Starting phenix.real_space_refine
on Wed Mar  4 01:06:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whm_32504/03_2026/7whm_32504.map"
  }
  resolution = 2.7
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    6048      2.51       5
     N    1706      2.21       5
     O    1857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9650
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1214, 9650
          Classifications: {'peptide': 1214}
          Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1171}
  Time building chain proxies: 2.24, per 1000 atoms: 0.23
  Number of scatterers: 9650
  At special positions: 0
  Unit cell: (110.448, 128.502, 133.812, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1857      8.00
     N    1706      7.00
     C    6048      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 384.2 milliseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2292

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      37.7% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 306 through 338
      removed outlier: 3.723A  pdb=" N   HIS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 372
      removed outlier: 3.534A  pdb=" N   ARG A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 631
      removed outlier: 3.562A  pdb=" N   ARG A 631 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 658
      removed outlier: 3.734A  pdb=" N   ASN A 655 " --> pdb=" O   MET A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 688
    Processing helix  chain 'A' and resid 718 through 724
    Processing helix  chain 'A' and resid 744 through 754
      removed outlier: 4.324A  pdb=" N   ARG A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 769
    Processing helix  chain 'A' and resid 773 through 777
    Processing helix  chain 'A' and resid 778 through 796
    Processing helix  chain 'A' and resid 800 through 814
      removed outlier: 3.739A  pdb=" N   ILE A 804 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 835
    Processing helix  chain 'A' and resid 835 through 850
    Processing helix  chain 'A' and resid 852 through 861
      removed outlier: 4.174A  pdb=" N   GLY A 861 " --> pdb=" O   THR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 885
    Processing helix  chain 'A' and resid 887 through 892
    Processing helix  chain 'A' and resid 897 through 901
    Processing helix  chain 'A' and resid 904 through 909
    Processing helix  chain 'A' and resid 909 through 923
    Processing helix  chain 'A' and resid 924 through 928
    Processing helix  chain 'A' and resid 932 through 937
    Processing helix  chain 'A' and resid 979 through 994
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing helix  chain 'A' and resid 1094 through 1105
    Processing helix  chain 'A' and resid 1123 through 1136
      removed outlier: 3.692A  pdb=" N   LEU A1133 " --> pdb=" O   MET A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1148 through 1161
      removed outlier: 4.027A  pdb=" N   PHE A1152 " --> pdb=" O   ASN A1148 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A1153 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1193
      removed outlier: 4.154A  pdb=" N   ALA A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1220
      removed outlier: 3.522A  pdb=" N   ARG A1220 " --> pdb=" O   LYS A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1236
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.934A  pdb=" N   ASN A 105 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   VAL A 235 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   GLN A 260 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   SER A 237 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   VAL A 258 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   HIS A 239 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   VAL A 256 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85
      removed outlier: 4.761A  pdb=" N   VAL A 296 " --> pdb=" O   LYS A1109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 181
      removed outlier: 6.390A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 149 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   TYR A 149 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   GLU A 157 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 139 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLN A 124 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ARG A 125 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 284 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   PHE A 127 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206
      removed outlier: 4.176A  pdb=" N   ASN A1053 " --> pdb=" O   ILE A1062 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE A1062 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A1063 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   ARG A1065 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 206
      removed outlier: 6.697A  pdb=" N   SER A1016 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 395
      removed outlier: 5.516A  pdb=" N   ARG A 382 " --> pdb=" O   ILE A 738 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ILE A 738 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   GLU A 384 " --> pdb=" O   ALA A 736 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ALA A 736 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ARG A 386 " --> pdb=" O   TRP A 734 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   TRP A 734 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ASP A 388 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   GLY A 732 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   THR A 725 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 725 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   VAL A 727 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   LEU A 568 " --> pdb=" O   VAL A 727 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 729 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU A 566 " --> pdb=" O   ARG A 729 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   HIS A 731 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   LEU A 564 " --> pdb=" O   HIS A 731 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASN A 733 " --> pdb=" O   GLY A 562 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLY A 562 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   SER A 735 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR A 560 " --> pdb=" O   SER A 735 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU A 573 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 409
      removed outlier: 6.814A  pdb=" N   GLN A 435 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   PHE A 676 " --> pdb=" O   GLN A 435 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ARG A 437 " --> pdb=" O   PHE A 676 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL A 678 " --> pdb=" O   ARG A 437 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ILE A 439 " --> pdb=" O   VAL A 678 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   THR A 673 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLU A 667 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 458
      removed outlier: 5.587A  pdb=" N   ASN A 449 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN A 472 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   SER A 451 " --> pdb=" O   TYR A 470 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   TYR A 470 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   PHE A 453 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   PHE A 468 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASN A 455 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU A 466 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU A 545 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   SER A 469 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   VAL A 543 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ARG A 471 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   ILE A 541 " --> pdb=" O   ARG A 471 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 604 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 545 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ILE A 602 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   LEU A 547 " --> pdb=" O   CYS A 600 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   CYS A 600 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   GLY A 549 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU A 598 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY A 593 " --> pdb=" O   THR A 589 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 502
      removed outlier: 6.989A  pdb=" N   THR A 510 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 531
    Processing sheet with id=AB2, first strand: chain 'A' and resid 864 through 865
      removed outlier: 6.561A  pdb=" N   ASN A 864 " --> pdb=" O   GLU A1119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    462 hydrogen bonds defined for protein.
    1320 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: 1.85

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3261
        1.34 -     1.45: 1325
        1.45 -     1.57: 5168
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9828
  Sorted by residual:
  bond pdb=" CB  THR A1007 "
       pdb=" CG2 THR A1007 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.54e+00
  bond pdb=" CG1 ILE A1048 "
       pdb=" CD1 ILE A1048 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.29e+00
  bond pdb=" CA  GLY A 204 "
       pdb=" C   GLY A 204 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 1.39e-02 5.18e+03 2.09e+00
  bond pdb=" CB  ASP A 182 "
       pdb=" CG  ASP A 182 "
    ideal  model  delta    sigma   weight residual
    1.516  1.482  0.034 2.50e-02 1.60e+03 1.88e+00
  bond pdb=" CB  ASN A1148 "
       pdb=" CG  ASN A1148 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.74e+00
  ... (remaining 9823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 12740
        1.36 -     2.72: 483
        2.72 -     4.09: 79
        4.09 -     5.45: 19
        5.45 -     6.81: 4
  Bond angle restraints: 13325
  Sorted by residual:
  angle pdb=" C   THR A 133 "
        pdb=" N   THR A 134 "
        pdb=" CA  THR A 134 "
      ideal   model   delta    sigma   weight residual
     122.74  129.54   -6.80 2.44e+00 1.68e-01 7.77e+00
  angle pdb=" C   TYR A 710 "
        pdb=" N   GLN A 711 "
        pdb=" CA  GLN A 711 "
      ideal   model   delta    sigma   weight residual
     122.61  126.39   -3.78 1.56e+00 4.11e-01 5.86e+00
  angle pdb=" N   LEU A 745 "
        pdb=" CA  LEU A 745 "
        pdb=" C   LEU A 745 "
      ideal   model   delta    sigma   weight residual
     109.81  115.13   -5.32 2.21e+00 2.05e-01 5.81e+00
  angle pdb=" CA  MET A 955 "
        pdb=" CB  MET A 955 "
        pdb=" CG  MET A 955 "
      ideal   model   delta    sigma   weight residual
     114.10  118.82   -4.72 2.00e+00 2.50e-01 5.57e+00
  angle pdb=" C   TYR A 615 "
        pdb=" N   LEU A 616 "
        pdb=" CA  LEU A 616 "
      ideal   model   delta    sigma   weight residual
     120.28  123.63   -3.35 1.44e+00 4.82e-01 5.42e+00
  ... (remaining 13320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5400
       17.65 -    35.30: 453
       35.30 -    52.96: 78
       52.96 -    70.61: 19
       70.61 -    88.26: 8
  Dihedral angle restraints: 5958
    sinusoidal: 2406
      harmonic: 3552
  Sorted by residual:
  dihedral pdb=" CA  ILE A 692 "
           pdb=" C   ILE A 692 "
           pdb=" N   SER A 693 "
           pdb=" CA  SER A 693 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  PRO A 700 "
           pdb=" C   PRO A 700 "
           pdb=" N   VAL A 701 "
           pdb=" CA  VAL A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.93  -22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  TYR A 706 "
           pdb=" C   TYR A 706 "
           pdb=" N   ALA A 707 "
           pdb=" CA  ALA A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.22  -17.78     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 969
       0.040 -    0.081: 378
       0.081 -    0.121: 150
       0.121 -    0.161: 18
       0.161 -    0.202: 2
  Chirality restraints: 1517
  Sorted by residual:
  chirality pdb=" CB  VAL A 904 "
            pdb=" CA  VAL A 904 "
            pdb=" CG1 VAL A 904 "
            pdb=" CG2 VAL A 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  THR A1007 "
            pdb=" CA  THR A1007 "
            pdb=" OG1 THR A1007 "
            pdb=" CG2 THR A1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  VAL A 113 "
            pdb=" N   VAL A 113 "
            pdb=" C   VAL A 113 "
            pdb=" CB  VAL A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  ... (remaining 1514 not shown)

  Planarity restraints: 1737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 134 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 135 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 135 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 135 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 398 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A 399 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 399 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 399 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 149 "   -0.009 2.00e-02 2.50e+03   9.94e-03 1.98e+00
        pdb=" CG  TYR A 149 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 149 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 149 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 149 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 149 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 149 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 149 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1734 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 240
        2.70 -     3.25: 9086
        3.25 -     3.80: 15015
        3.80 -     4.35: 19729
        4.35 -     4.90: 33490
  Nonbonded interactions: 77560
  Sorted by model distance:
  nonbonded pdb=" O   THR A  84 "
            pdb=" NH1 ARG A 960 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   LEU A 482 "
            pdb=" NE2 GLN A 531 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OH  TYR A 470 "
            pdb=" OE1 GLN A 472 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A 309 "
            pdb=" NH2 ARG A 312 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   TYR A  72 "
            pdb=" OG1 THR A  75 "
     model   vdw
     2.313 3.040
  ... (remaining 77555 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     9.810
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9828  Z= 0.263
  Angle     :  0.637   6.811  13325  Z= 0.364
  Chirality :  0.048   0.202   1517
  Planarity :  0.004   0.040   1737
  Dihedral  : 13.847  88.259   3666
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.23), residues: 1212
  helix:  1.29 (0.25), residues: 416
  sheet:  0.04 (0.29), residues: 292
  loop : -0.82 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 355 
 TYR   0.023   0.002   TYR A 149 
 PHE   0.022   0.002   PHE A 101 
 TRP   0.014   0.002   TRP A1099 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 9828)
  covalent geometry    : angle       0.63695 (13325)
  hydrogen bonds       : bond        0.16887 (  454)
  hydrogen bonds       : angle       6.25925 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  679 GLU cc_start: 0.7732 (tt0) cc_final: 0.7424 (tt0)
REVERT: A  733 ASN cc_start: 0.6813 (p0) cc_final: 0.6593 (p0)
REVERT: A 1186 MET cc_start: 0.9029 (tpt) cc_final: 0.8820 (tpt)
  outliers start: 0
  outliers final: 1
  residues processed: 155
  average time/residue: 0.7479
  time to fit residues: 122.2156
Evaluate side-chains
  137 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1190 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 260 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.140940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.097876 restraints weight = 11247.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.74
r_work: 0.2850 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.0869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9828  Z= 0.162
  Angle     :  0.546   7.053  13325  Z= 0.296
  Chirality :  0.045   0.161   1517
  Planarity :  0.004   0.041   1737
  Dihedral  :  5.082  52.279   1352
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  6.96 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.24), residues: 1212
  helix:  2.00 (0.25), residues: 406
  sheet:  0.39 (0.31), residues: 267
  loop : -0.74 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1212 
 TYR   0.015   0.002   TYR A 462 
 PHE   0.012   0.002   PHE A1003 
 TRP   0.011   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 9828)
  covalent geometry    : angle       0.54617 (13325)
  hydrogen bonds       : bond        0.05599 (  454)
  hydrogen bonds       : angle       4.77151 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  257 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: A  437 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6381 (ptt180)
REVERT: A  638 THR cc_start: 0.8820 (t) cc_final: 0.8509 (m)
REVERT: A  679 GLU cc_start: 0.7821 (tt0) cc_final: 0.7363 (tt0)
REVERT: A  733 ASN cc_start: 0.6740 (p0) cc_final: 0.6526 (p0)
REVERT: A 1131 ASP cc_start: 0.8775 (m-30) cc_final: 0.8574 (m-30)
REVERT: A 1212 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7744 (mtm-85)
  outliers start: 24
  outliers final: 8
  residues processed: 155
  average time/residue: 0.6892
  time to fit residues: 112.9619
Evaluate side-chains
  154 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue 1040 ASN
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1190 MET
Chi-restraints excluded: chain A residue 1216 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.143789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.100952 restraints weight = 11324.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.70
r_work: 0.2895 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9828  Z= 0.106
  Angle     :  0.473   5.529  13325  Z= 0.256
  Chirality :  0.043   0.152   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.451  22.697   1352
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.91 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.24), residues: 1212
  helix:  2.42 (0.26), residues: 404
  sheet:  0.47 (0.30), residues: 277
  loop : -0.47 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1212 
 TYR   0.017   0.001   TYR A 674 
 PHE   0.012   0.001   PHE A1003 
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 9828)
  covalent geometry    : angle       0.47350 (13325)
  hydrogen bonds       : bond        0.04389 (  454)
  hydrogen bonds       : angle       4.41459 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8658 (mt-10)
REVERT: A  161 LYS cc_start: 0.8789 (tmtp) cc_final: 0.8486 (tttp)
REVERT: A  257 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8013 (m-30)
REVERT: A  278 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8503 (mt-10)
REVERT: A  351 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7416 (tm-30)
REVERT: A  628 GLU cc_start: 0.5322 (pt0) cc_final: 0.3959 (tp30)
REVERT: A  638 THR cc_start: 0.8781 (t) cc_final: 0.8520 (m)
REVERT: A  672 MET cc_start: 0.6900 (mmt) cc_final: 0.6495 (mmt)
REVERT: A  679 GLU cc_start: 0.7631 (tt0) cc_final: 0.7276 (tt0)
  outliers start: 20
  outliers final: 5
  residues processed: 158
  average time/residue: 0.6981
  time to fit residues: 116.8325
Evaluate side-chains
  151 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 68 optimal weight:    0.1980
   chunk 100 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0010
   overall best weight:    1.1390

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.141486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.094914 restraints weight = 11186.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.58
r_work: 0.2796 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9828  Z= 0.129
  Angle     :  0.490   6.024  13325  Z= 0.264
  Chirality :  0.043   0.157   1517
  Planarity :  0.003   0.042   1737
  Dihedral  :  4.367  21.296   1349
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.49 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1212
  helix:  2.39 (0.25), residues: 406
  sheet:  0.73 (0.32), residues: 261
  loop : -0.53 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1212 
 TYR   0.014   0.001   TYR A 462 
 PHE   0.015   0.001   PHE A 676 
 TRP   0.011   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9828)
  covalent geometry    : angle       0.48952 (13325)
  hydrogen bonds       : bond        0.04737 (  454)
  hydrogen bonds       : angle       4.33680 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8251 (mt-10)
REVERT: A  161 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8368 (tmtp)
REVERT: A  257 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7978 (m-30)
REVERT: A  278 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8440 (mt-10)
REVERT: A  351 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7369 (tm-30)
REVERT: A  594 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7415 (tt0)
REVERT: A  628 GLU cc_start: 0.5104 (pt0) cc_final: 0.3826 (tp30)
REVERT: A  638 THR cc_start: 0.8710 (t) cc_final: 0.8462 (m)
REVERT: A  651 MET cc_start: 0.8386 (mpt) cc_final: 0.8136 (mtt)
REVERT: A  672 MET cc_start: 0.6768 (mmt) cc_final: 0.6468 (mmt)
REVERT: A  679 GLU cc_start: 0.7520 (tt0) cc_final: 0.7235 (tt0)
REVERT: A  841 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7149 (mtp180)
REVERT: A 1216 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8366 (mtpm)
  outliers start: 26
  outliers final: 8
  residues processed: 152
  average time/residue: 0.7059
  time to fit residues: 113.5397
Evaluate side-chains
  158 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1190 MET
Chi-restraints excluded: chain A residue 1216 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 37 optimal weight:    0.0670
   chunk 49 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 260 GLN
A 484 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.143644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.097479 restraints weight = 11178.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.58
r_work: 0.2859 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9828  Z= 0.096
  Angle     :  0.452   5.367  13325  Z= 0.244
  Chirality :  0.042   0.150   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.160  19.869   1349
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.23 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1212
  helix:  2.59 (0.25), residues: 406
  sheet:  0.68 (0.31), residues: 272
  loop : -0.42 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1212 
 TYR   0.013   0.001   TYR A1011 
 PHE   0.014   0.001   PHE A 676 
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 9828)
  covalent geometry    : angle       0.45194 (13325)
  hydrogen bonds       : bond        0.03992 (  454)
  hydrogen bonds       : angle       4.17648 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8393 (tmtp)
REVERT: A  206 ASP cc_start: 0.8619 (t0) cc_final: 0.8395 (t70)
REVERT: A  257 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (m-30)
REVERT: A  278 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8406 (mt-10)
REVERT: A  351 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7375 (tm-30)
REVERT: A  594 GLU cc_start: 0.8257 (pt0) cc_final: 0.7693 (tt0)
REVERT: A  628 GLU cc_start: 0.5079 (pt0) cc_final: 0.3975 (tp30)
REVERT: A  638 THR cc_start: 0.8705 (t) cc_final: 0.8468 (m)
REVERT: A  661 ASP cc_start: 0.7775 (m-30) cc_final: 0.7174 (m-30)
REVERT: A  672 MET cc_start: 0.6790 (mmt) cc_final: 0.6477 (mmt)
REVERT: A  679 GLU cc_start: 0.7564 (tt0) cc_final: 0.7098 (tt0)
REVERT: A  841 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7142 (mtp180)
REVERT: A  960 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8011 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7725 (pm20)
  outliers start: 24
  outliers final: 8
  residues processed: 157
  average time/residue: 0.6517
  time to fit residues: 108.5015
Evaluate side-chains
  157 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  981 GLU
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1231 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0870
   chunk 120 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.142458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.096005 restraints weight = 11174.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.58
r_work: 0.2803 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9828  Z= 0.116
  Angle     :  0.472   5.613  13325  Z= 0.253
  Chirality :  0.043   0.155   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.177  18.586   1349
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.53 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.24), residues: 1212
  helix:  2.52 (0.25), residues: 408
  sheet:  0.76 (0.31), residues: 268
  loop : -0.41 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1212 
 TYR   0.013   0.001   TYR A  72 
 PHE   0.013   0.001   PHE A 676 
 TRP   0.010   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9828)
  covalent geometry    : angle       0.47200 (13325)
  hydrogen bonds       : bond        0.04397 (  454)
  hydrogen bonds       : angle       4.17171 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8701 (mt-10)
REVERT: A  145 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8220 (mt-10)
REVERT: A  161 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8312 (tmtp)
REVERT: A  206 ASP cc_start: 0.8577 (t0) cc_final: 0.8319 (t70)
REVERT: A  257 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7962 (m-30)
REVERT: A  278 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8394 (mt-10)
REVERT: A  351 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7324 (tm-30)
REVERT: A  461 GLU cc_start: 0.7406 (tt0) cc_final: 0.6721 (tp30)
REVERT: A  462 TYR cc_start: 0.7479 (p90) cc_final: 0.7273 (p90)
REVERT: A  594 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7638 (tt0)
REVERT: A  628 GLU cc_start: 0.5008 (pt0) cc_final: 0.3938 (tp30)
REVERT: A  638 THR cc_start: 0.8659 (t) cc_final: 0.8437 (m)
REVERT: A  661 ASP cc_start: 0.7770 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  672 MET cc_start: 0.6869 (mmt) cc_final: 0.6585 (mmt)
REVERT: A  841 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7108 (mtp180)
REVERT: A  960 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7972 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7619 (pm20)
REVERT: A 1064 ASP cc_start: 0.8636 (m-30) cc_final: 0.8285 (m-30)
REVERT: A 1089 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7223 (mp10)
  outliers start: 26
  outliers final: 9
  residues processed: 152
  average time/residue: 0.6848
  time to fit residues: 110.1141
Evaluate side-chains
  160 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  675 THR
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  981 GLU
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1089 GLN
Chi-restraints excluded: chain A residue 1190 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0870
   chunk 78 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0980
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 484 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.144639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.098430 restraints weight = 11098.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.58
r_work: 0.2851 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9828  Z= 0.090
  Angle     :  0.447   5.797  13325  Z= 0.240
  Chirality :  0.042   0.149   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.021  17.755   1349
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.93 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.24), residues: 1212
  helix:  2.73 (0.25), residues: 406
  sheet:  0.81 (0.31), residues: 271
  loop : -0.36 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1212 
 TYR   0.012   0.001   TYR A1011 
 PHE   0.012   0.001   PHE A 676 
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.000   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 9828)
  covalent geometry    : angle       0.44724 (13325)
  hydrogen bonds       : bond        0.03756 (  454)
  hydrogen bonds       : angle       4.04988 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8709 (mt-10)
REVERT: A  161 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8120 (tmtp)
REVERT: A  206 ASP cc_start: 0.8527 (t0) cc_final: 0.8315 (t70)
REVERT: A  257 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7901 (m-30)
REVERT: A  278 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: A  351 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7184 (tm-30)
REVERT: A  461 GLU cc_start: 0.7387 (tt0) cc_final: 0.6731 (tp30)
REVERT: A  462 TYR cc_start: 0.7460 (p90) cc_final: 0.7172 (p90)
REVERT: A  548 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7327 (mp)
REVERT: A  594 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7574 (tt0)
REVERT: A  628 GLU cc_start: 0.5050 (pt0) cc_final: 0.4094 (tm-30)
REVERT: A  638 THR cc_start: 0.8640 (t) cc_final: 0.8426 (m)
REVERT: A  661 ASP cc_start: 0.7725 (m-30) cc_final: 0.7298 (m-30)
REVERT: A  672 MET cc_start: 0.6874 (mmt) cc_final: 0.6563 (mmt)
REVERT: A  841 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7042 (mtp180)
REVERT: A  960 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7922 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7528 (pm20)
REVERT: A 1064 ASP cc_start: 0.8665 (m-30) cc_final: 0.8300 (m-30)
REVERT: A 1194 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6198 (mp0)
REVERT: A 1231 LEU cc_start: 0.8560 (mm) cc_final: 0.7874 (tp)
  outliers start: 17
  outliers final: 4
  residues processed: 158
  average time/residue: 0.6732
  time to fit residues: 112.5603
Evaluate side-chains
  161 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  981 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0010
   chunk 94 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 754 HIS
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.140484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.093735 restraints weight = 11183.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.58
r_work: 0.2775 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9828  Z= 0.175
  Angle     :  0.525   6.621  13325  Z= 0.281
  Chirality :  0.045   0.161   1517
  Planarity :  0.004   0.048   1737
  Dihedral  :  4.325  17.794   1349
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.21 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.24), residues: 1212
  helix:  2.40 (0.25), residues: 406
  sheet:  0.73 (0.30), residues: 279
  loop : -0.43 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1212 
 TYR   0.015   0.002   TYR A1125 
 PHE   0.018   0.002   PHE A 676 
 TRP   0.010   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 9828)
  covalent geometry    : angle       0.52508 (13325)
  hydrogen bonds       : bond        0.05219 (  454)
  hydrogen bonds       : angle       4.25740 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8198 (mt-10)
REVERT: A  161 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8205 (tttp)
REVERT: A  206 ASP cc_start: 0.8545 (t0) cc_final: 0.8343 (t70)
REVERT: A  257 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7950 (m-30)
REVERT: A  278 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8463 (mt-10)
REVERT: A  346 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: A  351 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7388 (tm-30)
REVERT: A  437 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6131 (ptp-170)
REVERT: A  472 GLN cc_start: 0.7130 (tt0) cc_final: 0.6619 (tt0)
REVERT: A  594 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7621 (tt0)
REVERT: A  628 GLU cc_start: 0.5011 (pt0) cc_final: 0.4058 (tp30)
REVERT: A  672 MET cc_start: 0.6717 (mmt) cc_final: 0.6389 (mmt)
REVERT: A  841 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7013 (mtp180)
REVERT: A  960 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7996 (mtp-110)
REVERT: A 1064 ASP cc_start: 0.8641 (m-30) cc_final: 0.8267 (m-30)
REVERT: A 1089 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7161 (mp10)
  outliers start: 24
  outliers final: 8
  residues processed: 157
  average time/residue: 0.6876
  time to fit residues: 114.1249
Evaluate side-chains
  163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1089 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0670
   overall best weight:    0.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.142881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.096406 restraints weight = 11101.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.58
r_work: 0.2840 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9828  Z= 0.105
  Angle     :  0.471   6.492  13325  Z= 0.253
  Chirality :  0.042   0.153   1517
  Planarity :  0.003   0.048   1737
  Dihedral  :  4.165  17.839   1349
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.95 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1212
  helix:  2.57 (0.25), residues: 405
  sheet:  0.82 (0.31), residues: 271
  loop : -0.35 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1212 
 TYR   0.012   0.001   TYR A1011 
 PHE   0.017   0.001   PHE A 676 
 TRP   0.010   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9828)
  covalent geometry    : angle       0.47090 (13325)
  hydrogen bonds       : bond        0.04226 (  454)
  hydrogen bonds       : angle       4.13336 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8220 (mt-10)
REVERT: A  157 GLU cc_start: 0.8622 (tt0) cc_final: 0.8350 (tt0)
REVERT: A  161 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8308 (tmtp)
REVERT: A  206 ASP cc_start: 0.8556 (t0) cc_final: 0.8354 (t70)
REVERT: A  257 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7979 (m-30)
REVERT: A  278 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8417 (mt-10)
REVERT: A  346 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7869 (mm-30)
REVERT: A  351 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7332 (tm-30)
REVERT: A  594 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7632 (tt0)
REVERT: A  628 GLU cc_start: 0.4941 (pt0) cc_final: 0.3988 (tm-30)
REVERT: A  651 MET cc_start: 0.8683 (mtt) cc_final: 0.7950 (mtt)
REVERT: A  661 ASP cc_start: 0.7850 (m-30) cc_final: 0.7444 (m-30)
REVERT: A  672 MET cc_start: 0.6953 (mmt) cc_final: 0.6513 (mmt)
REVERT: A  841 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7171 (mtp180)
REVERT: A  960 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8039 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7726 (pm20)
REVERT: A 1064 ASP cc_start: 0.8667 (m-30) cc_final: 0.8327 (m-30)
REVERT: A 1194 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6357 (mp0)
  outliers start: 17
  outliers final: 8
  residues processed: 149
  average time/residue: 0.6822
  time to fit residues: 107.5499
Evaluate side-chains
  163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  981 GLU
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0060
   chunk 110 optimal weight:    0.0980
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.143539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.097070 restraints weight = 11048.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.58
r_work: 0.2855 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9828  Z= 0.101
  Angle     :  0.462   6.735  13325  Z= 0.248
  Chirality :  0.042   0.152   1517
  Planarity :  0.003   0.049   1737
  Dihedral  :  4.085  16.682   1349
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.41 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.24), residues: 1212
  helix:  2.64 (0.25), residues: 407
  sheet:  0.85 (0.31), residues: 273
  loop : -0.38 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1212 
 TYR   0.013   0.001   TYR A1011 
 PHE   0.016   0.001   PHE A 676 
 TRP   0.010   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9828)
  covalent geometry    : angle       0.46245 (13325)
  hydrogen bonds       : bond        0.04032 (  454)
  hydrogen bonds       : angle       4.07350 ( 1320)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (mt-10)
REVERT: A  157 GLU cc_start: 0.8588 (tt0) cc_final: 0.8294 (tt0)
REVERT: A  161 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8310 (tmtp)
REVERT: A  206 ASP cc_start: 0.8552 (t0) cc_final: 0.8349 (t70)
REVERT: A  257 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7967 (m-30)
REVERT: A  278 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: A  346 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7883 (mm-30)
REVERT: A  351 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7371 (tm-30)
REVERT: A  461 GLU cc_start: 0.7337 (tt0) cc_final: 0.6719 (tp30)
REVERT: A  594 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7641 (tt0)
REVERT: A  628 GLU cc_start: 0.5098 (pt0) cc_final: 0.4161 (tm-30)
REVERT: A  651 MET cc_start: 0.8695 (mtt) cc_final: 0.8004 (mtt)
REVERT: A  661 ASP cc_start: 0.7886 (m-30) cc_final: 0.7519 (m-30)
REVERT: A  672 MET cc_start: 0.6901 (mmt) cc_final: 0.6525 (mmt)
REVERT: A  841 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7101 (mtp180)
REVERT: A  960 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8032 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7684 (pm20)
REVERT: A 1064 ASP cc_start: 0.8648 (m-30) cc_final: 0.8317 (m-30)
REVERT: A 1194 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6313 (mp0)
  outliers start: 17
  outliers final: 7
  residues processed: 157
  average time/residue: 0.6679
  time to fit residues: 111.2854
Evaluate side-chains
  165 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  741 THR
Chi-restraints excluded: chain A residue  841 ARG
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  981 GLU
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 17 optimal weight:    0.4980
   chunk 118 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.095955 restraints weight = 11137.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.58
r_work: 0.2835 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9828  Z= 0.118
  Angle     :  0.474   6.350  13325  Z= 0.254
  Chirality :  0.043   0.155   1517
  Planarity :  0.003   0.041   1737
  Dihedral  :  4.148  16.937   1349
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.60 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1212
  helix:  2.54 (0.25), residues: 408
  sheet:  0.83 (0.31), residues: 277
  loop : -0.35 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1212 
 TYR   0.012   0.001   TYR A  72 
 PHE   0.018   0.001   PHE A 676 
 TRP   0.010   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9828)
  covalent geometry    : angle       0.47411 (13325)
  hydrogen bonds       : bond        0.04389 (  454)
  hydrogen bonds       : angle       4.11765 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4054.09 seconds
wall clock time: 69 minutes 31.09 seconds (4171.09 seconds total)