Starting phenix.real_space_refine
on Sat Aug 23 04:18:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5v_44226/08_2025/9b5v_44226.map"
  }
  resolution = 3.94
  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=   0.000 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      42      5.16       5
     C    6074      2.51       5
     N    1573      2.21       5
     O    1833      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 9527
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.51, per 1000 atoms: 0.26
  Number of scatterers: 9527
  At special positions: 0
  Unit cell: (91.504, 100.016, 121.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       3     15.00
     Mg      2     11.99
     O    1833      8.00
     N    1573      7.00
     C    6074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.93

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 326.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      46.8% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 4.063A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.936A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.887A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.510A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 146
      removed outlier: 3.707A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 224
      removed outlier: 3.796A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.428A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.727A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.565A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.875A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
      removed outlier: 3.627A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.625A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.562A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 583
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.515A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.521A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.996A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.626A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.671A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 41
    Processing helix  chain 'D' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.939A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.046A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.046A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.518A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 907
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923
      removed outlier: 6.321A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ASP A 996 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   VAL A 942 " --> pdb=" O   ASP A 996 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923
      removed outlier: 6.321A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.332A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16
      removed outlier: 8.804A  pdb=" N   LEU D  67 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   PHE D   4 " --> pdb=" O   LEU D  67 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   LEU D  69 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS D   6 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1272 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: 1.74

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1616
        1.27 -     1.40: 2291
        1.40 -     1.54: 5657
        1.54 -     1.67: 110
        1.67 -     1.81: 64
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" C04 A1AIV D 101 "
       pdb=" C05 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.525 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.76e+00
  bond pdb=" C   SER A 589 "
       pdb=" N   PHE A 590 "
    ideal  model  delta    sigma   weight residual
    1.339  1.277  0.062 5.57e-02 3.22e+02 1.25e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.519  0.012 1.20e-02 6.94e+03 9.88e-01
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 8.68e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 12916
        1.35 -     2.70: 192
        2.70 -     4.05: 76
        4.05 -     5.40: 9
        5.40 -     6.74: 2
  Bond angle restraints: 13195
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  127.93   -6.23 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.32    3.21 1.18e+00 7.24e-01 7.47e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.91    4.28 1.76e+00 3.23e-01 5.92e+00
  angle pdb=" C1' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     110.58  103.84    6.74 2.79e+00 1.28e-01 5.83e+00
  angle pdb=" C4' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.06  106.03    5.03 2.50e+00 1.60e-01 4.05e+00
  ... (remaining 13190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 5695
       18.05 -    36.10: 188
       36.10 -    54.15: 42
       54.15 -    72.21: 1
       72.21 -    90.26: 3
  Dihedral angle restraints: 5929
    sinusoidal: 2424
      harmonic: 3505
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.26   90.26     1      1.00e+01 1.00e-02 9.64e+01
  dihedral pdb=" CB  ARG D  74 "
           pdb=" CG  ARG D  74 "
           pdb=" CD  ARG D  74 "
           pdb=" NE  ARG D  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.00   54.00     3      1.50e+01 4.44e-03 9.25e+00
  dihedral pdb=" N   GLU A 869 "
           pdb=" CA  GLU A 869 "
           pdb=" CB  GLU A 869 "
           pdb=" CG  GLU A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.49   53.49     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 5926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1274
       0.054 -    0.108: 160
       0.108 -    0.161: 34
       0.161 -    0.215: 1
       0.215 -    0.269: 2
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.95    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.88    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.71    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  67 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.06e+00
        pdb=" C   LEU D  67 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LEU D  67 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   HIS D  68 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 120 "   -0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO C 121 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO C 121 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 121 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  60 "   -0.015 5.00e-02 4.00e+02   2.33e-02 8.69e-01
        pdb=" N   PRO C  61 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO C  61 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C  61 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 108
        2.56 -     3.14: 7921
        3.14 -     3.73: 14486
        3.73 -     4.31: 20176
        4.31 -     4.90: 34385
  Nonbonded interactions: 77076
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     1.969 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.020 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O3G ATP A1103 "
     model   vdw
     2.020 2.170
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.102 2.170
  nonbonded pdb=" OE2 GLU A 468 "
            pdb="MG    MG A1102 "
     model   vdw
     2.137 2.170
  ... (remaining 77071 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.030
  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:             0.030
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.510
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.010   0.896   9741  Z= 0.496
  Angle     :  0.727  58.761  13197  Z= 0.364
  Chirality :  0.040   0.269   1471
  Planarity :  0.003   0.027   1707
  Dihedral  :  9.567  80.529   3662
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.83 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  2.54 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.41 (0.25), residues: 1199
  helix:  1.95 (0.25), residues: 476
  sheet:  0.28 (0.37), residues: 217
  loop :  0.37 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 133 
 TYR   0.009   0.001   TYR C 134 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.009   0.001   TRP A 702 
 HIS   0.004   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9738)
  covalent geometry    : angle       0.51127 (13195)
  SS BOND              : bond        0.89638 (    1)
  SS BOND              : angle      42.00556 (    2)
  hydrogen bonds       : bond        0.14974 (  454)
  hydrogen bonds       : angle       5.78454 ( 1272)
  Misc. bond           : bond        0.08646 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.9489 (m) cc_final: 0.9288 (m)
REVERT: A  162 ILE cc_start: 0.9638 (mt) cc_final: 0.9426 (mm)
REVERT: A  235 TYR cc_start: 0.8418 (m-80) cc_final: 0.8048 (m-10)
REVERT: A  345 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8892 (mm-30)
REVERT: A  353 ASP cc_start: 0.8282 (t0) cc_final: 0.7796 (m-30)
REVERT: A  357 MET cc_start: 0.8930 (mmm) cc_final: 0.8714 (mmm)
REVERT: A  445 ASN cc_start: 0.9149 (m-40) cc_final: 0.8497 (m-40)
REVERT: A  448 MET cc_start: 0.9487 (mmp) cc_final: 0.9212 (mmm)
REVERT: A  526 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8668 (t80)
REVERT: A  557 LEU cc_start: 0.9055 (mt) cc_final: 0.8851 (mp)
REVERT: A  562 LEU cc_start: 0.9130 (tp) cc_final: 0.8729 (pp)
REVERT: A  606 ILE cc_start: 0.9407 (mt) cc_final: 0.9140 (mm)
REVERT: A  622 ASP cc_start: 0.9196 (m-30) cc_final: 0.8778 (t0)
REVERT: A  919 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6914 (ptp-170)
REVERT: A  955 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8897 (m-40)
REVERT: C   28 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (t70)
REVERT: C   67 VAL cc_start: 0.9346 (t) cc_final: 0.9115 (t)
REVERT: C   88 ILE cc_start: 0.9083 (pt) cc_final: 0.8615 (mp)
REVERT: D   50 LEU cc_start: 0.8222 (mt) cc_final: 0.7606 (mt)
  outliers start: 25
  outliers final: 6
  residues processed: 197
  average time/residue: 0.0919
  time to fit residues: 24.4981
Evaluate side-chains
  87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  955 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   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 = 0.3227 r_free = 0.3227 target = 0.049822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.038310 restraints weight = 60462.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.039601 restraints weight = 35139.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.040504 restraints weight = 24036.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.041107 restraints weight = 18203.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.041576 restraints weight = 14938.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9741  Z= 0.190
  Angle     :  0.626   8.983  13197  Z= 0.323
  Chirality :  0.044   0.188   1471
  Planarity :  0.004   0.060   1707
  Dihedral  :  5.844  60.759   1341
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  7.73 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.49 (0.25), residues: 1199
  helix:  1.87 (0.24), residues: 499
  sheet:  0.65 (0.38), residues: 204
  loop :  0.34 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 406 
 TYR   0.018   0.001   TYR A  25 
 PHE   0.012   0.001   PHE A 237 
 TRP   0.010   0.002   TRP C  33 
 HIS   0.005   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9738)
  covalent geometry    : angle       0.62440 (13195)
  SS BOND              : bond        0.01361 (    1)
  SS BOND              : angle       3.95879 (    2)
  hydrogen bonds       : bond        0.04297 (  454)
  hydrogen bonds       : angle       4.83289 ( 1272)
  Misc. bond           : bond        0.00462 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 TYR cc_start: 0.8270 (m-80) cc_final: 0.7990 (m-10)
REVERT: A  253 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8090 (p)
REVERT: A  285 MET cc_start: 0.8645 (pmm) cc_final: 0.8079 (mpp)
REVERT: A  345 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8911 (mm-30)
REVERT: A  353 ASP cc_start: 0.8146 (t0) cc_final: 0.7840 (m-30)
REVERT: A  445 ASN cc_start: 0.9148 (m-40) cc_final: 0.8658 (m-40)
REVERT: A  464 MET cc_start: 0.8867 (pmt) cc_final: 0.8212 (pmt)
REVERT: A  526 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8436 (t80)
REVERT: A  562 LEU cc_start: 0.9124 (tp) cc_final: 0.8908 (tp)
REVERT: A  622 ASP cc_start: 0.9508 (m-30) cc_final: 0.8776 (t0)
REVERT: A  626 MET cc_start: 0.9199 (mmp) cc_final: 0.8799 (mmp)
REVERT: A  707 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7537 (mtt90)
REVERT: A  869 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8656 (mm-30)
REVERT: A  906 MET cc_start: 0.7521 (tmm) cc_final: 0.7289 (tmm)
REVERT: C   38 MET cc_start: 0.7756 (mmm) cc_final: 0.6917 (mmm)
REVERT: C  130 ASP cc_start: 0.8810 (t0) cc_final: 0.8304 (p0)
REVERT: D   73 LEU cc_start: 0.9243 (pt) cc_final: 0.8972 (mt)
  outliers start: 23
  outliers final: 11
  residues processed: 100
  average time/residue: 0.0789
  time to fit residues: 11.4194
Evaluate side-chains
  79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 104 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.049662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.038329 restraints weight = 60937.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.039610 restraints weight = 35410.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.040495 restraints weight = 24262.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.041101 restraints weight = 18403.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.041554 restraints weight = 15051.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9741  Z= 0.147
  Angle     :  0.570   9.974  13197  Z= 0.287
  Chirality :  0.042   0.153   1471
  Planarity :  0.004   0.043   1707
  Dihedral  :  5.535  57.641   1334
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.14 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.58 (0.25), residues: 1199
  helix:  1.90 (0.24), residues: 500
  sheet:  0.71 (0.38), residues: 205
  loop :  0.43 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C   5 
 TYR   0.014   0.001   TYR A 250 
 PHE   0.022   0.001   PHE A 633 
 TRP   0.007   0.001   TRP C  93 
 HIS   0.004   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9738)
  covalent geometry    : angle       0.56846 (13195)
  SS BOND              : bond        0.00901 (    1)
  SS BOND              : angle       3.03761 (    2)
  hydrogen bonds       : bond        0.03662 (  454)
  hydrogen bonds       : angle       4.62788 ( 1272)
  Misc. bond           : bond        0.00012 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7975 (tpt)
REVERT: A  235 TYR cc_start: 0.8303 (m-80) cc_final: 0.8049 (m-10)
REVERT: A  285 MET cc_start: 0.8623 (pmm) cc_final: 0.8119 (mpp)
REVERT: A  345 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8871 (mm-30)
REVERT: A  353 ASP cc_start: 0.8151 (t0) cc_final: 0.7766 (m-30)
REVERT: A  445 ASN cc_start: 0.9084 (m-40) cc_final: 0.8570 (m-40)
REVERT: A  464 MET cc_start: 0.8862 (pmt) cc_final: 0.8278 (pmt)
REVERT: A  526 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8402 (t80)
REVERT: A  562 LEU cc_start: 0.9108 (tp) cc_final: 0.8870 (tp)
REVERT: A  622 ASP cc_start: 0.9485 (m-30) cc_final: 0.8753 (t0)
REVERT: A  626 MET cc_start: 0.9293 (mmp) cc_final: 0.8743 (mmp)
REVERT: A  707 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7702 (mtt180)
REVERT: A  906 MET cc_start: 0.7509 (tmm) cc_final: 0.7165 (tmm)
REVERT: A  945 LEU cc_start: 0.9500 (mt) cc_final: 0.9184 (mt)
REVERT: C   52 LEU cc_start: 0.9144 (mp) cc_final: 0.8878 (mt)
REVERT: C  130 ASP cc_start: 0.8765 (t0) cc_final: 0.8387 (p0)
REVERT: D    1 MET cc_start: 0.4879 (tmm) cc_final: 0.4655 (tmm)
REVERT: D   50 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8693 (mp)
REVERT: D   73 LEU cc_start: 0.9261 (pt) cc_final: 0.9030 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0791
  time to fit residues: 9.3772
Evaluate side-chains
  76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 100 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.049681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.038334 restraints weight = 61473.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.039606 restraints weight = 35518.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.040486 restraints weight = 24250.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041114 restraints weight = 18431.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.041536 restraints weight = 15055.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9741  Z= 0.141
  Angle     :  0.554   8.836  13197  Z= 0.281
  Chirality :  0.042   0.226   1471
  Planarity :  0.004   0.053   1707
  Dihedral  :  5.413  57.091   1333
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.14 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.58 (0.25), residues: 1199
  helix:  1.85 (0.24), residues: 500
  sheet:  0.65 (0.37), residues: 205
  loop :  0.52 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C   5 
 TYR   0.009   0.001   TYR A  25 
 PHE   0.014   0.001   PHE A 633 
 TRP   0.006   0.001   TRP A 702 
 HIS   0.002   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9738)
  covalent geometry    : angle       0.55360 (13195)
  SS BOND              : bond        0.00591 (    1)
  SS BOND              : angle       2.36649 (    2)
  hydrogen bonds       : bond        0.03413 (  454)
  hydrogen bonds       : angle       4.63129 ( 1272)
  Misc. bond           : bond        0.00076 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8823 (p)
REVERT: A  235 TYR cc_start: 0.8299 (m-80) cc_final: 0.8014 (m-10)
REVERT: A  285 MET cc_start: 0.8620 (pmm) cc_final: 0.8084 (mpp)
REVERT: A  353 ASP cc_start: 0.8230 (t0) cc_final: 0.7765 (m-30)
REVERT: A  445 ASN cc_start: 0.9100 (m-40) cc_final: 0.8565 (m-40)
REVERT: A  464 MET cc_start: 0.8857 (pmt) cc_final: 0.8314 (pmt)
REVERT: A  526 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8329 (t80)
REVERT: A  562 LEU cc_start: 0.9122 (tp) cc_final: 0.8880 (tp)
REVERT: A  622 ASP cc_start: 0.9482 (m-30) cc_final: 0.8756 (t0)
REVERT: A  626 MET cc_start: 0.9345 (mmp) cc_final: 0.8861 (mmp)
REVERT: A  869 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: A  906 MET cc_start: 0.7444 (tmm) cc_final: 0.7112 (tmm)
REVERT: C   52 LEU cc_start: 0.9178 (mp) cc_final: 0.8930 (mt)
REVERT: C  130 ASP cc_start: 0.8750 (t0) cc_final: 0.8453 (p0)
REVERT: D    1 MET cc_start: 0.4891 (tmm) cc_final: 0.4090 (tmm)
REVERT: D   72 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7133 (ttp80)
REVERT: D   73 LEU cc_start: 0.9285 (pt) cc_final: 0.8934 (mt)
  outliers start: 25
  outliers final: 13
  residues processed: 90
  average time/residue: 0.0747
  time to fit residues: 9.7168
Evaluate side-chains
  80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   72 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.049779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.038367 restraints weight = 61467.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.039631 restraints weight = 35818.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.040531 restraints weight = 24586.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041159 restraints weight = 18716.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.041585 restraints weight = 15318.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9741  Z= 0.122
  Angle     :  0.561   8.778  13197  Z= 0.281
  Chirality :  0.042   0.219   1471
  Planarity :  0.004   0.050   1707
  Dihedral  :  5.282  58.992   1333
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.43 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.68 (0.26), residues: 1199
  helix:  1.95 (0.24), residues: 500
  sheet:  0.71 (0.37), residues: 211
  loop :  0.57 (0.31), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 406 
 TYR   0.011   0.001   TYR A 250 
 PHE   0.013   0.001   PHE A 633 
 TRP   0.006   0.001   TRP A 702 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9738)
  covalent geometry    : angle       0.56039 (13195)
  SS BOND              : bond        0.00749 (    1)
  SS BOND              : angle       2.04023 (    2)
  hydrogen bonds       : bond        0.03298 (  454)
  hydrogen bonds       : angle       4.50442 ( 1272)
  Misc. bond           : bond        0.00058 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8693 (ppp)
REVERT: A  112 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8798 (p)
REVERT: A  218 MET cc_start: 0.4980 (mmm) cc_final: 0.4610 (mmm)
REVERT: A  235 TYR cc_start: 0.8327 (m-80) cc_final: 0.8038 (m-10)
REVERT: A  285 MET cc_start: 0.8643 (pmm) cc_final: 0.8315 (pmm)
REVERT: A  345 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8808 (mm-30)
REVERT: A  353 ASP cc_start: 0.8188 (t0) cc_final: 0.7741 (m-30)
REVERT: A  445 ASN cc_start: 0.9113 (m-40) cc_final: 0.8576 (m-40)
REVERT: A  464 MET cc_start: 0.8904 (pmt) cc_final: 0.8383 (pmt)
REVERT: A  526 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8326 (t80)
REVERT: A  562 LEU cc_start: 0.9126 (tp) cc_final: 0.8897 (tp)
REVERT: A  622 ASP cc_start: 0.9488 (m-30) cc_final: 0.8757 (t0)
REVERT: A  626 MET cc_start: 0.9352 (mmp) cc_final: 0.8872 (mmp)
REVERT: A  707 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8347 (mtt180)
REVERT: A  869 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8686 (mm-30)
REVERT: A  906 MET cc_start: 0.7418 (tmm) cc_final: 0.7077 (tmm)
REVERT: C   52 LEU cc_start: 0.9210 (mp) cc_final: 0.8997 (mt)
REVERT: C  130 ASP cc_start: 0.8736 (t0) cc_final: 0.8480 (p0)
REVERT: D    1 MET cc_start: 0.5408 (tmm) cc_final: 0.4525 (tmm)
REVERT: D   72 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7165 (ttp80)
REVERT: D   73 LEU cc_start: 0.9293 (pt) cc_final: 0.8971 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 82
  average time/residue: 0.0718
  time to fit residues: 8.6292
Evaluate side-chains
  81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   72 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.049599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.038239 restraints weight = 61469.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.039480 restraints weight = 36367.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.040387 restraints weight = 25228.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.040980 restraints weight = 19190.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.041414 restraints weight = 15781.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9741  Z= 0.129
  Angle     :  0.546   9.523  13197  Z= 0.275
  Chirality :  0.042   0.216   1471
  Planarity :  0.004   0.050   1707
  Dihedral  :  5.195  59.379   1333
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  :  9.05 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.72 (0.26), residues: 1199
  helix:  2.03 (0.24), residues: 500
  sheet:  0.64 (0.37), residues: 211
  loop :  0.57 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   8 
 TYR   0.014   0.001   TYR D  59 
 PHE   0.014   0.001   PHE A 934 
 TRP   0.005   0.001   TRP A 702 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9738)
  covalent geometry    : angle       0.54521 (13195)
  SS BOND              : bond        0.00451 (    1)
  SS BOND              : angle       1.76451 (    2)
  hydrogen bonds       : bond        0.03148 (  454)
  hydrogen bonds       : angle       4.45117 ( 1272)
  Misc. bond           : bond        0.00063 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8709 (ppp)
REVERT: A  112 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8799 (p)
REVERT: A  196 MET cc_start: 0.6158 (mmm) cc_final: 0.5850 (mmm)
REVERT: A  218 MET cc_start: 0.4903 (mmm) cc_final: 0.4459 (mmm)
REVERT: A  235 TYR cc_start: 0.8292 (m-80) cc_final: 0.7995 (m-10)
REVERT: A  285 MET cc_start: 0.8534 (pmm) cc_final: 0.8209 (pmm)
REVERT: A  353 ASP cc_start: 0.8202 (t0) cc_final: 0.7800 (m-30)
REVERT: A  445 ASN cc_start: 0.9123 (m-40) cc_final: 0.8600 (m-40)
REVERT: A  464 MET cc_start: 0.8933 (pmt) cc_final: 0.8458 (pmt)
REVERT: A  526 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8269 (t80)
REVERT: A  562 LEU cc_start: 0.9083 (tp) cc_final: 0.8839 (tp)
REVERT: A  618 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8027 (tppt)
REVERT: A  622 ASP cc_start: 0.9459 (m-30) cc_final: 0.8755 (t0)
REVERT: A  626 MET cc_start: 0.9313 (mmp) cc_final: 0.8848 (mmp)
REVERT: A  707 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8420 (mtt180)
REVERT: A  908 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8158 (p)
REVERT: D    1 MET cc_start: 0.5308 (tmm) cc_final: 0.4196 (tmm)
REVERT: D   72 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7187 (ttp80)
REVERT: D   73 LEU cc_start: 0.9291 (pt) cc_final: 0.8981 (mt)
  outliers start: 31
  outliers final: 16
  residues processed: 87
  average time/residue: 0.0749
  time to fit residues: 9.6234
Evaluate side-chains
  80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   72 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0050
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.9400

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.048811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.037535 restraints weight = 62352.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.038748 restraints weight = 36757.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.039603 restraints weight = 25474.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.040122 restraints weight = 19450.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.040563 restraints weight = 16193.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9741  Z= 0.187
  Angle     :  0.600   9.793  13197  Z= 0.303
  Chirality :  0.042   0.161   1471
  Planarity :  0.004   0.051   1707
  Dihedral  :  5.354  59.919   1333
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.80 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.59 (0.25), residues: 1199
  helix:  1.94 (0.24), residues: 501
  sheet:  0.49 (0.37), residues: 203
  loop :  0.52 (0.30), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   5 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.014   0.001   PHE A 633 
 TRP   0.007   0.001   TRP A 702 
 HIS   0.003   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 9738)
  covalent geometry    : angle       0.59967 (13195)
  SS BOND              : bond        0.00422 (    1)
  SS BOND              : angle       1.79578 (    2)
  hydrogen bonds       : bond        0.03334 (  454)
  hydrogen bonds       : angle       4.61695 ( 1272)
  Misc. bond           : bond        0.00063 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 60
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 MET cc_start: 0.4167 (mmm) cc_final: 0.3955 (mmm)
REVERT: A  235 TYR cc_start: 0.8378 (m-80) cc_final: 0.8062 (m-10)
REVERT: A  285 MET cc_start: 0.8558 (pmm) cc_final: 0.8208 (pmm)
REVERT: A  445 ASN cc_start: 0.9134 (m-40) cc_final: 0.8605 (m-40)
REVERT: A  464 MET cc_start: 0.8938 (pmt) cc_final: 0.8464 (pmt)
REVERT: A  526 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8248 (t80)
REVERT: A  562 LEU cc_start: 0.9034 (tp) cc_final: 0.8786 (tp)
REVERT: A  606 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9092 (mp)
REVERT: A  618 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8111 (tppt)
REVERT: A  622 ASP cc_start: 0.9478 (m-30) cc_final: 0.8777 (t0)
REVERT: A  626 MET cc_start: 0.9284 (mmp) cc_final: 0.8864 (mmp)
REVERT: A  707 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8461 (mtt180)
REVERT: D    1 MET cc_start: 0.5154 (tmm) cc_final: 0.4216 (tmm)
REVERT: D   43 LEU cc_start: 0.9159 (tp) cc_final: 0.8881 (tp)
REVERT: D   72 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7339 (ttp80)
  outliers start: 27
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0855
  time to fit residues: 10.1710
Evaluate side-chains
  77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   72 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0070
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.049759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.038555 restraints weight = 60998.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.039785 restraints weight = 36215.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.040620 restraints weight = 25085.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.041213 restraints weight = 19271.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.041604 restraints weight = 15856.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9741  Z= 0.107
  Angle     :  0.565   9.050  13197  Z= 0.281
  Chirality :  0.042   0.290   1471
  Planarity :  0.004   0.052   1707
  Dihedral  :  5.141  57.429   1333
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.46 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.56 (0.25), residues: 1199
  helix:  1.96 (0.24), residues: 502
  sheet:  0.40 (0.37), residues: 209
  loop :  0.49 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 406 
 TYR   0.008   0.001   TYR A 627 
 PHE   0.013   0.001   PHE A 633 
 TRP   0.007   0.001   TRP A 702 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9738)
  covalent geometry    : angle       0.56485 (13195)
  SS BOND              : bond        0.00591 (    1)
  SS BOND              : angle       1.51975 (    2)
  hydrogen bonds       : bond        0.03054 (  454)
  hydrogen bonds       : angle       4.40533 ( 1272)
  Misc. bond           : bond        0.00057 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8687 (ppp)
REVERT: A  235 TYR cc_start: 0.8346 (m-80) cc_final: 0.8010 (m-10)
REVERT: A  285 MET cc_start: 0.8539 (pmm) cc_final: 0.8218 (pmm)
REVERT: A  345 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8781 (mm-30)
REVERT: A  353 ASP cc_start: 0.7955 (t0) cc_final: 0.7729 (m-30)
REVERT: A  445 ASN cc_start: 0.9103 (m-40) cc_final: 0.8580 (m-40)
REVERT: A  464 MET cc_start: 0.8947 (pmt) cc_final: 0.8469 (pmt)
REVERT: A  562 LEU cc_start: 0.9010 (tp) cc_final: 0.8761 (tp)
REVERT: A  606 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9157 (mp)
REVERT: A  618 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8231 (tppt)
REVERT: A  622 ASP cc_start: 0.9444 (m-30) cc_final: 0.8733 (t0)
REVERT: A  626 MET cc_start: 0.9296 (mmp) cc_final: 0.8861 (mmp)
REVERT: D    1 MET cc_start: 0.5422 (tmm) cc_final: 0.4439 (tmm)
REVERT: D   62 GLN cc_start: 0.6575 (pt0) cc_final: 0.6327 (pt0)
REVERT: D   72 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7180 (ttp80)
REVERT: D   73 LEU cc_start: 0.9306 (pt) cc_final: 0.9067 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 79
  average time/residue: 0.0889
  time to fit residues: 10.0905
Evaluate side-chains
  77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   72 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0270
   chunk 62 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0170
   chunk 118 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5676

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.049972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.038770 restraints weight = 61065.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.039992 restraints weight = 36393.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.040831 restraints weight = 25250.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.041442 restraints weight = 19331.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.041853 restraints weight = 15820.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9741  Z= 0.106
  Angle     :  0.584   9.942  13197  Z= 0.290
  Chirality :  0.042   0.307   1471
  Planarity :  0.004   0.057   1707
  Dihedral  :  4.890  56.045   1331
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.84 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.56 (0.25), residues: 1199
  helix:  1.96 (0.24), residues: 501
  sheet:  0.41 (0.37), residues: 209
  loop :  0.48 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 707 
 TYR   0.009   0.001   TYR D  59 
 PHE   0.012   0.001   PHE A 633 
 TRP   0.006   0.001   TRP C  33 
 HIS   0.002   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9738)
  covalent geometry    : angle       0.58414 (13195)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       1.40280 (    2)
  hydrogen bonds       : bond        0.02960 (  454)
  hydrogen bonds       : angle       4.31922 ( 1272)
  Misc. bond           : bond        0.00145 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8661 (ppp)
REVERT: A  235 TYR cc_start: 0.8341 (m-80) cc_final: 0.7999 (m-10)
REVERT: A  285 MET cc_start: 0.8569 (pmm) cc_final: 0.8216 (pmm)
REVERT: A  345 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8788 (mm-30)
REVERT: A  353 ASP cc_start: 0.7954 (t0) cc_final: 0.7747 (m-30)
REVERT: A  445 ASN cc_start: 0.9102 (m-40) cc_final: 0.8572 (m-40)
REVERT: A  464 MET cc_start: 0.8933 (pmt) cc_final: 0.8512 (pmt)
REVERT: A  562 LEU cc_start: 0.9021 (tp) cc_final: 0.8764 (tp)
REVERT: A  606 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9149 (mp)
REVERT: A  618 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8230 (tppt)
REVERT: A  622 ASP cc_start: 0.9444 (m-30) cc_final: 0.8733 (t0)
REVERT: A  626 MET cc_start: 0.9315 (mmp) cc_final: 0.8853 (mmp)
  outliers start: 16
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0902
  time to fit residues: 9.3636
Evaluate side-chains
  74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   31 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0370
   chunk 91 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.3221 r_free = 0.3221 target = 0.050081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.038870 restraints weight = 61182.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.040077 restraints weight = 36394.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.040899 restraints weight = 25372.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.041506 restraints weight = 19589.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.041885 restraints weight = 16076.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9741  Z= 0.107
  Angle     :  0.595  10.871  13197  Z= 0.290
  Chirality :  0.044   0.421   1471
  Planarity :  0.004   0.057   1707
  Dihedral  :  4.598  51.863   1330
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.22 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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: 1199
  helix:  1.97 (0.24), residues: 501
  sheet:  0.47 (0.37), residues: 207
  loop :  0.51 (0.30), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 481 
 TYR   0.008   0.001   TYR A 627 
 PHE   0.012   0.001   PHE A 633 
 TRP   0.006   0.001   TRP C  33 
 HIS   0.002   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9738)
  covalent geometry    : angle       0.59289 (13195)
  SS BOND              : bond        0.00429 (    1)
  SS BOND              : angle       4.48331 (    2)
  hydrogen bonds       : bond        0.02851 (  454)
  hydrogen bonds       : angle       4.27839 ( 1272)
  Misc. bond           : bond        0.00167 (    2)

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 TYR cc_start: 0.8358 (m-80) cc_final: 0.7997 (m-10)
REVERT: A  285 MET cc_start: 0.8553 (pmm) cc_final: 0.8204 (pmm)
REVERT: A  345 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8778 (mm-30)
REVERT: A  445 ASN cc_start: 0.9060 (m-40) cc_final: 0.8528 (m-40)
REVERT: A  464 MET cc_start: 0.8958 (pmt) cc_final: 0.8554 (pmt)
REVERT: A  562 LEU cc_start: 0.9004 (tp) cc_final: 0.8748 (tp)
REVERT: A  606 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9180 (mp)
REVERT: A  618 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8206 (tppt)
REVERT: A  622 ASP cc_start: 0.9428 (m-30) cc_final: 0.8730 (t0)
REVERT: A  626 MET cc_start: 0.9274 (mmp) cc_final: 0.8810 (mmp)
  outliers start: 15
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0874
  time to fit residues: 8.5927
Evaluate side-chains
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue   81 ASN
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue   39 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 79 optimal weight:    0.5980
   chunk 116 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3210 r_free = 0.3210 target = 0.049646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.038622 restraints weight = 61374.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.039838 restraints weight = 36413.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.040660 restraints weight = 25267.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041247 restraints weight = 19427.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.041610 restraints weight = 15924.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9741  Z= 0.124
  Angle     :  0.594  10.342  13197  Z= 0.291
  Chirality :  0.043   0.324   1471
  Planarity :  0.004   0.050   1707
  Dihedral  :  4.586  51.064   1330
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.22 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.62 (0.26), residues: 1199
  helix:  1.99 (0.24), residues: 501
  sheet:  0.46 (0.38), residues: 205
  loop :  0.52 (0.30), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 481 
 TYR   0.009   0.001   TYR D  59 
 PHE   0.013   0.001   PHE A 633 
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9738)
  covalent geometry    : angle       0.59267 (13195)
  SS BOND              : bond        0.00910 (    1)
  SS BOND              : angle       3.13089 (    2)
  hydrogen bonds       : bond        0.02874 (  454)
  hydrogen bonds       : angle       4.28968 ( 1272)
  Misc. bond           : bond        0.00016 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 1234.59 seconds
wall clock time: 21 minutes 53.75 seconds (1313.75 seconds total)