Starting phenix.real_space_refine
on Wed Sep 17 16:15:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5u_44225/09_2025/9b5u_44225.cif"
  }
  resolution = 3.67
  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=   0.046
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 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.36, per 1000 atoms: 0.25
  Number of scatterers: 9527
  At special positions: 0
  Unit cell: (100.016, 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=2.92

  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: 0.93
  Conformation dependent library (CDL) restraints added in 348.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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
      46.6% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.968A  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: 3.842A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.911A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 3.552A  pdb=" N   VAL A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.616A  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 144
      removed outlier: 3.751A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 224
      removed outlier: 3.844A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.412A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.671A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.679A  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: 4.619A  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: 3.786A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.574A  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: 3.537A  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: 3.662A  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
    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: 3.578A  pdb=" N   THR A 636 " --> pdb=" O   ASN A 632 " (cutoff:3.500A)
      removed outlier: 3.544A  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
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 4.045A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 3.909A  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: 3.546A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.705A  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 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    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: 6.774A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   ILE A  43 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 278 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
      removed outlier: 8.977A  pdb=" N   ASP A 387 " --> 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: 3.525A  pdb=" N   VAL A 210 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.635A  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: 3.525A  pdb=" N   VAL A 210 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
      removed outlier: 3.942A  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: 6.544A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.155A  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: 6.407A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 6.090A  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: 6.407A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 4.323A  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: 6.153A  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

    464 hydrogen bonds defined for protein.
    1254 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: 1.94

  Time building geometry restraints manager: 1.22 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  1.528 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.65e+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 9.25e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.404  0.012 1.30e-02 5.92e+03 8.07e-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 7.82e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 12988
        1.32 -     2.64: 127
        2.64 -     3.97: 68
        3.97 -     5.29: 7
        5.29 -     6.61: 5
  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  128.31   -6.61 1.80e+00 3.09e-01 1.35e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.26    3.27 1.18e+00 7.24e-01 7.76e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.64    4.55 1.76e+00 3.23e-01 6.68e+00
  angle pdb=" C1' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     110.58  104.17    6.41 2.79e+00 1.28e-01 5.26e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  106.44    5.39 2.67e+00 1.40e-01 4.08e+00
  ... (remaining 13190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.86: 5580
       13.86 -    27.72: 266
       27.72 -    41.57: 60
       41.57 -    55.43: 17
       55.43 -    69.29: 6
  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 -148.51   62.51     1      1.00e+01 1.00e-02 5.17e+01
  dihedral pdb=" N   GLU A 587 "
           pdb=" CA  GLU A 587 "
           pdb=" CB  GLU A 587 "
           pdb=" CG  GLU A 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.20   59.20     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG D  74 "
           pdb=" CB  ARG D  74 "
           pdb=" CG  ARG D  74 "
           pdb=" CD  ARG D  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.13   56.13     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 5926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1277
       0.055 -    0.110: 166
       0.110 -    0.165: 25
       0.165 -    0.220: 0
       0.220 -    0.275: 3
  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   -2.96    0.28 2.00e-01 2.50e+01 1.89e+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    0.24 2.00e-01 2.50e+01 1.46e+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    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  39 "   -0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO C  40 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C  40 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  40 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D  42 "   -0.005 2.00e-02 2.50e+03   1.06e-02 1.13e+00
        pdb=" C   ARG D  42 "    0.018 2.00e-02 2.50e+03
        pdb=" O   ARG D  42 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   LEU D  43 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 922 "    0.017 5.00e-02 4.00e+02   2.54e-02 1.04e+00
        pdb=" N   PRO A 923 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 923 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 923 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 86
        2.57 -     3.15: 7939
        3.15 -     3.74: 14087
        3.74 -     4.32: 19920
        4.32 -     4.90: 34050
  Nonbonded interactions: 76082
  Sorted by model distance:
  nonbonded pdb=" O   SER A 589 "
            pdb=" NH2 ARG C  90 "
     model   vdw
     1.989 3.120
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.001 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     2.006 2.170
  nonbonded pdb=" OD2 ASP A 463 "
            pdb=" O3' ATP A1103 "
     model   vdw
     2.075 3.040
  nonbonded pdb="MG    MG A1101 "
            pdb=" O3G ATP A1103 "
     model   vdw
     2.095 2.170
  ... (remaining 76077 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:             4.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.880
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
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   0.892   9741  Z= 0.495
  Angle     :  0.733  64.502  13197  Z= 0.360
  Chirality :  0.041   0.275   1471
  Planarity :  0.003   0.037   1707
  Dihedral  :  9.224  69.288   3662
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  2.83 %
    Favored  : 95.48 %
  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:  1.42 (0.25), residues: 1199
  helix:  1.82 (0.25), residues: 492
  sheet:  0.50 (0.37), residues: 203
  loop :  0.37 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 131 
 TYR   0.010   0.001   TYR A 732 
 PHE   0.008   0.001   PHE A 842 
 TRP   0.005   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9738)
  covalent geometry    : angle       0.47157 (13195)
  SS BOND              : bond        0.89242 (    1)
  SS BOND              : angle      45.61322 (    2)
  hydrogen bonds       : bond        0.15663 (  450)
  hydrogen bonds       : angle       6.00215 ( 1254)
  Misc. bond           : bond        0.07961 (    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: 18
    poor density    : 184
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.9041 (mtp) cc_final: 0.8702 (mmm)
REVERT: A  442 MET cc_start: 0.9481 (tpp) cc_final: 0.9080 (mmm)
REVERT: A  510 GLN cc_start: 0.8583 (pt0) cc_final: 0.8306 (pp30)
REVERT: A  650 ASN cc_start: 0.9079 (m-40) cc_final: 0.8652 (t0)
REVERT: A  669 TRP cc_start: 0.9314 (t60) cc_final: 0.9039 (t60)
REVERT: A  675 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8967 (m-30)
REVERT: A  676 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8690 (tppt)
REVERT: A  811 GLU cc_start: 0.8348 (tp30) cc_final: 0.8059 (tp30)
REVERT: A  936 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8784 (ptpp)
REVERT: A  937 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (mm-30)
REVERT: A  992 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: D   24 ASP cc_start: 0.7949 (m-30) cc_final: 0.7499 (t0)
  outliers start: 18
  outliers final: 7
  residues processed: 198
  average time/residue: 0.1436
  time to fit residues: 36.8831
Evaluate side-chains
  100 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.071603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054532 restraints weight = 37363.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.056496 restraints weight = 19171.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.057835 restraints weight = 12349.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.058747 restraints weight = 9206.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.059272 restraints weight = 7525.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   9741  Z= 0.153
  Angle     :  0.608  10.329  13197  Z= 0.307
  Chirality :  0.043   0.253   1471
  Planarity :  0.004   0.046   1707
  Dihedral  :  6.280  65.464   1349
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  8.48 %
    Favored  : 89.54 %
  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:  1.64 (0.25), residues: 1199
  helix:  1.84 (0.24), residues: 500
  sheet:  1.02 (0.38), residues: 199
  loop :  0.47 (0.30), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  42 
 TYR   0.009   0.001   TYR C 145 
 PHE   0.016   0.001   PHE A 633 
 TRP   0.007   0.001   TRP C  93 
 HIS   0.004   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9738)
  covalent geometry    : angle       0.60457 (13195)
  SS BOND              : bond        0.00768 (    1)
  SS BOND              : angle       5.12026 (    2)
  hydrogen bonds       : bond        0.04439 (  450)
  hydrogen bonds       : angle       4.65667 ( 1254)
  Misc. bond           : bond        0.00142 (    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
  117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.9094 (mtp) cc_final: 0.8825 (mmm)
REVERT: A  154 ASP cc_start: 0.7584 (t0) cc_final: 0.6847 (m-30)
REVERT: A  196 MET cc_start: 0.8675 (mmm) cc_final: 0.8405 (mmm)
REVERT: A  357 MET cc_start: 0.8573 (mmm) cc_final: 0.8316 (tpt)
REVERT: A  442 MET cc_start: 0.9425 (tpp) cc_final: 0.9018 (mmm)
REVERT: A  669 TRP cc_start: 0.9356 (t60) cc_final: 0.9091 (t60)
REVERT: A  675 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8827 (m-30)
REVERT: A  676 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8685 (tppt)
REVERT: A  811 GLU cc_start: 0.8273 (tp30) cc_final: 0.8007 (tp30)
REVERT: A  937 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8765 (mm-30)
REVERT: C   38 MET cc_start: 0.8436 (mpp) cc_final: 0.7356 (mpp)
REVERT: C   72 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7974 (mtp85)
REVERT: C  122 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: D    1 MET cc_start: 0.5037 (ppp) cc_final: 0.4489 (pmm)
REVERT: D    2 GLN cc_start: 0.8414 (pm20) cc_final: 0.8192 (pm20)
  outliers start: 21
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1240
  time to fit residues: 18.9788
Evaluate side-chains
  91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  646 GLU
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   72 ARG
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain D residue   48 LYS
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.070229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.052689 restraints weight = 37600.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.054607 restraints weight = 19615.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.055918 restraints weight = 12873.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.056800 restraints weight = 9706.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.057251 restraints weight = 8035.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9741  Z= 0.139
  Angle     :  0.543   8.947  13197  Z= 0.275
  Chirality :  0.042   0.227   1471
  Planarity :  0.004   0.039   1707
  Dihedral  :  5.869  61.494   1337
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.99 %
    Favored  : 88.31 %
  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:  1.81 (0.24), residues: 502
  sheet:  0.91 (0.37), residues: 210
  loop :  0.43 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 919 
 TYR   0.019   0.001   TYR C 134 
 PHE   0.013   0.001   PHE A 633 
 TRP   0.007   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9738)
  covalent geometry    : angle       0.54111 (13195)
  SS BOND              : bond        0.01129 (    1)
  SS BOND              : angle       3.52254 (    2)
  hydrogen bonds       : bond        0.03745 (  450)
  hydrogen bonds       : angle       4.35502 ( 1254)
  Misc. bond           : bond        0.00046 (    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
  101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.9070 (mtp) cc_final: 0.8851 (mmm)
REVERT: A  154 ASP cc_start: 0.7693 (t0) cc_final: 0.6753 (m-30)
REVERT: A  196 MET cc_start: 0.8760 (mmm) cc_final: 0.8308 (mmm)
REVERT: A  357 MET cc_start: 0.8607 (mmm) cc_final: 0.8310 (tpt)
REVERT: A  442 MET cc_start: 0.9381 (tpp) cc_final: 0.9097 (mmm)
REVERT: A  668 MET cc_start: 0.8356 (tmm) cc_final: 0.8083 (tmm)
REVERT: A  669 TRP cc_start: 0.9410 (t60) cc_final: 0.9142 (t60)
REVERT: A  675 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8787 (m-30)
REVERT: A  676 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8665 (tppt)
REVERT: A  811 GLU cc_start: 0.8259 (tp30) cc_final: 0.8044 (tp30)
REVERT: A  937 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8741 (mp0)
REVERT: A  944 MET cc_start: 0.7919 (tmm) cc_final: 0.7699 (tmm)
REVERT: C   38 MET cc_start: 0.8442 (mpp) cc_final: 0.7365 (mpp)
REVERT: C  122 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: D    1 MET cc_start: 0.5455 (ppp) cc_final: 0.4975 (pmm)
REVERT: D   42 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8265 (mmt-90)
  outliers start: 18
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1102
  time to fit residues: 14.6685
Evaluate side-chains
  86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 49 optimal weight:    0.8980
   chunk 117 optimal weight:    0.0020
   chunk 100 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 87 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.071467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.054215 restraints weight = 37936.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.056196 restraints weight = 19307.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.057522 restraints weight = 12423.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.058408 restraints weight = 9287.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.059083 restraints weight = 7632.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9741  Z= 0.098
  Angle     :  0.501   8.725  13197  Z= 0.252
  Chirality :  0.041   0.212   1471
  Planarity :  0.003   0.040   1707
  Dihedral  :  5.629  57.510   1337
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.37 %
    Favored  : 88.31 %
  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:  1.65 (0.25), residues: 1199
  helix:  1.83 (0.24), residues: 504
  sheet:  0.97 (0.37), residues: 209
  loop :  0.49 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 919 
 TYR   0.019   0.001   TYR C 134 
 PHE   0.015   0.001   PHE A 633 
 TRP   0.005   0.001   TRP C  93 
 HIS   0.001   0.000   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9738)
  covalent geometry    : angle       0.49969 (13195)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       2.47051 (    2)
  hydrogen bonds       : bond        0.03286 (  450)
  hydrogen bonds       : angle       4.16514 ( 1254)
  Misc. bond           : bond        0.00065 (    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
  104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASP cc_start: 0.7612 (t0) cc_final: 0.6767 (m-30)
REVERT: A  196 MET cc_start: 0.8682 (mmm) cc_final: 0.8266 (mmm)
REVERT: A  357 MET cc_start: 0.8531 (mmm) cc_final: 0.8211 (tpp)
REVERT: A  442 MET cc_start: 0.9335 (tpp) cc_final: 0.9058 (mmm)
REVERT: A  668 MET cc_start: 0.8406 (tmm) cc_final: 0.8113 (tmm)
REVERT: A  669 TRP cc_start: 0.9382 (t60) cc_final: 0.9045 (t60)
REVERT: A  675 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8741 (m-30)
REVERT: A  676 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8649 (tppt)
REVERT: A  811 GLU cc_start: 0.8265 (tp30) cc_final: 0.8024 (tp30)
REVERT: A  937 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8737 (mp0)
REVERT: C   38 MET cc_start: 0.8388 (mpp) cc_final: 0.7303 (mpp)
REVERT: C  122 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8463 (tm-30)
REVERT: D    1 MET cc_start: 0.5268 (ppp) cc_final: 0.4996 (pmm)
REVERT: D   42 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8172 (mmt-90)
  outliers start: 14
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1252
  time to fit residues: 17.1918
Evaluate side-chains
  89 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 118 optimal weight:    5.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.070778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.053355 restraints weight = 38033.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.055295 restraints weight = 19604.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.056613 restraints weight = 12740.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057374 restraints weight = 9542.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.058148 restraints weight = 7936.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9741  Z= 0.121
  Angle     :  0.520  12.795  13197  Z= 0.258
  Chirality :  0.041   0.208   1471
  Planarity :  0.003   0.038   1707
  Dihedral  :  5.580  56.633   1337
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.31 %
    Favored  : 87.09 %
  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 (0.25), residues: 1199
  helix:  1.88 (0.24), residues: 505
  sheet:  1.00 (0.37), residues: 209
  loop :  0.55 (0.31), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 919 
 TYR   0.023   0.001   TYR C 134 
 PHE   0.016   0.001   PHE A 633 
 TRP   0.004   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9738)
  covalent geometry    : angle       0.51895 (13195)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       2.32586 (    2)
  hydrogen bonds       : bond        0.03316 (  450)
  hydrogen bonds       : angle       4.17119 ( 1254)
  Misc. bond           : bond        0.00014 (    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
  99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 MET cc_start: 0.8701 (mmm) cc_final: 0.8464 (mmm)
REVERT: A  442 MET cc_start: 0.9327 (tpp) cc_final: 0.9070 (mmm)
REVERT: A  668 MET cc_start: 0.8474 (tmm) cc_final: 0.8168 (tmm)
REVERT: A  669 TRP cc_start: 0.9384 (t60) cc_final: 0.9121 (t60)
REVERT: A  675 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8722 (m-30)
REVERT: A  676 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8630 (tppt)
REVERT: A  811 GLU cc_start: 0.8276 (tp30) cc_final: 0.8045 (tp30)
REVERT: A  869 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8350 (mm-30)
REVERT: A  937 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8743 (mp0)
REVERT: C   38 MET cc_start: 0.8414 (mpp) cc_final: 0.7334 (mpp)
REVERT: C  122 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: D    1 MET cc_start: 0.5429 (ppp) cc_final: 0.5142 (pmm)
  outliers start: 17
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1187
  time to fit residues: 15.5471
Evaluate side-chains
  86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue  142 THR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 82 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0570
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.8502

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.070560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.053251 restraints weight = 37982.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.055172 restraints weight = 19526.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.056472 restraints weight = 12678.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.057378 restraints weight = 9506.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.057875 restraints weight = 7807.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9741  Z= 0.115
  Angle     :  0.515  12.467  13197  Z= 0.257
  Chirality :  0.041   0.208   1471
  Planarity :  0.003   0.048   1707
  Dihedral  :  5.509  57.035   1337
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.69 %
    Favored  : 86.80 %
  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:  1.73 (0.25), residues: 1199
  helix:  1.89 (0.24), residues: 505
  sheet:  1.00 (0.38), residues: 208
  loop :  0.56 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 919 
 TYR   0.025   0.001   TYR C 134 
 PHE   0.020   0.001   PHE A 633 
 TRP   0.008   0.001   TRP C 141 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9738)
  covalent geometry    : angle       0.51459 (13195)
  SS BOND              : bond        0.00600 (    1)
  SS BOND              : angle       1.92758 (    2)
  hydrogen bonds       : bond        0.03269 (  450)
  hydrogen bonds       : angle       4.13109 ( 1254)
  Misc. bond           : bond        0.00023 (    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: 16
    poor density    : 79
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8102 (tm-30)
REVERT: A  196 MET cc_start: 0.8661 (mmm) cc_final: 0.8225 (mmm)
REVERT: A  218 MET cc_start: 0.7295 (mmt) cc_final: 0.6951 (mmt)
REVERT: A  442 MET cc_start: 0.9308 (tpp) cc_final: 0.9060 (mmm)
REVERT: A  668 MET cc_start: 0.8492 (tmm) cc_final: 0.8183 (tmm)
REVERT: A  669 TRP cc_start: 0.9385 (t60) cc_final: 0.9129 (t60)
REVERT: A  676 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8647 (tppt)
REVERT: A  937 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8723 (mp0)
REVERT: A  944 MET cc_start: 0.7497 (tmm) cc_final: 0.7146 (tmm)
REVERT: C   38 MET cc_start: 0.8457 (mpp) cc_final: 0.7447 (mpp)
REVERT: C  122 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8456 (tm-30)
REVERT: D   42 ARG cc_start: 0.8797 (mtm180) cc_final: 0.8346 (mmt-90)
REVERT: D   71 LEU cc_start: 0.8108 (mp) cc_final: 0.7567 (tp)
  outliers start: 16
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1261
  time to fit residues: 15.8676
Evaluate side-chains
  81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   chunk 43 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0170
   chunk 49 optimal weight:    0.9990
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.071397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.054420 restraints weight = 37954.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.056346 restraints weight = 19279.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057659 restraints weight = 12409.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058557 restraints weight = 9235.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.059055 restraints weight = 7565.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9741  Z= 0.098
  Angle     :  0.511  12.736  13197  Z= 0.255
  Chirality :  0.041   0.197   1471
  Planarity :  0.003   0.049   1707
  Dihedral  :  5.301  57.639   1335
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.97 %
    Favored  : 86.43 %
  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:  1.74 (0.25), residues: 1199
  helix:  1.91 (0.24), residues: 504
  sheet:  1.02 (0.38), residues: 208
  loop :  0.55 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 919 
 TYR   0.025   0.001   TYR C 134 
 PHE   0.020   0.001   PHE A 633 
 TRP   0.005   0.001   TRP C 141 
 HIS   0.002   0.000   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 9738)
  covalent geometry    : angle       0.51082 (13195)
  SS BOND              : bond        0.00995 (    1)
  SS BOND              : angle       1.66566 (    2)
  hydrogen bonds       : bond        0.03142 (  450)
  hydrogen bonds       : angle       4.05643 ( 1254)
  Misc. bond           : bond        0.00031 (    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
  90 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8063 (tm-30)
REVERT: A  196 MET cc_start: 0.8611 (mmm) cc_final: 0.7151 (mmm)
REVERT: A  218 MET cc_start: 0.6994 (mmt) cc_final: 0.6642 (mmt)
REVERT: A  357 MET cc_start: 0.8172 (tpp) cc_final: 0.7914 (tpt)
REVERT: A  442 MET cc_start: 0.9300 (tpp) cc_final: 0.9053 (mmm)
REVERT: A  668 MET cc_start: 0.8477 (tmm) cc_final: 0.8191 (tmm)
REVERT: A  669 TRP cc_start: 0.9376 (t60) cc_final: 0.9125 (t60)
REVERT: A  944 MET cc_start: 0.7666 (tmm) cc_final: 0.7157 (tmm)
REVERT: C   38 MET cc_start: 0.8464 (mpp) cc_final: 0.7535 (mpp)
REVERT: C  122 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8487 (tm-30)
REVERT: D    1 MET cc_start: 0.4794 (pmm) cc_final: 0.2578 (ppp)
REVERT: D   42 ARG cc_start: 0.8606 (mtm180) cc_final: 0.8257 (mmt-90)
REVERT: D   71 LEU cc_start: 0.8232 (mp) cc_final: 0.7615 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1114
  time to fit residues: 13.5720
Evaluate side-chains
  79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.070016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053252 restraints weight = 37755.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.055146 restraints weight = 19370.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.056419 restraints weight = 12615.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.057268 restraints weight = 9455.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.057849 restraints weight = 7821.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9741  Z= 0.114
  Angle     :  0.518  12.270  13197  Z= 0.260
  Chirality :  0.041   0.197   1471
  Planarity :  0.003   0.049   1707
  Dihedral  :  5.058  57.838   1332
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.44 %
    Favored  : 86.15 %
  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:  1.77 (0.25), residues: 1199
  helix:  1.93 (0.24), residues: 503
  sheet:  0.98 (0.38), residues: 212
  loop :  0.59 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 919 
 TYR   0.028   0.001   TYR C 134 
 PHE   0.041   0.001   PHE A 254 
 TRP   0.004   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9738)
  covalent geometry    : angle       0.51774 (13195)
  SS BOND              : bond        0.00873 (    1)
  SS BOND              : angle       1.68744 (    2)
  hydrogen bonds       : bond        0.03165 (  450)
  hydrogen bonds       : angle       4.08717 ( 1254)
  Misc. bond           : bond        0.00066 (    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: 15
    poor density    : 70
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8108 (tm-30)
REVERT: A  196 MET cc_start: 0.8796 (mmm) cc_final: 0.8538 (mmm)
REVERT: A  218 MET cc_start: 0.7027 (mmt) cc_final: 0.6760 (mmt)
REVERT: A  668 MET cc_start: 0.8371 (tmm) cc_final: 0.8107 (tmm)
REVERT: A  669 TRP cc_start: 0.9371 (t60) cc_final: 0.9128 (t60)
REVERT: A  944 MET cc_start: 0.7853 (tmm) cc_final: 0.7373 (tmm)
REVERT: C   38 MET cc_start: 0.8494 (mpp) cc_final: 0.7582 (mpp)
REVERT: C  122 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: D    1 MET cc_start: 0.4831 (pmm) cc_final: 0.2510 (ppp)
REVERT: D   42 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8268 (mmt-90)
REVERT: D   71 LEU cc_start: 0.8213 (mp) cc_final: 0.7708 (tp)
  outliers start: 15
  outliers final: 13
  residues processed: 82
  average time/residue: 0.1232
  time to fit residues: 13.9356
Evaluate side-chains
  79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   74 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:    0.0870
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    0.4980
   chunk 62 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0020
   chunk 76 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 118 optimal weight:    7.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.4366

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.070509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.053926 restraints weight = 37745.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.055840 restraints weight = 19234.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.057122 restraints weight = 12460.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.058002 restraints weight = 9304.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.058535 restraints weight = 7633.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9741  Z= 0.098
  Angle     :  0.524  12.647  13197  Z= 0.261
  Chirality :  0.041   0.200   1471
  Planarity :  0.004   0.048   1707
  Dihedral  :  4.994  59.084   1332
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.63 %
    Favored  : 85.96 %
  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:  1.77 (0.25), residues: 1199
  helix:  1.93 (0.24), residues: 501
  sheet:  1.00 (0.38), residues: 212
  loop :  0.58 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 143 
 TYR   0.028   0.001   TYR C 134 
 PHE   0.037   0.001   PHE A 254 
 TRP   0.011   0.001   TRP A 446 
 HIS   0.001   0.000   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9738)
  covalent geometry    : angle       0.52325 (13195)
  SS BOND              : bond        0.00478 (    1)
  SS BOND              : angle       1.54010 (    2)
  hydrogen bonds       : bond        0.03044 (  450)
  hydrogen bonds       : angle       4.04514 ( 1254)
  Misc. bond           : bond        0.00022 (    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
  86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8061 (tm-30)
REVERT: A  218 MET cc_start: 0.6968 (mmt) cc_final: 0.6719 (mmt)
REVERT: A  510 GLN cc_start: 0.8190 (pt0) cc_final: 0.7953 (pp30)
REVERT: A  668 MET cc_start: 0.8375 (tmm) cc_final: 0.8102 (tmm)
REVERT: A  669 TRP cc_start: 0.9345 (t60) cc_final: 0.9111 (t60)
REVERT: A  944 MET cc_start: 0.7875 (tmm) cc_final: 0.7374 (tmm)
REVERT: C   38 MET cc_start: 0.8499 (mpp) cc_final: 0.7575 (mpp)
REVERT: C  122 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: C  135 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8605 (mm-30)
REVERT: D    1 MET cc_start: 0.4958 (pmm) cc_final: 0.3049 (ppp)
REVERT: D   42 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8277 (mmt-90)
REVERT: D   71 LEU cc_start: 0.8216 (mp) cc_final: 0.7716 (tp)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1066
  time to fit residues: 12.6162
Evaluate side-chains
  83 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  526 PHE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0040
   chunk 18 optimal weight:    4.9990
   chunk 87 optimal weight:    0.4980
   chunk 84 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.070408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053773 restraints weight = 37857.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.055693 restraints weight = 19297.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.056975 restraints weight = 12485.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.057859 restraints weight = 9334.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.058460 restraints weight = 7655.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9741  Z= 0.105
  Angle     :  0.548  14.641  13197  Z= 0.268
  Chirality :  0.041   0.184   1471
  Planarity :  0.003   0.049   1707
  Dihedral  :  4.987  59.695   1332
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.63 %
    Favored  : 85.96 %
  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:  1.76 (0.25), residues: 1199
  helix:  1.92 (0.24), residues: 501
  sheet:  1.00 (0.38), residues: 212
  loop :  0.58 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 143 
 TYR   0.026   0.001   TYR C 134 
 PHE   0.036   0.001   PHE A 254 
 TRP   0.020   0.001   TRP A 446 
 HIS   0.001   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9738)
  covalent geometry    : angle       0.54795 (13195)
  SS BOND              : bond        0.00649 (    1)
  SS BOND              : angle       1.51347 (    2)
  hydrogen bonds       : bond        0.03047 (  450)
  hydrogen bonds       : angle       4.06637 ( 1254)
  Misc. bond           : bond        0.00053 (    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
  86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8069 (tm-30)
REVERT: A  218 MET cc_start: 0.6945 (mmt) cc_final: 0.6712 (mmt)
REVERT: A  510 GLN cc_start: 0.8179 (pt0) cc_final: 0.7949 (pp30)
REVERT: A  668 MET cc_start: 0.8345 (tmm) cc_final: 0.8132 (tmm)
REVERT: A  669 TRP cc_start: 0.9351 (t60) cc_final: 0.9117 (t60)
REVERT: A  944 MET cc_start: 0.7865 (tmm) cc_final: 0.7404 (tmm)
REVERT: C   38 MET cc_start: 0.8504 (mpp) cc_final: 0.7591 (mpp)
REVERT: C  122 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: C  135 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: D    1 MET cc_start: 0.4832 (pmm) cc_final: 0.2752 (ppp)
REVERT: D   42 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8290 (mmt-90)
REVERT: D   71 LEU cc_start: 0.8230 (mp) cc_final: 0.7916 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1106
  time to fit residues: 12.9181
Evaluate side-chains
  82 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain D residue   74 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 102 optimal weight:    0.4980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.070960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.054308 restraints weight = 37754.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.056241 restraints weight = 19186.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.057527 restraints weight = 12331.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.058384 restraints weight = 9180.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.059026 restraints weight = 7538.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9741  Z= 0.106
  Angle     :  0.538  12.370  13197  Z= 0.264
  Chirality :  0.041   0.181   1471
  Planarity :  0.003   0.048   1707
  Dihedral  :  4.949  59.892   1332
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.44 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.78 (0.25), residues: 1199
  helix:  1.92 (0.24), residues: 502
  sheet:  1.01 (0.38), residues: 212
  loop :  0.61 (0.30), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 143 
 TYR   0.028   0.001   TYR C 134 
 PHE   0.035   0.001   PHE A 254 
 TRP   0.014   0.001   TRP A 446 
 HIS   0.001   0.000   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9738)
  covalent geometry    : angle       0.53750 (13195)
  SS BOND              : bond        0.00521 (    1)
  SS BOND              : angle       1.54641 (    2)
  hydrogen bonds       : bond        0.03025 (  450)
  hydrogen bonds       : angle       4.04338 ( 1254)
  Misc. bond           : bond        0.00032 (    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: 1675.25 seconds
wall clock time: 29 minutes 27.51 seconds (1767.51 seconds total)