z= 0.105
  Angle     :  0.490   8.845  13496  Z= 0.238
  Chirality :  0.036   0.120   1525
  Planarity :  0.003   0.038   1701
  Dihedral  :  3.580  17.184   1287
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.48 %
    Favored  : 85.34 %
  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:  2.59 (0.25), residues: 1186
  helix:  2.58 (0.18), residues: 870
  sheet:  None (None), residues: 0
  loop : -0.84 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.017   0.001   TYR A 301 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.003   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9965)
  covalent geometry    : angle       0.49018 (13496)
  hydrogen bonds       : bond        0.02916 (  618)
  hydrogen bonds       : angle       3.89237 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  142 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8665 (tpt)
REVERT: A  452 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7513 (mtp180)
REVERT: A  627 MET cc_start: 0.8806 (ptm) cc_final: 0.8284 (ppp)
  outliers start: 13
  outliers final: 10
  residues processed: 47
  average time/residue: 0.0739
  time to fit residues: 5.3284
Evaluate side-chains
  48 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  452 ARG
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0570
   chunk 85 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0170
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.3124 r_free = 0.3124 target = 0.050767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.036371 restraints weight = 54304.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 4.89
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9965  Z= 0.088
  Angle     :  0.479   9.062  13496  Z= 0.233
  Chirality :  0.036   0.117   1525
  Planarity :  0.003   0.037   1701
  Dihedral  :  3.519  16.870   1287
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.67 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.52 (0.25), residues: 1186
  helix:  2.56 (0.18), residues: 869
  sheet:  None (None), residues: 0
  loop : -0.95 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  26 
 TYR   0.017   0.001   TYR A 404 
 PHE   0.010   0.001   PHE A 206 
 TRP   0.008   0.001   TRP A 807 
 HIS   0.002   0.000   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 9965)
  covalent geometry    : angle       0.47874 (13496)
  hydrogen bonds       : bond        0.02567 (  618)
  hydrogen bonds       : angle       3.82330 ( 1828)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  452 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7551 (mtp180)
REVERT: A  627 MET cc_start: 0.8793 (ptm) cc_final: 0.7972 (ppp)
  outliers start: 10
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0797
  time to fit residues: 6.0315
Evaluate side-chains
  47 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  452 ARG
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1125 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.050112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.035220 restraints weight = 69836.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2620 rms_B_bonded: 5.54
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9965  Z= 0.101
  Angle     :  0.486   9.258  13496  Z= 0.236
  Chirality :  0.036   0.119   1525
  Planarity :  0.003   0.037   1701
  Dihedral  :  3.508  17.024   1287
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.39 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.59 (0.25), residues: 1186
  helix:  2.60 (0.18), residues: 869
  sheet:  None (None), residues: 0
  loop : -0.89 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  26 
 TYR   0.016   0.001   TYR A 301 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.009   0.001   TRP A 807 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9965)
  covalent geometry    : angle       0.48552 (13496)
  hydrogen bonds       : bond        0.02759 (  618)
  hydrogen bonds       : angle       3.84241 ( 1828)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1556.35 seconds
wall clock time: 27 minutes 31.28 seconds (1651.28 seconds total)