Starting phenix.real_space_refine
on Sun Jul 27 21:48:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_32504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_32504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_32504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_32504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whm_32504/07_2025/7whm_32504.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.25, per 1000 atoms: 0.65
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.33
  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: 3.78

  Time building geometry restraints manager: 3.05 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:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:12.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.880
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.014   0.002   TRP A1099 
 HIS   0.008   0.001   HIS A 195 
 PHE   0.022   0.002   PHE A 101 
 TYR   0.023   0.002   TYR A 149 
 ARG   0.010   0.001   ARG A 355 

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

*********************** 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  : 1.139 
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: 1.5427
  time to fit residues: 252.9743
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  : 1.101 
-------------------------------------------------------------------------------
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 102 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0980
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 109 optimal weight:    0.8980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.141016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.097432 restraints weight = 11157.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.68
r_work: 0.2859 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.0848

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= 0.157
  Angle     :  0.546   6.723  13325  Z= 0.296
  Chirality :  0.045   0.160   1517
  Planarity :  0.004   0.041   1737
  Dihedral  :  5.074  52.280   1352
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  7.15 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1212
  helix:  2.01 (0.25), residues: 402
  sheet:  0.35 (0.31), residues: 271
  loop : -0.73 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.012   0.002   PHE A 128 
 TYR   0.015   0.002   TYR A  72 
 ARG   0.011   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05642 (  454)
  hydrogen bonds       : angle       4.79676 ( 1320)
  covalent geometry    : bond        0.00367 ( 9828)
  covalent geometry    : angle       0.54607 (13325)

*********************** 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
  175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.8813 (tmtp) cc_final: 0.8508 (tmtp)
REVERT: A  257 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: A  437 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6352 (ptt180)
REVERT: A  638 THR cc_start: 0.8813 (t) cc_final: 0.8493 (m)
REVERT: A  679 GLU cc_start: 0.7820 (tt0) cc_final: 0.7367 (tt0)
REVERT: A  733 ASN cc_start: 0.6731 (p0) cc_final: 0.6514 (p0)
REVERT: A 1212 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7667 (mtm-85)
  outliers start: 24
  outliers final: 9
  residues processed: 154
  average time/residue: 1.5030
  time to fit residues: 245.3106
Evaluate side-chains
  154 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  673 THR
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 101 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0010
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** A1030 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.141988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.099015 restraints weight = 11353.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.74
r_work: 0.2841 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9828  Z= 0.136
  Angle     :  0.504   6.209  13325  Z= 0.273
  Chirality :  0.044   0.156   1517
  Planarity :  0.004   0.041   1737
  Dihedral  :  4.625  29.800   1352
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.82 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1212
  helix:  2.25 (0.25), residues: 406
  sheet:  0.66 (0.31), residues: 262
  loop : -0.58 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.018   0.002   TYR A 674 
 ARG   0.006   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  454)
  hydrogen bonds       : angle       4.49088 ( 1320)
  covalent geometry    : bond        0.00316 ( 9828)
  covalent geometry    : angle       0.50395 (13325)

*********************** 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
  176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8502 (tmtp)
REVERT: A  257 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8040 (m-30)
REVERT: A  278 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8560 (mt-10)
REVERT: A  351 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7540 (tm-30)
REVERT: A  594 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7599 (tt0)
REVERT: A  628 GLU cc_start: 0.5362 (pt0) cc_final: 0.3954 (tp30)
REVERT: A  638 THR cc_start: 0.8798 (t) cc_final: 0.8539 (m)
REVERT: A  672 MET cc_start: 0.6813 (mmt) cc_final: 0.6443 (mmt)
REVERT: A  679 GLU cc_start: 0.7695 (tt0) cc_final: 0.7320 (tt0)
REVERT: A  733 ASN cc_start: 0.6550 (p0) cc_final: 0.6349 (p0)
  outliers start: 23
  outliers final: 7
  residues processed: 155
  average time/residue: 1.5029
  time to fit residues: 247.5397
Evaluate side-chains
  155 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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  436 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  741 THR
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 48 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.138414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.091749 restraints weight = 11123.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.57
r_work: 0.2768 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2659 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9828  Z= 0.223
  Angle     :  0.572   8.506  13325  Z= 0.308
  Chirality :  0.047   0.165   1517
  Planarity :  0.004   0.066   1737
  Dihedral  :  4.754  22.821   1349
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  9.94 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1212
  helix:  2.07 (0.25), residues: 406
  sheet:  0.50 (0.30), residues: 277
  loop : -0.59 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1099 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.015   0.002   PHE A 676 
 TYR   0.020   0.002   TYR A 674 
 ARG   0.007   0.000   ARG A 841 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06070 (  454)
  hydrogen bonds       : angle       4.57267 ( 1320)
  covalent geometry    : bond        0.00543 ( 9828)
  covalent geometry    : angle       0.57234 (13325)

*********************** 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: 30
    poor density    : 141
  time to evaluate  : 1.242 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8606 (mt-10)
REVERT: A  145 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (mt-10)
REVERT: A  161 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8561 (tmtp)
REVERT: A  257 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (m-30)
REVERT: A  278 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8479 (mt-10)
REVERT: A  351 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7427 (tm-30)
REVERT: A  628 GLU cc_start: 0.5040 (pt0) cc_final: 0.3703 (tp30)
REVERT: A  638 THR cc_start: 0.8708 (t) cc_final: 0.8477 (m)
REVERT: A  672 MET cc_start: 0.6924 (mmt) cc_final: 0.6582 (mmt)
REVERT: A  841 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7141 (mtp180)
REVERT: A  960 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8036 (mtp-110)
REVERT: A 1216 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8428 (mtpm)
  outliers start: 30
  outliers final: 11
  residues processed: 149
  average time/residue: 1.7133
  time to fit residues: 273.7470
Evaluate side-chains
  158 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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  585 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  666 THR
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 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 102 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 120 optimal weight:    0.6980
   chunk 55 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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
A 754 HIS
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.140347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.093866 restraints weight = 11114.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.57
r_work: 0.2767 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2659 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9828  Z= 0.141
  Angle     :  0.505   6.628  13325  Z= 0.273
  Chirality :  0.044   0.158   1517
  Planarity :  0.004   0.041   1737
  Dihedral  :  4.526  22.376   1349
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 10.96 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.24), residues: 1212
  helix:  2.27 (0.25), residues: 406
  sheet:  0.55 (0.31), residues: 272
  loop : -0.55 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 452 
 PHE   0.013   0.001   PHE A 676 
 TYR   0.017   0.001   TYR A 462 
 ARG   0.006   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05010 (  454)
  hydrogen bonds       : angle       4.39406 ( 1320)
  covalent geometry    : bond        0.00333 ( 9828)
  covalent geometry    : angle       0.50459 (13325)

*********************** 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: 30
    poor density    : 143
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8646 (mt-10)
REVERT: A  145 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8229 (mt-10)
REVERT: A  161 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8391 (tmtp)
REVERT: A  240 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8398 (mt)
REVERT: A  257 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7980 (m-30)
REVERT: A  278 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8446 (mt-10)
REVERT: A  351 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7370 (tm-30)
REVERT: A  437 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6291 (ptp90)
REVERT: A  479 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7167 (m)
REVERT: A  594 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7486 (tt0)
REVERT: A  628 GLU cc_start: 0.4996 (pt0) cc_final: 0.3730 (tp30)
REVERT: A  638 THR cc_start: 0.8683 (t) cc_final: 0.8465 (m)
REVERT: A  651 MET cc_start: 0.8417 (mpt) cc_final: 0.8144 (mtt)
REVERT: A  672 MET cc_start: 0.6861 (mmt) cc_final: 0.6546 (mmt)
REVERT: A  841 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7150 (mtp180)
REVERT: A  981 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7655 (pm20)
  outliers start: 30
  outliers final: 11
  residues processed: 154
  average time/residue: 1.4729
  time to fit residues: 240.7340
Evaluate side-chains
  165 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
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  240 LEU
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  437 ARG
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  585 VAL
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  981 GLU
Chi-restraints excluded: chain A residue 1007 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1190 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0570
   chunk 110 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.7704

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 472 GLN
A 484 GLN
A 754 HIS
A1089 GLN
A1139 GLN
A1179 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.139522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.092888 restraints weight = 11134.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.58
r_work: 0.2761 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1276

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= 0.173
  Angle     :  0.525   6.861  13325  Z= 0.283
  Chirality :  0.045   0.161   1517
  Planarity :  0.004   0.046   1737
  Dihedral  :  4.580  21.677   1349
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.51 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.24), residues: 1212
  helix:  2.22 (0.25), residues: 406
  sheet:  0.54 (0.31), residues: 272
  loop : -0.55 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 754 
 PHE   0.015   0.002   PHE A 676 
 TYR   0.016   0.002   TYR A 462 
 ARG   0.007   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05424 (  454)
  hydrogen bonds       : angle       4.41630 ( 1320)
  covalent geometry    : bond        0.00416 ( 9828)
  covalent geometry    : angle       0.52511 (13325)

*********************** 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
  181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8112 (mt-10)
REVERT: A  161 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8337 (tmtp)
REVERT: A  240 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8354 (mt)
REVERT: A  257 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7958 (m-30)
REVERT: A  278 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8428 (mt-10)
REVERT: A  346 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: A  351 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7389 (tm-30)
REVERT: A  437 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6187 (ptp90)
REVERT: A  472 GLN cc_start: 0.7002 (tt0) cc_final: 0.6794 (tt0)
REVERT: A  594 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7427 (tt0)
REVERT: A  628 GLU cc_start: 0.4949 (pt0) cc_final: 0.3707 (tp30)
REVERT: A  638 THR cc_start: 0.8635 (t) cc_final: 0.8428 (m)
REVERT: A  651 MET cc_start: 0.8376 (mpt) cc_final: 0.8119 (mtt)
REVERT: A  672 MET cc_start: 0.6805 (mmt) cc_final: 0.6473 (mmt)
REVERT: A  841 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7056 (mtp180)
REVERT: A  960 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8004 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7630 (pm20)
REVERT: A 1216 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8323 (mtpm)
  outliers start: 31
  outliers final: 11
  residues processed: 159
  average time/residue: 1.4425
  time to fit residues: 243.7144
Evaluate side-chains
  170 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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  240 LEU
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  437 ARG
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  585 VAL
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 1063 ILE
Chi-restraints excluded: chain A residue 1190 MET
Chi-restraints excluded: chain A residue 1216 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.141581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.096789 restraints weight = 11169.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 1.71
r_work: 0.2804 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1484

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= 0.115
  Angle     :  0.477   5.872  13325  Z= 0.258
  Chirality :  0.043   0.154   1517
  Planarity :  0.004   0.041   1737
  Dihedral  :  4.364  20.925   1349
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.09 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1212
  helix:  2.44 (0.25), residues: 406
  sheet:  0.60 (0.31), residues: 272
  loop : -0.50 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 452 
 PHE   0.015   0.001   PHE A 676 
 TYR   0.015   0.001   TYR A 462 
 ARG   0.010   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  454)
  hydrogen bonds       : angle       4.26390 ( 1320)
  covalent geometry    : bond        0.00261 ( 9828)
  covalent geometry    : angle       0.47739 (13325)

*********************** 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
  172 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (mt-10)
REVERT: A  161 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8352 (tttp)
REVERT: A  240 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8304 (mt)
REVERT: A  257 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7999 (m-30)
REVERT: A  278 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: A  346 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: A  351 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7378 (tm-30)
REVERT: A  437 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6112 (ptp90)
REVERT: A  594 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7659 (tt0)
REVERT: A  628 GLU cc_start: 0.4914 (pt0) cc_final: 0.3738 (tp30)
REVERT: A  638 THR cc_start: 0.8670 (t) cc_final: 0.8458 (m)
REVERT: A  672 MET cc_start: 0.6827 (mmt) cc_final: 0.6516 (mmt)
REVERT: A  841 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7135 (mtp180)
REVERT: A  960 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8053 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7671 (pm20)
REVERT: A 1216 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8388 (mtpm)
  outliers start: 24
  outliers final: 8
  residues processed: 153
  average time/residue: 1.5351
  time to fit residues: 249.1533
Evaluate side-chains
  164 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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  240 LEU
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  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
Chi-restraints excluded: chain A residue 1216 LYS
Chi-restraints excluded: chain A residue 1231 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0030
   chunk 6 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.1196

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.141291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.094719 restraints weight = 11239.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 1.59
r_work: 0.2815 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9828  Z= 0.127
  Angle     :  0.490   5.979  13325  Z= 0.264
  Chirality :  0.043   0.156   1517
  Planarity :  0.004   0.042   1737
  Dihedral  :  4.349  19.852   1349
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.37 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1212
  helix:  2.44 (0.25), residues: 405
  sheet:  0.61 (0.31), residues: 273
  loop : -0.46 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.017   0.001   PHE A 676 
 TYR   0.013   0.001   TYR A  72 
 ARG   0.009   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04687 (  454)
  hydrogen bonds       : angle       4.25009 ( 1320)
  covalent geometry    : bond        0.00295 ( 9828)
  covalent geometry    : angle       0.49011 (13325)

*********************** 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
  177 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8642 (mt-10)
REVERT: A  145 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (mt-10)
REVERT: A  161 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (tttt)
REVERT: A  240 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8322 (mt)
REVERT: A  257 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8006 (m-30)
REVERT: A  278 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8510 (mt-10)
REVERT: A  346 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7882 (mm-30)
REVERT: A  351 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (tm-30)
REVERT: A  437 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6171 (ptp-170)
REVERT: A  594 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7658 (tt0)
REVERT: A  628 GLU cc_start: 0.4877 (pt0) cc_final: 0.3728 (tp30)
REVERT: A  638 THR cc_start: 0.8681 (t) cc_final: 0.8472 (m)
REVERT: A  672 MET cc_start: 0.6823 (mmt) cc_final: 0.6541 (mmt)
REVERT: A  841 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7152 (mtp180)
REVERT: A  960 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8030 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7712 (pm20)
REVERT: A 1216 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8425 (mtpm)
  outliers start: 28
  outliers final: 8
  residues processed: 157
  average time/residue: 1.5921
  time to fit residues: 265.7672
Evaluate side-chains
  166 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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  240 LEU
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  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 1063 ILE
Chi-restraints excluded: chain A residue 1216 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 109 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.1980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
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 = 0.3560 r_free = 0.3560 target = 0.142940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.096626 restraints weight = 11108.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.58
r_work: 0.2843 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1677

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= 0.103
  Angle     :  0.468   6.548  13325  Z= 0.252
  Chirality :  0.042   0.152   1517
  Planarity :  0.003   0.045   1737
  Dihedral  :  4.207  19.060   1349
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.67 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.24), residues: 1212
  helix:  2.55 (0.25), residues: 407
  sheet:  0.65 (0.31), residues: 273
  loop : -0.44 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 317 
 PHE   0.014   0.001   PHE A 676 
 TYR   0.013   0.001   TYR A1011 
 ARG   0.010   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  454)
  hydrogen bonds       : angle       4.14558 ( 1320)
  covalent geometry    : bond        0.00230 ( 9828)
  covalent geometry    : angle       0.46800 (13325)

*********************** 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
  169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8633 (mt-10)
REVERT: A  161 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8304 (tttp)
REVERT: A  206 ASP cc_start: 0.8573 (t0) cc_final: 0.8348 (t70)
REVERT: A  257 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8003 (m-30)
REVERT: A  278 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8386 (mt-10)
REVERT: A  346 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: A  351 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7358 (tm-30)
REVERT: A  437 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6205 (ptp-170)
REVERT: A  594 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7653 (tt0)
REVERT: A  628 GLU cc_start: 0.5104 (pt0) cc_final: 0.4032 (tp30)
REVERT: A  638 THR cc_start: 0.8688 (t) cc_final: 0.8481 (m)
REVERT: A  661 ASP cc_start: 0.7835 (m-30) cc_final: 0.7410 (m-30)
REVERT: A  672 MET cc_start: 0.6798 (mmt) cc_final: 0.6557 (mmt)
REVERT: A  841 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7155 (mtp180)
REVERT: A  960 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8023 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7661 (pm20)
REVERT: A 1216 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8451 (mtpm)
  outliers start: 18
  outliers final: 7
  residues processed: 155
  average time/residue: 1.7842
  time to fit residues: 293.9900
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  : 1.181 
-------------------------------------------------------------------------------
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  436 VAL
Chi-restraints excluded: chain A residue  437 ARG
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 1063 ILE
Chi-restraints excluded: chain A residue 1216 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 24 optimal weight:    0.0040
   chunk 4 optimal weight:    0.3980
   chunk 111 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 68 optimal weight:    9.9990
   chunk 116 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0670
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.4130

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.145854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.099849 restraints weight = 11239.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 1.59
r_work: 0.2898 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9828  Z= 0.084
  Angle     :  0.439   6.925  13325  Z= 0.236
  Chirality :  0.041   0.146   1517
  Planarity :  0.003   0.046   1737
  Dihedral  :  3.972  16.928   1349
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.23 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1212
  helix:  2.75 (0.25), residues: 405
  sheet:  0.76 (0.31), residues: 273
  loop : -0.32 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.002   0.000   HIS A 452 
 PHE   0.014   0.001   PHE A 676 
 TYR   0.013   0.001   TYR A1011 
 ARG   0.011   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  454)
  hydrogen bonds       : angle       4.00588 ( 1320)
  covalent geometry    : bond        0.00179 ( 9828)
  covalent geometry    : angle       0.43870 (13325)

********************** 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
  181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 1.188 
Fit side-chains
REVERT: A   86 ASN cc_start: 0.8967 (p0) cc_final: 0.8698 (p0)
REVERT: A   89 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8343 (mt-10)
REVERT: A  161 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8318 (tmtp)
REVERT: A  206 ASP cc_start: 0.8541 (t0) cc_final: 0.8334 (t70)
REVERT: A  257 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7988 (m-30)
REVERT: A  278 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8435 (mt-10)
REVERT: A  315 MET cc_start: 0.8861 (mmm) cc_final: 0.8518 (mmt)
REVERT: A  346 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7862 (mm-30)
REVERT: A  351 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7246 (tm-30)
REVERT: A  461 GLU cc_start: 0.7265 (tt0) cc_final: 0.6709 (tp30)
REVERT: A  511 ILE cc_start: 0.8494 (pt) cc_final: 0.8255 (pp)
REVERT: A  594 GLU cc_start: 0.8258 (pt0) cc_final: 0.7637 (tt0)
REVERT: A  628 GLU cc_start: 0.5093 (pt0) cc_final: 0.4180 (tm-30)
REVERT: A  638 THR cc_start: 0.8696 (t) cc_final: 0.8490 (m)
REVERT: A  651 MET cc_start: 0.8637 (mtt) cc_final: 0.7963 (mtt)
REVERT: A  661 ASP cc_start: 0.7775 (m-30) cc_final: 0.7375 (m-30)
REVERT: A  672 MET cc_start: 0.6757 (mmt) cc_final: 0.6486 (mmt)
REVERT: A  841 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7167 (mtp180)
REVERT: A  960 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7960 (mtp-110)
REVERT: A  981 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7618 (pm20)
REVERT: A 1089 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7095 (mp10)
REVERT: A 1212 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7405 (mtm-85)
REVERT: A 1231 LEU cc_start: 0.8653 (mm) cc_final: 0.7961 (tp)
  outliers start: 17
  outliers final: 3
  residues processed: 166
  average time/residue: 1.4884
  time to fit residues: 262.2148
Evaluate side-chains
  162 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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  649 SER
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 1089 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.1784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.141925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.095245 restraints weight = 11097.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.57
r_work: 0.2823 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9828  Z= 0.131
  Angle     :  0.501   6.216  13325  Z= 0.268
  Chirality :  0.044   0.158   1517
  Planarity :  0.004   0.053   1737
  Dihedral  :  4.200  16.850   1349
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.62 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.24), residues: 1212
  helix:  2.52 (0.25), residues: 405
  sheet:  0.59 (0.30), residues: 293
  loop : -0.19 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.005   0.001   HIS A 317 
 PHE   0.016   0.001   PHE A 676 
 TYR   0.014   0.001   TYR A  72 
 ARG   0.011   0.000   ARG A1212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04630 (  454)
  hydrogen bonds       : angle       4.17291 ( 1320)
  covalent geometry    : bond        0.00306 ( 9828)
  covalent geometry    : angle       0.50100 (13325)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9094.21 seconds
wall clock time: 159 minutes 56.99 seconds (9596.99 seconds total)