Starting phenix.real_space_refine
on Thu Jan 16 13:47:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5o_44219/01_2025/9b5o_44219.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.059
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 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.75, per 1000 atoms: 0.71
  Number of scatterers: 9527
  At special positions: 0
  Unit cell: (91.504, 100.016, 120.232, 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=2.89

  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: 2.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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:
      52 helices and 10 sheets defined
      47.6% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.839A  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 73 through 79
      removed outlier: 3.685A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.880A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.297A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.560A  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: 3.738A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 3.573A  pdb=" N   ASP A 223 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.353A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.629A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.622A  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 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.391A  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: 3.682A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.509A  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
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.763A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.847A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.523A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.518A  pdb=" N   SER A 581 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 582'
    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 630
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.680A  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
      removed outlier: 3.509A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.580A  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: 4.002A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 3.862A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
    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: 3.625A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.557A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 879 through 883'
    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: 6.850A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.398A  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: 4.211A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.227A  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: 4.211A  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: 6.511A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.275A  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 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.406A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.515A  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 922
      removed outlier: 6.406A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.442A  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 26
      removed outlier: 3.653A  pdb=" N   GLY C  24 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16

    468 hydrogen bonds defined for protein.
    1275 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: 3.79

  Time building geometry restraints manager: 2.92 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: 5650
        1.54 -     1.67: 117
        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 1.30e+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 2.81e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 8.69e-01
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.133  0.018 2.00e-02 2.50e+03 8.35e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.406  0.010 1.30e-02 5.92e+03 5.66e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 13037
        1.30 -     2.60: 79
        2.60 -     3.90: 69
        3.90 -     5.20: 7
        5.20 -     6.51: 3
  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  128.21   -6.51 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.20    3.33 1.18e+00 7.24e-01 8.02e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.74    4.45 1.76e+00 3.23e-01 6.39e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.67    6.16 2.67e+00 1.40e-01 5.32e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  106.25    5.58 2.67e+00 1.40e-01 4.37e+00
  ... (remaining 13190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5722
       17.98 -    35.95: 166
       35.95 -    53.92: 31
       53.92 -    71.90: 8
       71.90 -    89.87: 2
  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 -146.74   60.74     1      1.00e+01 1.00e-02 4.91e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.17   15.83     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  LEU A 870 "
           pdb=" CB  LEU A 870 "
           pdb=" CG  LEU A 870 "
           pdb=" CD1 LEU A 870 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.22  -59.22     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1268
       0.052 -    0.104: 145
       0.104 -    0.156: 55
       0.156 -    0.208: 0
       0.208 -    0.260: 3
  Chirality restraints: 1471
  Sorted by residual:
  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   -2.89    0.26 2.00e-01 2.50e+01 1.69e+00
  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   -2.94    0.26 2.00e-01 2.50e+01 1.66e+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   -2.72    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO C  95 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  17 "    0.018 5.00e-02 4.00e+02   2.70e-02 1.17e+00
        pdb=" N   PRO C  18 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO C  18 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C  18 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 259 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.42e-01
        pdb=" N   PRO A 260 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 260 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 260 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 67
        2.60 -     3.17: 8137
        3.17 -     3.75: 13881
        3.75 -     4.32: 20449
        4.32 -     4.90: 34623
  Nonbonded interactions: 77157
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.022 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.039 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.053 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O3G ATP A1103 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" OD2 ASP A 463 "
            pdb=" O3' ATP A1103 "
     model   vdw
     2.172 3.040
  ... (remaining 77152 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.030
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.040
  Process input model:                     26.600
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
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      :  0.003   0.072   9738  Z= 0.187
  Angle     :  0.438   6.505  13195  Z= 0.220
  Chirality :  0.041   0.260   1471
  Planarity :  0.003   0.031   1707
  Dihedral  :  9.279  89.875   3662
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  2.17 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1199
  helix:  1.91 (0.25), residues: 493
  sheet:  0.36 (0.36), residues: 196
  loop :  0.43 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 608 
 HIS   0.002   0.000   HIS A 988 
 PHE   0.009   0.001   PHE A 842 
 TYR   0.006   0.001   TYR A  81 
 ARG   0.001   0.000   ARG A 409 

*********************** 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
  183 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 174
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 MET cc_start: 0.5436 (mtt) cc_final: 0.5196 (mmt)
REVERT: A  227 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7401 (mmt90)
REVERT: A  562 LEU cc_start: 0.8946 (tp) cc_final: 0.8711 (tp)
REVERT: A  567 ASN cc_start: 0.8789 (p0) cc_final: 0.8580 (p0)
REVERT: A  643 ASN cc_start: 0.8425 (m-40) cc_final: 0.8200 (t0)
REVERT: A  649 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8103 (mm-30)
REVERT: A  937 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8107 (mp0)
REVERT: A  994 CYS cc_start: 0.7878 (m) cc_final: 0.7428 (m)
REVERT: C   59 ASP cc_start: 0.7994 (m-30) cc_final: 0.7578 (t0)
REVERT: C  116 ASP cc_start: 0.8084 (m-30) cc_final: 0.7498 (t0)
REVERT: C  117 ASP cc_start: 0.8755 (t0) cc_final: 0.8494 (t70)
REVERT: C  130 ASP cc_start: 0.6472 (t0) cc_final: 0.5956 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 180
  average time/residue: 0.3436
  time to fit residues: 79.3923
Evaluate side-chains
  102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.135997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.085643 restraints weight = 13614.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 3.03
r_work: 0.2914 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9738  Z= 0.276
  Angle     :  0.545   6.929  13195  Z= 0.278
  Chirality :  0.044   0.265   1471
  Planarity :  0.004   0.046   1707
  Dihedral  :  6.327  87.002   1333
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  6.88 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1199
  helix:  1.79 (0.24), residues: 503
  sheet:  0.47 (0.36), residues: 201
  loop :  0.39 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.009   0.001   HIS D  68 
 PHE   0.018   0.001   PHE A 956 
 TYR   0.011   0.001   TYR C  74 
 ARG   0.008   0.001   ARG A 406 

*********************** 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
  122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.120 
Fit side-chains
REVERT: A   80 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7431 (tm-30)
REVERT: A  197 LEU cc_start: 0.6283 (mp) cc_final: 0.5708 (mt)
REVERT: A  464 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7538 (pmt)
REVERT: A  567 ASN cc_start: 0.8678 (p0) cc_final: 0.8394 (p0)
REVERT: A  603 GLU cc_start: 0.8701 (mp0) cc_final: 0.8301 (mp0)
REVERT: A  649 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8450 (mm-30)
REVERT: A  739 LYS cc_start: 0.8979 (tppt) cc_final: 0.8464 (ttpp)
REVERT: A  937 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8727 (mm-30)
REVERT: C    7 ASN cc_start: 0.8873 (t0) cc_final: 0.8454 (p0)
REVERT: C   59 ASP cc_start: 0.8148 (m-30) cc_final: 0.7616 (t0)
REVERT: C  116 ASP cc_start: 0.8027 (m-30) cc_final: 0.7628 (t0)
REVERT: D   42 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7251 (mtp180)
  outliers start: 17
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2881
  time to fit residues: 45.0410
Evaluate side-chains
  99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 67 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.136349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.085836 restraints weight = 13794.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 3.06
r_work: 0.2916 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9738  Z= 0.221
  Angle     :  0.508   8.384  13195  Z= 0.262
  Chirality :  0.043   0.152   1471
  Planarity :  0.004   0.045   1707
  Dihedral  :  6.029  74.606   1332
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.92 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1199
  helix:  1.76 (0.24), residues: 498
  sheet:  0.58 (0.36), residues: 201
  loop :  0.39 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  93 
 HIS   0.003   0.001   HIS D  68 
 PHE   0.014   0.001   PHE A 956 
 TYR   0.010   0.001   TYR C 134 
 ARG   0.009   0.001   ARG A 841 

*********************** 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
  110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.7418 (tm-30)
REVERT: A  154 ASP cc_start: 0.7747 (m-30) cc_final: 0.7494 (m-30)
REVERT: A  218 MET cc_start: 0.4374 (mmt) cc_final: 0.3895 (mmt)
REVERT: A  464 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7524 (pmt)
REVERT: A  567 ASN cc_start: 0.8660 (p0) cc_final: 0.8382 (p0)
REVERT: A  603 GLU cc_start: 0.8675 (mp0) cc_final: 0.8264 (mp0)
REVERT: A  649 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8413 (mm-30)
REVERT: A  739 LYS cc_start: 0.9006 (tppt) cc_final: 0.8571 (ttpp)
REVERT: C   38 MET cc_start: 0.8348 (mmm) cc_final: 0.7931 (mmm)
REVERT: C   59 ASP cc_start: 0.8091 (m-30) cc_final: 0.7563 (t0)
REVERT: C   92 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6355 (tm-30)
REVERT: C  116 ASP cc_start: 0.7967 (m-30) cc_final: 0.7581 (t0)
REVERT: D   42 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7278 (mtp180)
  outliers start: 13
  outliers final: 7
  residues processed: 106
  average time/residue: 0.3131
  time to fit residues: 43.5041
Evaluate side-chains
  99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0270
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0470
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 79 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.137353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.086760 restraints weight = 13644.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 3.06
r_work: 0.2936 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9738  Z= 0.158
  Angle     :  0.485   7.209  13195  Z= 0.250
  Chirality :  0.042   0.272   1471
  Planarity :  0.004   0.062   1707
  Dihedral  :  5.722  79.294   1329
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.63 %
    Favored  : 91.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1199
  helix:  1.81 (0.24), residues: 498
  sheet:  0.64 (0.36), residues: 207
  loop :  0.35 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  93 
 HIS   0.003   0.000   HIS D  68 
 PHE   0.011   0.001   PHE A 956 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.008   0.001   ARG C 143 

*********************** 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
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASP cc_start: 0.7713 (m-30) cc_final: 0.7457 (m-30)
REVERT: A  218 MET cc_start: 0.4497 (mmt) cc_final: 0.4089 (mmt)
REVERT: A  227 ARG cc_start: 0.6646 (mmm-85) cc_final: 0.6174 (mmt90)
REVERT: A  464 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7568 (pmt)
REVERT: A  567 ASN cc_start: 0.8626 (p0) cc_final: 0.8382 (p0)
REVERT: A  603 GLU cc_start: 0.8654 (mp0) cc_final: 0.8227 (mp0)
REVERT: A  649 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8382 (mm-30)
REVERT: A  739 LYS cc_start: 0.9051 (tppt) cc_final: 0.8616 (ttpp)
REVERT: C    7 ASN cc_start: 0.8913 (t0) cc_final: 0.8546 (p0)
REVERT: C   38 MET cc_start: 0.8347 (mmm) cc_final: 0.7895 (mmm)
REVERT: C   59 ASP cc_start: 0.8007 (m-30) cc_final: 0.7408 (t70)
REVERT: C   72 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7733 (mtm-85)
REVERT: C   92 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6430 (tm-30)
REVERT: C  116 ASP cc_start: 0.7934 (m-30) cc_final: 0.7559 (t0)
REVERT: C  131 ARG cc_start: 0.7422 (tpt170) cc_final: 0.6916 (tpt90)
REVERT: D   42 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7201 (mtp180)
  outliers start: 11
  outliers final: 5
  residues processed: 102
  average time/residue: 0.3091
  time to fit residues: 41.6231
Evaluate side-chains
  98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 76 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 104 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0870
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.136620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.085944 restraints weight = 13600.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.06
r_work: 0.2919 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9738  Z= 0.197
  Angle     :  0.499   9.329  13195  Z= 0.254
  Chirality :  0.042   0.194   1471
  Planarity :  0.004   0.061   1707
  Dihedral  :  5.668  76.030   1329
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.39 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1199
  helix:  1.84 (0.24), residues: 499
  sheet:  0.52 (0.35), residues: 210
  loop :  0.38 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  93 
 HIS   0.003   0.001   HIS D  68 
 PHE   0.011   0.001   PHE D   4 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.011   0.000   ARG A 841 

*********************** 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
  109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7450 (tm-30)
REVERT: A  154 ASP cc_start: 0.7747 (m-30) cc_final: 0.7507 (m-30)
REVERT: A  333 GLN cc_start: 0.8558 (mp10) cc_final: 0.7446 (tm-30)
REVERT: A  464 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7601 (pmt)
REVERT: A  567 ASN cc_start: 0.8653 (p0) cc_final: 0.8404 (p0)
REVERT: A  603 GLU cc_start: 0.8676 (mp0) cc_final: 0.8383 (mp0)
REVERT: A  649 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8370 (mm-30)
REVERT: A  739 LYS cc_start: 0.9107 (tppt) cc_final: 0.8652 (ttpp)
REVERT: C    7 ASN cc_start: 0.8835 (t0) cc_final: 0.8340 (t0)
REVERT: C   38 MET cc_start: 0.8364 (mmm) cc_final: 0.7886 (mmm)
REVERT: C   59 ASP cc_start: 0.8010 (m-30) cc_final: 0.7436 (t70)
REVERT: C   72 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7843 (mtm-85)
REVERT: C   92 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6506 (tm-30)
REVERT: C  116 ASP cc_start: 0.7920 (m-30) cc_final: 0.7567 (t0)
REVERT: D   42 ARG cc_start: 0.7545 (mtm180) cc_final: 0.7176 (mtp180)
  outliers start: 14
  outliers final: 7
  residues processed: 105
  average time/residue: 0.2948
  time to fit residues: 41.3630
Evaluate side-chains
  97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0370
   chunk 100 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0070
   chunk 37 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.137123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.086596 restraints weight = 13679.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 3.05
r_work: 0.2937 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9738  Z= 0.168
  Angle     :  0.499   8.560  13195  Z= 0.252
  Chirality :  0.042   0.255   1471
  Planarity :  0.004   0.056   1707
  Dihedral  :  5.673  78.209   1329
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.77 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1199
  helix:  1.83 (0.24), residues: 498
  sheet:  0.32 (0.35), residues: 217
  loop :  0.45 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.000   HIS D  68 
 PHE   0.011   0.001   PHE D   4 
 TYR   0.008   0.001   TYR C 134 
 ARG   0.009   0.000   ARG C 143 

*********************** 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
  104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASP cc_start: 0.7727 (m-30) cc_final: 0.7467 (m-30)
REVERT: A  218 MET cc_start: 0.4167 (mmt) cc_final: 0.3964 (mmt)
REVERT: A  333 GLN cc_start: 0.8581 (mp10) cc_final: 0.7503 (tm-30)
REVERT: A  464 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7495 (pmt)
REVERT: A  567 ASN cc_start: 0.8624 (p0) cc_final: 0.8380 (p0)
REVERT: A  603 GLU cc_start: 0.8665 (mp0) cc_final: 0.8372 (mp0)
REVERT: A  649 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8390 (mm-30)
REVERT: A  739 LYS cc_start: 0.9126 (tppt) cc_final: 0.8653 (ttpp)
REVERT: C   38 MET cc_start: 0.8316 (mmm) cc_final: 0.7857 (mmm)
REVERT: C   59 ASP cc_start: 0.7983 (m-30) cc_final: 0.7395 (t0)
REVERT: C   72 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7964 (mtm-85)
REVERT: C   92 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6402 (tm-30)
REVERT: C  116 ASP cc_start: 0.7869 (m-30) cc_final: 0.7541 (t0)
REVERT: D   42 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7247 (mtp180)
  outliers start: 14
  outliers final: 9
  residues processed: 100
  average time/residue: 0.3154
  time to fit residues: 41.4913
Evaluate side-chains
  96 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0170
   chunk 20 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.136600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.086102 restraints weight = 13679.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.05
r_work: 0.2927 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9738  Z= 0.186
  Angle     :  0.493   8.982  13195  Z= 0.250
  Chirality :  0.042   0.164   1471
  Planarity :  0.004   0.054   1707
  Dihedral  :  5.574  74.629   1329
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.14 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.25), residues: 1199
  helix:  1.86 (0.24), residues: 498
  sheet:  0.61 (0.35), residues: 209
  loop :  0.41 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.000   HIS D  68 
 PHE   0.010   0.001   PHE D   4 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.010   0.000   ARG C 143 

*********************** 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
  101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 MET cc_start: 0.4082 (mmt) cc_final: 0.3839 (mmt)
REVERT: A  333 GLN cc_start: 0.8580 (mp10) cc_final: 0.7505 (tm-30)
REVERT: A  464 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7509 (pmt)
REVERT: A  567 ASN cc_start: 0.8625 (p0) cc_final: 0.8378 (p0)
REVERT: A  603 GLU cc_start: 0.8684 (mp0) cc_final: 0.8371 (mp0)
REVERT: A  649 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8271 (mm-30)
REVERT: A  739 LYS cc_start: 0.9135 (tppt) cc_final: 0.8712 (ttpp)
REVERT: C   38 MET cc_start: 0.8243 (mmm) cc_final: 0.7747 (mmm)
REVERT: C   59 ASP cc_start: 0.7999 (m-30) cc_final: 0.7409 (t0)
REVERT: C   72 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7990 (mtm-85)
REVERT: C   92 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6563 (tm-30)
REVERT: C  116 ASP cc_start: 0.7844 (m-30) cc_final: 0.7571 (t0)
REVERT: C  144 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8141 (mtmm)
REVERT: D   42 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7235 (mtp180)
  outliers start: 11
  outliers final: 9
  residues processed: 99
  average time/residue: 0.3048
  time to fit residues: 40.1640
Evaluate side-chains
  97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 82 optimal weight:    0.0070
   chunk 40 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.136517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.086233 restraints weight = 13880.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 3.03
r_work: 0.2929 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9738  Z= 0.184
  Angle     :  0.506  13.358  13195  Z= 0.254
  Chirality :  0.042   0.165   1471
  Planarity :  0.004   0.055   1707
  Dihedral  :  5.591  75.563   1329
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.14 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1199
  helix:  1.83 (0.24), residues: 498
  sheet:  0.57 (0.35), residues: 209
  loop :  0.41 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.000   HIS D  68 
 PHE   0.024   0.001   PHE D  45 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.005   0.000   ARG C 131 

*********************** 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
  101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7907 (mtt) cc_final: 0.7469 (tpp)
REVERT: A  205 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7299 (pt0)
REVERT: A  218 MET cc_start: 0.4095 (mmt) cc_final: 0.3841 (mmt)
REVERT: A  333 GLN cc_start: 0.8612 (mp10) cc_final: 0.7537 (tm-30)
REVERT: A  464 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7498 (pmt)
REVERT: A  567 ASN cc_start: 0.8625 (p0) cc_final: 0.8375 (p0)
REVERT: A  603 GLU cc_start: 0.8679 (mp0) cc_final: 0.8350 (mp0)
REVERT: A  649 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8274 (mm-30)
REVERT: A  739 LYS cc_start: 0.9128 (tppt) cc_final: 0.8714 (ttpp)
REVERT: C   38 MET cc_start: 0.8245 (mmm) cc_final: 0.7750 (mmm)
REVERT: C   59 ASP cc_start: 0.8005 (m-30) cc_final: 0.7404 (t0)
REVERT: C   72 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7980 (mtm-85)
REVERT: C   92 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6584 (tm-30)
REVERT: C  116 ASP cc_start: 0.7842 (m-30) cc_final: 0.7571 (t0)
REVERT: D   42 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7064 (mtm180)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.3092
  time to fit residues: 40.5974
Evaluate side-chains
  100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 105 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.134693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.084295 restraints weight = 13735.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 3.03
r_work: 0.2893 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9738  Z= 0.278
  Angle     :  0.543  13.526  13195  Z= 0.272
  Chirality :  0.043   0.151   1471
  Planarity :  0.004   0.052   1707
  Dihedral  :  5.714  71.376   1329
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.43 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.25), residues: 1199
  helix:  1.70 (0.24), residues: 499
  sheet:  0.45 (0.35), residues: 209
  loop :  0.33 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.013   0.001   PHE D  45 
 TYR   0.012   0.001   TYR A  81 
 ARG   0.011   0.001   ARG C 143 

*********************** 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
  100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7434 (tm-30)
REVERT: A  184 MET cc_start: 0.7933 (mtt) cc_final: 0.7510 (tpp)
REVERT: A  205 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7311 (pt0)
REVERT: A  218 MET cc_start: 0.4120 (mmt) cc_final: 0.3873 (mmt)
REVERT: A  333 GLN cc_start: 0.8630 (mp10) cc_final: 0.7580 (tm-30)
REVERT: A  464 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7352 (pmt)
REVERT: A  567 ASN cc_start: 0.8679 (p0) cc_final: 0.8370 (p0)
REVERT: A  603 GLU cc_start: 0.8748 (mp0) cc_final: 0.8514 (mp0)
REVERT: A  649 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8195 (mm-30)
REVERT: A  739 LYS cc_start: 0.9126 (tppt) cc_final: 0.8737 (ttpp)
REVERT: C   38 MET cc_start: 0.8225 (mmm) cc_final: 0.7725 (mmm)
REVERT: C   59 ASP cc_start: 0.8160 (m-30) cc_final: 0.7582 (t0)
REVERT: C   72 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8135 (mtm-85)
REVERT: C   92 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6604 (tm-30)
REVERT: C  101 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7946 (mmmt)
REVERT: C  116 ASP cc_start: 0.7868 (m-30) cc_final: 0.7616 (t0)
REVERT: C  144 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8185 (mtmm)
REVERT: D   42 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7092 (mtm180)
  outliers start: 13
  outliers final: 10
  residues processed: 96
  average time/residue: 0.3057
  time to fit residues: 38.5976
Evaluate side-chains
  98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   chunk 94 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.135445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.085031 restraints weight = 13922.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.06
r_work: 0.2906 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9738  Z= 0.201
  Angle     :  0.524  13.914  13195  Z= 0.261
  Chirality :  0.042   0.149   1471
  Planarity :  0.004   0.051   1707
  Dihedral  :  5.709  74.774   1329
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.61 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1199
  helix:  1.72 (0.24), residues: 499
  sheet:  0.48 (0.35), residues: 209
  loop :  0.34 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  93 
 HIS   0.002   0.000   HIS C  32 
 PHE   0.013   0.001   PHE D  45 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.005   0.000   ARG C 143 

********************** 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
  104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7481 (tm-30)
REVERT: A  184 MET cc_start: 0.7910 (mtt) cc_final: 0.7515 (tpp)
REVERT: A  218 MET cc_start: 0.4087 (mmt) cc_final: 0.3837 (mmt)
REVERT: A  333 GLN cc_start: 0.8636 (mp10) cc_final: 0.7478 (tm-30)
REVERT: A  464 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7396 (pmt)
REVERT: A  567 ASN cc_start: 0.8684 (p0) cc_final: 0.8386 (p0)
REVERT: A  603 GLU cc_start: 0.8747 (mp0) cc_final: 0.8527 (mp0)
REVERT: A  649 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8058 (mm-30)
REVERT: A  739 LYS cc_start: 0.9129 (tppt) cc_final: 0.8742 (ttpp)
REVERT: C   38 MET cc_start: 0.8262 (mmm) cc_final: 0.7762 (mmm)
REVERT: C   59 ASP cc_start: 0.8098 (m-30) cc_final: 0.7441 (t0)
REVERT: C   92 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6756 (tm-30)
REVERT: C  101 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7940 (mmmt)
REVERT: C  116 ASP cc_start: 0.7856 (m-30) cc_final: 0.7614 (t0)
REVERT: C  144 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8180 (mtmm)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.3221
  time to fit residues: 41.9473
Evaluate side-chains
  100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue  898 SER
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.134689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.084333 restraints weight = 13784.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.03
r_work: 0.2897 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9738  Z= 0.255
  Angle     :  0.538  13.565  13195  Z= 0.268
  Chirality :  0.043   0.180   1471
  Planarity :  0.004   0.052   1707
  Dihedral  :  5.747  72.820   1329
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.43 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1199
  helix:  1.66 (0.24), residues: 501
  sheet:  0.46 (0.35), residues: 209
  loop :  0.34 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.011   0.001   PHE D  45 
 TYR   0.011   0.001   TYR A 235 
 ARG   0.006   0.001   ARG C  72 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 4976.59 seconds
wall clock time: 89 minutes 46.53 seconds (5386.53 seconds total)