Starting phenix.real_space_refine
on Wed Sep 17 22:58:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzn_51728/09_2025/9gzn_51728.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      57      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    7247      2.51       5
     N    2082      2.21       5
     O    2187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11637
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1000, 7928
          Classifications: {'peptide': 1000}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 64, 'TRANS': 935}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 32
    Chain: "N"
      Number of atoms: 518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 518
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "T"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 508
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2597
          Classifications: {'peptide': 326}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 21, 'TRANS': 304}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 41
    Chain: "R"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 53
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.85, per 1000 atoms: 0.24
  Number of scatterers: 11637
  At special positions: 0
  Unit cell: (101.7, 135, 114.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P      57     15.00
     Mg      1     11.99
     O    2187      8.00
     N    2082      7.00
     C    7247      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 518.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2516

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 11 sheets defined
      58.7% alpha, 6.3% beta
      12 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 220 through 237
      removed outlier: 3.850A  pdb=" N   LEU A 227 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 252
      removed outlier: 3.765A  pdb=" N   ALA A 242 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 4.173A  pdb=" N   LYS A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 275
      removed outlier: 3.522A  pdb=" N   TYR A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 291
      removed outlier: 3.781A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.561A  pdb=" N   TYR A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 327
    Processing helix  chain 'A' and resid 329 through 335
      removed outlier: 3.801A  pdb=" N   LEU A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 352
    Processing helix  chain 'A' and resid 392 through 410
    Processing helix  chain 'A' and resid 424 through 461
    Processing helix  chain 'A' and resid 467 through 472
    Processing helix  chain 'A' and resid 475 through 489
    Processing helix  chain 'A' and resid 497 through 521
    Processing helix  chain 'A' and resid 521 through 534
      removed outlier: 3.891A  pdb=" N   ALA A 525 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 556
    Processing helix  chain 'A' and resid 568 through 587
      removed outlier: 3.573A  pdb=" N   THR A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 635
      removed outlier: 3.559A  pdb=" N   VAL A 628 " --> pdb=" O   HIS A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 686
    Processing helix  chain 'A' and resid 688 through 691
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 711 through 724
      removed outlier: 3.591A  pdb=" N   ALA A 723 " --> pdb=" O   GLN A 719 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS A 724 " --> pdb=" O   LEU A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 789
    Processing helix  chain 'A' and resid 818 through 824
    Processing helix  chain 'A' and resid 837 through 850
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 884 through 888
    Processing helix  chain 'A' and resid 893 through 907
      removed outlier: 3.556A  pdb=" N   ASN A 903 " --> pdb=" O   MET A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 912
    Processing helix  chain 'A' and resid 925 through 936
    Processing helix  chain 'A' and resid 937 through 944
    Processing helix  chain 'A' and resid 954 through 974
      removed outlier: 3.663A  pdb=" N   GLY A 958 " --> pdb=" O   ASP A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 981
      removed outlier: 3.610A  pdb=" N   GLN A 979 " --> pdb=" O   MET A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 998
      removed outlier: 4.062A  pdb=" N   VAL A 990 " --> pdb=" O   THR A 986 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLN A 992 " --> pdb=" O   LYS A 988 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   THR A 993 " --> pdb=" O   VAL A 989 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 998 " --> pdb=" O   VAL A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1015
    Processing helix  chain 'A' and resid 1021 through 1023
      No H-bonds generated for 'chain 'A' and resid 1021 through 1023'
    Processing helix  chain 'A' and resid 1024 through 1039
      removed outlier: 3.557A  pdb=" N   HIS A1030 " --> pdb=" O   TRP A1026 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG A1034 " --> pdb=" O   HIS A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1064
      removed outlier: 4.067A  pdb=" N   MET A1064 " --> pdb=" O   LEU A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1111 through 1142
      removed outlier: 3.641A  pdb=" N   GLY A1118 " --> pdb=" O   LYS A1114 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE A1119 " --> pdb=" O   GLN A1115 " (cutoff:3.500A)
      Proline residue:  A1120  - end of helix
      removed outlier: 3.750A  pdb=" N   LYS A1142 " --> pdb=" O   HIS A1138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1177
      removed outlier: 3.932A  pdb=" N   GLU A1177 " --> pdb=" O   ARG A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1193
      removed outlier: 3.751A  pdb=" N   SER A1193 " --> pdb=" O   LYS A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1209
    Processing helix  chain 'A' and resid 1218 through 1224
    Processing helix  chain 'B' and resid 77 through 89
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 128 through 137
      removed outlier: 4.514A  pdb=" N   HIS B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 154
      removed outlier: 3.797A  pdb=" N   LEU B 154 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 176
    Processing helix  chain 'B' and resid 199 through 213
    Processing helix  chain 'B' and resid 216 through 221
      removed outlier: 4.007A  pdb=" N   PHE B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLY B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 216 through 221'
    Processing helix  chain 'B' and resid 230 through 238
    Processing helix  chain 'B' and resid 248 through 258
    Processing helix  chain 'B' and resid 267 through 269
      No H-bonds generated for 'chain 'B' and resid 267 through 269'
    Processing helix  chain 'B' and resid 281 through 292
      removed outlier: 3.516A  pdb=" N   ARG B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG B 286 " --> pdb=" O   ASN B 282 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP B 290 " --> pdb=" O   ARG B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 328
      removed outlier: 3.526A  pdb=" N   PHE B 320 " --> pdb=" O   ASN B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 343
      removed outlier: 3.789A  pdb=" N   HIS B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 355
    Processing helix  chain 'B' and resid 366 through 379
    Processing helix  chain 'B' and resid 390 through 394
    Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496
    Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 709
    Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800
    Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1069 through 1071
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1091
      removed outlier: 3.534A  pdb=" N   ILE A1098 " --> pdb=" O   ILE A1091 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1147 through 1149
      removed outlier: 3.739A  pdb=" N   VAL A1147 " --> pdb=" O   TRP A1154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75
    Processing sheet with id=AB2, first strand: chain 'B' and resid 144 through 148
      removed outlier: 6.648A  pdb=" N   VAL B 120 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   ILE B 147 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ALA B 122 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU B  99 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   LEU B 123 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   GLU B 101 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU B 100 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   MET B 194 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   CYS B 102 " --> pdb=" O   MET B 194 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B 264 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLN B 300 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL B 262 " --> pdb=" O   GLN B 300 " (cutoff:3.500A)

    551 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      29 hydrogen bonds
      58 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1740
        1.31 -     1.43: 3335
        1.43 -     1.56: 6742
        1.56 -     1.68: 110
        1.68 -     1.81: 96
  Bond restraints: 12023
  Sorted by residual:
  bond pdb=" O3'  DT T  19 "
       pdb=" P    DA T  20 "
    ideal  model  delta    sigma   weight residual
    1.607  1.474  0.133 1.50e-02 4.44e+03 7.89e+01
  bond pdb=" C3'  DC T  11 "
       pdb=" C2'  DC T  11 "
    ideal  model  delta    sigma   weight residual
    1.525  1.649 -0.124 2.00e-02 2.50e+03 3.84e+01
  bond pdb=" O3'  DC N  35 "
       pdb=" P    DG N  36 "
    ideal  model  delta    sigma   weight residual
    1.607  1.683 -0.076 1.50e-02 4.44e+03 2.54e+01
  bond pdb=" C   LEU A 526 "
       pdb=" O   LEU A 526 "
    ideal  model  delta    sigma   weight residual
    1.237  1.180  0.057 1.17e-02 7.31e+03 2.39e+01
  bond pdb=" O3'  DT N  45 "
       pdb=" P    DA N  46 "
    ideal  model  delta    sigma   weight residual
    1.607  1.548  0.059 1.50e-02 4.44e+03 1.54e+01
  ... (remaining 12018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 16146
        3.09 -     6.18: 317
        6.18 -     9.27: 53
        9.27 -    12.36: 16
       12.36 -    15.45: 5
  Bond angle restraints: 16537
  Sorted by residual:
  angle pdb=" C3'  DC T   9 "
        pdb=" O3'  DC T   9 "
        pdb=" P    DT T  10 "
      ideal   model   delta    sigma   weight residual
     120.20  105.04   15.16 1.50e+00 4.44e-01 1.02e+02
  angle pdb=" C3'  DC T  11 "
        pdb=" O3'  DC T  11 "
        pdb=" P    DC T  12 "
      ideal   model   delta    sigma   weight residual
     120.20  105.47   14.73 1.50e+00 4.44e-01 9.64e+01
  angle pdb=" C3'  DA N  46 "
        pdb=" O3'  DA N  46 "
        pdb=" P    DA N  47 "
      ideal   model   delta    sigma   weight residual
     120.20  107.18   13.02 1.50e+00 4.44e-01 7.54e+01
  angle pdb=" C3'  DC N  34 "
        pdb=" O3'  DC N  34 "
        pdb=" P    DC N  35 "
      ideal   model   delta    sigma   weight residual
     120.20  108.07   12.13 1.50e+00 4.44e-01 6.54e+01
  angle pdb=" C3'  DG T  15 "
        pdb=" O3'  DG T  15 "
        pdb=" P    DC T  16 "
      ideal   model   delta    sigma   weight residual
     120.20  108.62   11.58 1.50e+00 4.44e-01 5.96e+01
  ... (remaining 16532 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.10: 6745
       31.10 -    62.21: 403
       62.21 -    93.31: 14
       93.31 -   124.42: 4
      124.42 -   155.52: 3
  Dihedral angle restraints: 7169
    sinusoidal: 3293
      harmonic: 3876
  Sorted by residual:
  dihedral pdb=" C4'   A R 102 "
           pdb=" C3'   A R 102 "
           pdb=" C2'   A R 102 "
           pdb=" C1'   A R 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34   -8.91   45.26     1      3.10e+00 1.04e-01 2.96e+02
  dihedral pdb=" O4'   A R 102 "
           pdb=" C2'   A R 102 "
           pdb=" C1'   A R 102 "
           pdb=" C3'   A R 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.59  -27.69   53.29     3      3.80e+00 6.93e-02 1.43e+02
  dihedral pdb=" C4'   A R 102 "
           pdb=" O4'   A R 102 "
           pdb=" C1'   A R 102 "
           pdb=" C2'   A R 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.88  -37.16   41.04     3      5.00e+00 4.00e-02 6.60e+01
  ... (remaining 7166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1756
       0.128 -    0.255: 37
       0.255 -    0.383: 8
       0.383 -    0.510: 28
       0.510 -    0.638: 9
  Chirality restraints: 1838
  Sorted by residual:
  chirality pdb=" P    DA N  24 "
            pdb=" OP1  DA N  24 "
            pdb=" OP2  DA N  24 "
            pdb=" O5'  DA N  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DC T  11 "
            pdb=" OP1  DC T  11 "
            pdb=" OP2  DC T  11 "
            pdb=" O5'  DC T  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.58 2.00e-01 2.50e+01 8.43e+00
  chirality pdb=" P     A R 102 "
            pdb=" OP1   A R 102 "
            pdb=" OP2   A R 102 "
            pdb=" O5'   A R 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.74   -0.57 2.00e-01 2.50e+01 8.07e+00
  ... (remaining 1835 not shown)

  Planarity restraints: 1938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 517 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   GLN A 517 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLN A 517 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 518 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 522 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.75e+00
        pdb=" C   GLN A 522 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLN A 522 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 523 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 527 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.21e+00
        pdb=" C   GLN A 527 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   GLN A 527 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 528 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1935 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 23
        2.45 -     3.07: 7383
        3.07 -     3.68: 16946
        3.68 -     4.29: 24589
        4.29 -     4.90: 41416
  Nonbonded interactions: 90357
  Sorted by model distance:
  nonbonded pdb=" O2B GTP A1301 "
            pdb="MG    MG A1302 "
     model   vdw
     1.843 2.170
  nonbonded pdb=" OD1 ASP B 186 "
            pdb=" N   ILE B 187 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" O   GLY A 923 "
            pdb="MG    MG A1302 "
     model   vdw
     2.217 2.170
  nonbonded pdb=" O   LYS B 236 "
            pdb=" OG  SER B 251 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" NZ  LYS B  91 "
            pdb=" O   SER B  93 "
     model   vdw
     2.264 3.120
  ... (remaining 90352 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  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:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.280
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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   0.133  12024  Z= 0.334
  Angle     :  1.059  15.453  16537  Z= 0.594
  Chirality :  0.083   0.638   1838
  Planarity :  0.006   0.063   1938
  Dihedral  : 17.761 155.520   4653
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.56 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  0.79 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.23), residues: 1320
  helix:  2.05 (0.20), residues: 718
  sheet: -0.52 (0.55), residues: 80
  loop : -0.65 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1224 
 TYR   0.016   0.001   TYR B 247 
 PHE   0.029   0.001   PHE A 497 
 TRP   0.023   0.001   TRP B 387 
 HIS   0.009   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (12023)
  covalent geometry    : angle       1.05857 (16537)
  hydrogen bonds       : bond        0.15122 (  580)
  hydrogen bonds       : angle       5.75372 ( 1660)
  Misc. bond           : bond        0.05711 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.7646 (mtt) cc_final: 0.7380 (mtt)
REVERT: A  512 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7733 (t70)
REVERT: B  172 LEU cc_start: 0.8580 (tp) cc_final: 0.8201 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 128
  average time/residue: 0.1060
  time to fit residues: 19.8502
Evaluate side-chains
  81 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  510 SER
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
A 565 GLN
** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 ASN ** 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 = 0.3217 r_free = 0.3217 target = 0.054958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.042443 restraints weight = 60292.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.043812 restraints weight = 32535.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044723 restraints weight = 21989.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.045345 restraints weight = 16967.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.045724 restraints weight = 14308.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12024  Z= 0.200
  Angle     :  0.627   9.311  16537  Z= 0.321
  Chirality :  0.039   0.159   1838
  Planarity :  0.005   0.059   1938
  Dihedral  : 18.289 148.923   2055
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.71 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  7.39 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.23), residues: 1320
  helix:  2.38 (0.19), residues: 724
  sheet: -0.48 (0.55), residues: 84
  loop : -0.68 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 613 
 TYR   0.022   0.002   TYR A1100 
 PHE   0.014   0.001   PHE A 285 
 TRP   0.008   0.001   TRP B 387 
 HIS   0.004   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (12023)
  covalent geometry    : angle       0.62700 (16537)
  hydrogen bonds       : bond        0.05212 (  580)
  hydrogen bonds       : angle       4.01498 ( 1660)
  Misc. bond           : bond        0.00071 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 MET cc_start: 0.9546 (tmm) cc_final: 0.9261 (tpp)
REVERT: A  563 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8244 (ptm-80)
REVERT: B  172 LEU cc_start: 0.9611 (tp) cc_final: 0.9268 (tt)
REVERT: B  227 MET cc_start: 0.8743 (mmp) cc_final: 0.8394 (mmp)
  outliers start: 19
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1080
  time to fit residues: 15.1327
Evaluate side-chains
  82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 117 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 249 HIS
A 274 GLN
A 565 GLN
A1041 GLN
A1103 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.055407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.042785 restraints weight = 59978.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.044128 restraints weight = 32357.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.045046 restraints weight = 22027.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.045636 restraints weight = 17038.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046068 restraints weight = 14473.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12024  Z= 0.134
  Angle     :  0.566  12.259  16537  Z= 0.285
  Chirality :  0.037   0.198   1838
  Planarity :  0.005   0.058   1938
  Dihedral  : 18.009 148.526   2053
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.11 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.12 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.24), residues: 1320
  helix:  2.61 (0.19), residues: 719
  sheet: -0.33 (0.55), residues: 90
  loop : -0.52 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 613 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 277 
 TRP   0.007   0.001   TRP B 387 
 HIS   0.006   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (12023)
  covalent geometry    : angle       0.56604 (16537)
  hydrogen bonds       : bond        0.04412 (  580)
  hydrogen bonds       : angle       3.61534 ( 1660)
  Misc. bond           : bond        0.00090 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8916 (mtt) cc_final: 0.8441 (mpp)
REVERT: A  268 MET cc_start: 0.9504 (mtp) cc_final: 0.9237 (mtp)
REVERT: A  323 MET cc_start: 0.9566 (tmm) cc_final: 0.9302 (tpp)
REVERT: B  172 LEU cc_start: 0.9616 (tp) cc_final: 0.9282 (tt)
REVERT: B  227 MET cc_start: 0.8598 (mmp) cc_final: 0.8166 (mmp)
  outliers start: 12
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1089
  time to fit residues: 14.5035
Evaluate side-chains
  82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 125 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 GLN
A 916 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.054065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.041470 restraints weight = 60839.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.042772 restraints weight = 33324.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.043661 restraints weight = 22907.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.044210 restraints weight = 17863.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.044640 restraints weight = 15271.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12024  Z= 0.183
  Angle     :  0.578   8.444  16537  Z= 0.292
  Chirality :  0.037   0.157   1838
  Planarity :  0.005   0.056   1938
  Dihedral  : 17.783 139.738   2053
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.18 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.44 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.24), residues: 1320
  helix:  2.57 (0.19), residues: 725
  sheet: -0.58 (0.53), residues: 96
  loop : -0.61 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 613 
 TYR   0.014   0.001   TYR B 247 
 PHE   0.012   0.001   PHE A 285 
 TRP   0.005   0.001   TRP A 840 
 HIS   0.005   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12023)
  covalent geometry    : angle       0.57844 (16537)
  hydrogen bonds       : bond        0.04598 (  580)
  hydrogen bonds       : angle       3.67680 ( 1660)
  Misc. bond           : bond        0.00059 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8923 (mtt) cc_final: 0.8454 (mpp)
REVERT: A  323 MET cc_start: 0.9550 (tmm) cc_final: 0.9268 (tpp)
REVERT: A  495 GLU cc_start: 0.8719 (tp30) cc_final: 0.8503 (tp30)
REVERT: A 1090 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7829 (tp-100)
REVERT: B  172 LEU cc_start: 0.9641 (tp) cc_final: 0.9335 (tt)
REVERT: B  227 MET cc_start: 0.8646 (mmp) cc_final: 0.8210 (mmp)
  outliers start: 18
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1101
  time to fit residues: 14.3912
Evaluate side-chains
  82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  781 TYR
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1090 GLN
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 38 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 GLN
B 148 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.053844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.041269 restraints weight = 60585.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.042564 restraints weight = 33175.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.043448 restraints weight = 22721.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.044057 restraints weight = 17753.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.044411 restraints weight = 15013.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12024  Z= 0.172
  Angle     :  0.569   8.616  16537  Z= 0.286
  Chirality :  0.037   0.163   1838
  Planarity :  0.005   0.056   1938
  Dihedral  : 17.643 130.854   2053
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.18 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.03 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.23), residues: 1320
  helix:  2.54 (0.19), residues: 733
  sheet: -0.59 (0.53), residues: 96
  loop : -0.57 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 613 
 TYR   0.012   0.001   TYR B 247 
 PHE   0.012   0.001   PHE A 285 
 TRP   0.007   0.001   TRP A 567 
 HIS   0.005   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12023)
  covalent geometry    : angle       0.56863 (16537)
  hydrogen bonds       : bond        0.04410 (  580)
  hydrogen bonds       : angle       3.61275 ( 1660)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8896 (mtt) cc_final: 0.8443 (mpp)
REVERT: A  323 MET cc_start: 0.9540 (tmm) cc_final: 0.9248 (tpp)
REVERT: A 1090 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7916 (tp-100)
REVERT: B  172 LEU cc_start: 0.9615 (tp) cc_final: 0.9329 (tt)
REVERT: B  227 MET cc_start: 0.8637 (mmp) cc_final: 0.8195 (mmp)
  outliers start: 18
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1122
  time to fit residues: 14.3644
Evaluate side-chains
  84 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  781 TYR
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1041 GLN
Chi-restraints excluded: chain A residue 1090 GLN
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   chunk 84 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 127 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.054878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.042218 restraints weight = 60159.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.043541 restraints weight = 32423.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.044452 restraints weight = 22118.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.045068 restraints weight = 17165.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.045466 restraints weight = 14471.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12024  Z= 0.118
  Angle     :  0.542   8.627  16537  Z= 0.271
  Chirality :  0.036   0.157   1838
  Planarity :  0.004   0.056   1938
  Dihedral  : 17.497 124.349   2053
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.03 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.82 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.24), residues: 1320
  helix:  2.69 (0.19), residues: 731
  sheet: -0.43 (0.52), residues: 102
  loop : -0.59 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 613 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.010   0.001   PHE A 285 
 TRP   0.006   0.001   TRP B 387 
 HIS   0.005   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12023)
  covalent geometry    : angle       0.54219 (16537)
  hydrogen bonds       : bond        0.03979 (  580)
  hydrogen bonds       : angle       3.36468 ( 1660)
  Misc. bond           : bond        0.00077 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8905 (mtt) cc_final: 0.8460 (mpp)
REVERT: A  323 MET cc_start: 0.9537 (tmm) cc_final: 0.9257 (tpp)
REVERT: B  111 GLN cc_start: 0.9432 (tp-100) cc_final: 0.8858 (tp-100)
REVERT: B  172 LEU cc_start: 0.9619 (tp) cc_final: 0.9351 (tt)
REVERT: B  227 MET cc_start: 0.8659 (mmp) cc_final: 0.8217 (mmp)
REVERT: B  327 CYS cc_start: 0.9235 (m) cc_final: 0.8996 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1052
  time to fit residues: 14.4862
Evaluate side-chains
  83 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1041 GLN
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 293 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.053442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.040777 restraints weight = 61842.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042046 restraints weight = 33555.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.042875 restraints weight = 23030.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.043490 restraints weight = 18198.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.043862 restraints weight = 15422.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12024  Z= 0.191
  Angle     :  0.602  11.378  16537  Z= 0.297
  Chirality :  0.037   0.172   1838
  Planarity :  0.005   0.055   1938
  Dihedral  : 17.455 111.530   2051
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.82 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.23), residues: 1320
  helix:  2.61 (0.19), residues: 731
  sheet: -0.58 (0.53), residues: 96
  loop : -0.52 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 613 
 TYR   0.012   0.001   TYR B 247 
 PHE   0.009   0.001   PHE A 285 
 TRP   0.005   0.001   TRP A 553 
 HIS   0.011   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (12023)
  covalent geometry    : angle       0.60155 (16537)
  hydrogen bonds       : bond        0.04452 (  580)
  hydrogen bonds       : angle       3.61881 ( 1660)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8990 (mtt) cc_final: 0.8488 (mpp)
REVERT: A  268 MET cc_start: 0.9528 (mtp) cc_final: 0.9281 (mtp)
REVERT: A  306 MET cc_start: 0.9405 (mmm) cc_final: 0.8959 (tpp)
REVERT: A  323 MET cc_start: 0.9535 (tmm) cc_final: 0.9236 (tpp)
REVERT: A  495 GLU cc_start: 0.8672 (tp30) cc_final: 0.8462 (tm-30)
REVERT: A 1145 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8629 (p)
REVERT: B  172 LEU cc_start: 0.9613 (tp) cc_final: 0.9388 (tt)
REVERT: B  227 MET cc_start: 0.8611 (mmp) cc_final: 0.8240 (mmp)
  outliers start: 19
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1070
  time to fit residues: 13.4287
Evaluate side-chains
  80 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  781 TYR
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1041 GLN
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.053499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.040756 restraints weight = 60824.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.042034 restraints weight = 33128.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.042911 restraints weight = 22779.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.043498 restraints weight = 17822.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.043858 restraints weight = 15165.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12024  Z= 0.169
  Angle     :  0.589  10.241  16537  Z= 0.292
  Chirality :  0.037   0.160   1838
  Planarity :  0.005   0.056   1938
  Dihedral  : 17.322 115.376   2051
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.03 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.00 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.23), residues: 1320
  helix:  2.59 (0.19), residues: 732
  sheet: -0.55 (0.53), residues: 96
  loop : -0.52 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 613 
 TYR   0.011   0.001   TYR B 247 
 PHE   0.010   0.001   PHE A 285 
 TRP   0.005   0.001   TRP A 840 
 HIS   0.005   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12023)
  covalent geometry    : angle       0.58860 (16537)
  hydrogen bonds       : bond        0.04276 (  580)
  hydrogen bonds       : angle       3.57870 ( 1660)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8986 (mtt) cc_final: 0.8498 (mpp)
REVERT: A  306 MET cc_start: 0.9418 (mmm) cc_final: 0.9061 (tpp)
REVERT: A  323 MET cc_start: 0.9530 (tmm) cc_final: 0.9225 (tpp)
REVERT: A 1090 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8047 (tp-100)
REVERT: A 1145 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8596 (p)
REVERT: B  172 LEU cc_start: 0.9605 (tp) cc_final: 0.9384 (tt)
REVERT: B  227 MET cc_start: 0.8618 (mmp) cc_final: 0.8293 (mmp)
  outliers start: 18
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1064
  time to fit residues: 13.5706
Evaluate side-chains
  81 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1090 GLN
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain A residue 1145 THR
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9980
   chunk 128 optimal weight:    0.0770
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.9940

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

Flipped N/Q/H residues before XYZ refinement:
A 953 GLN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.054167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.041624 restraints weight = 59798.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.042905 restraints weight = 32810.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.043789 restraints weight = 22469.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.044334 restraints weight = 17539.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.044748 restraints weight = 14978.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12024  Z= 0.124
  Angle     :  0.585  11.199  16537  Z= 0.288
  Chirality :  0.036   0.184   1838
  Planarity :  0.005   0.057   1938
  Dihedral  : 17.098 117.925   2051
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.14 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.24), residues: 1320
  helix:  2.71 (0.19), residues: 730
  sheet: -0.33 (0.52), residues: 102
  loop : -0.55 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 613 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.010   0.001   PHE A 285 
 TRP   0.007   0.001   TRP B 387 
 HIS   0.011   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12023)
  covalent geometry    : angle       0.58462 (16537)
  hydrogen bonds       : bond        0.03934 (  580)
  hydrogen bonds       : angle       3.39691 ( 1660)
  Misc. bond           : bond        0.00071 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8959 (mtt) cc_final: 0.8497 (mpp)
REVERT: A  306 MET cc_start: 0.9382 (mmm) cc_final: 0.8839 (tpp)
REVERT: A  323 MET cc_start: 0.9519 (tmm) cc_final: 0.9225 (tpp)
REVERT: A  646 VAL cc_start: 0.9136 (t) cc_final: 0.8887 (m)
REVERT: A 1043 MET cc_start: 0.8884 (mmm) cc_final: 0.8278 (mmm)
REVERT: A 1132 MET cc_start: 0.9682 (tmm) cc_final: 0.8965 (tmm)
REVERT: B  172 LEU cc_start: 0.9612 (tp) cc_final: 0.9399 (tt)
REVERT: B  227 MET cc_start: 0.8624 (mmp) cc_final: 0.8420 (mmp)
REVERT: B  327 CYS cc_start: 0.9230 (m) cc_final: 0.8994 (m)
  outliers start: 11
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1099
  time to fit residues: 13.9973
Evaluate side-chains
  80 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  565 GLN
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Chi-restraints excluded: chain B residue  394 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0470
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    1.0882

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

Flipped N/Q/H residues before XYZ refinement:
B 235 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.054309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.041764 restraints weight = 60008.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.043052 restraints weight = 32705.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.043916 restraints weight = 22417.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.044490 restraints weight = 17502.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.044881 restraints weight = 14867.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12024  Z= 0.125
  Angle     :  0.600  11.573  16537  Z= 0.294
  Chirality :  0.036   0.178   1838
  Planarity :  0.005   0.056   1938
  Dihedral  : 16.936 119.078   2051
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.03 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 15.49 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.24), residues: 1320
  helix:  2.75 (0.19), residues: 729
  sheet: -0.32 (0.53), residues: 102
  loop : -0.55 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 613 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.012   0.001   PHE A 285 
 TRP   0.006   0.001   TRP B 387 
 HIS   0.008   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (12023)
  covalent geometry    : angle       0.59972 (16537)
  hydrogen bonds       : bond        0.03818 (  580)
  hydrogen bonds       : angle       3.34770 ( 1660)
  Misc. bond           : bond        0.00069 (    1)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.8975 (mtt) cc_final: 0.8454 (mpp)
REVERT: A  306 MET cc_start: 0.8935 (mmm) cc_final: 0.8463 (tpp)
REVERT: A  323 MET cc_start: 0.9518 (tmm) cc_final: 0.9221 (tpp)
REVERT: A  646 VAL cc_start: 0.9166 (t) cc_final: 0.8941 (m)
REVERT: A 1043 MET cc_start: 0.8916 (mmm) cc_final: 0.8287 (mmm)
REVERT: A 1132 MET cc_start: 0.9680 (tmm) cc_final: 0.8971 (tmm)
REVERT: B  327 CYS cc_start: 0.9227 (m) cc_final: 0.8992 (m)
  outliers start: 12
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1102
  time to fit residues: 13.3885
Evaluate side-chains
  81 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  565 GLN
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1103 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  276 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 56 optimal weight:    0.0670
   chunk 12 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 135 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.3980
   chunk 76 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.0322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.054508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.041930 restraints weight = 59451.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.043214 restraints weight = 32659.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.044102 restraints weight = 22397.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.044638 restraints weight = 17433.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.045054 restraints weight = 14888.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12024  Z= 0.122
  Angle     :  0.599  11.889  16537  Z= 0.295
  Chirality :  0.036   0.162   1838
  Planarity :  0.005   0.055   1938
  Dihedral  : 16.816 119.423   2051
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.95 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.40 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.24), residues: 1320
  helix:  2.76 (0.19), residues: 730
  sheet: -0.26 (0.53), residues: 102
  loop : -0.56 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 613 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.012   0.001   PHE A 285 
 TRP   0.007   0.001   TRP B 387 
 HIS   0.008   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12023)
  covalent geometry    : angle       0.59877 (16537)
  hydrogen bonds       : bond        0.03796 (  580)
  hydrogen bonds       : angle       3.33126 ( 1660)
  Misc. bond           : bond        0.00069 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1970.67 seconds
wall clock time: 34 minutes 45.57 seconds (2085.57 seconds total)